42 results on '"Ezequiel Petrillo"'
Search Results
2. Halting ErbB-2 isoforms retrograde transport to the nucleus as a new theragnostic approach for triple-negative breast cancer
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Santiago Madera, Franco Izzo, María F. Chervo, Agustina Dupont, Violeta A. Chiauzzi, Sofia Bruni, Ezequiel Petrillo, Sharon S. Merin, Mara De Martino, Diego Montero, Claudio Levit, Gabriel Lebersztein, Fabiana Anfuso, Agustina Roldán Deamicis, María F. Mercogliano, Cecilia J. Proietti, Roxana Schillaci, Patricia V. Elizalde, and Rosalía I. Cordo Russo
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Cytology ,QH573-671 - Abstract
Abstract Triple-negative breast cancer (TNBC) is clinically defined by the absence of estrogen and progesterone receptors and the lack of membrane overexpression or gene amplification of receptor tyrosine kinase ErbB-2/HER2. Due to TNBC heterogeneity, clinical biomarkers and targeted therapies for this disease remain elusive. We demonstrated that ErbB-2 is localized in the nucleus (NErbB-2) of TNBC cells and primary tumors, from where it drives growth. We also discovered that TNBC expresses both wild-type ErbB-2 (WTErbB-2) and alternative ErbB-2 isoform c (ErbB-2c). Here, we revealed that the inhibitors of the retrograde transport Retro-2 and its cyclic derivative Retro-2.1 evict both WTErbB-2 and ErbB-2c from the nucleus of BC cells and tumors. Using BC cells from several molecular subtypes, as well as normal breast cells, we demonstrated that Retro-2 specifically blocks proliferation of BC cells expressing NErbB-2. Importantly, Retro-2 eviction of both ErbB-2 isoforms from the nucleus resulted in a striking growth abrogation in multiple TNBC preclinical models, including tumor explants and xenografts. Our mechanistic studies in TNBC cells revealed that Retro-2 induces a differential accumulation of WTErbB-2 at the early endosomes and the plasma membrane, and of ErbB-2c at the Golgi, shedding new light both on Retro-2 action on endogenous protein cargoes undergoing retrograde transport, and on the biology of ErbB-2 splicing variants. In addition, we revealed that the presence of a functional signal peptide and a nuclear export signal (NES), both located at the N-terminus of WTErbB-2, and absent in ErbB-2c, accounts for the differential subcellular distribution of ErbB-2 isoforms upon Retro-2 treatment. Our present discoveries provide evidence for the rational repurposing of Retro-2 as a novel therapeutic agent for TNBC.
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- 2022
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3. DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2
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Alexander Yermanos, Kai-Lin Hong, Andreas Agrafiotis, Jiami Han, Sarah Nadeau, Cecilia Valenzuela, Asli Azizoglu, Roy Ehling, Beichen Gao, Michael Spahr, Daniel Neumeier, Ching-Hsiang Chang, Andreas Dounas, Ezequiel Petrillo, Ina Nissen, Elodie Burcklen, Mirjam Feldkamp, Christian Beisel, Annette Oxenius, Miodrag Savic, Tanja Stadler, Fabian Rudolf, and Sai T. Reddy
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. Results Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. Conclusions DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. Graphical abstract DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com .
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- 2022
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4. Apoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature
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Javier Martínez Pacheco, Philippe Ranocha, Luciana Kasulin, Corina M. Fusari, Lucas Servi, Ariel. A. Aptekmann, Victoria Berdion Gabarain, Juan Manuel Peralta, Cecilia Borassi, Eliana Marzol, Diana Rosa Rodríguez-Garcia, Yossmayer del Carmen Rondón Guerrero, Mariana Carignani Sardoy, Lucía Ferrero, Javier F. Botto, Claudio Meneses, Federico Ariel, Alejandro D. Nadra, Ezequiel Petrillo, Christophe Dunand, and José M. Estevez
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Science - Abstract
Arabidopsis root hair growth is enhanced at low temperatures. Here the authors show that the class III peroxidases PRX62 and PRX69 modulate ROS homeostasis and cell wall characteristics, and promote root hair elongation at low temperature.
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- 2022
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5. Editorial: Regulation of alternative splicing in plant stress responses
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Kranthi K. Mandadi, Ezequiel Petrillo, Alexandra S. Dubrovina, and Konstantin V. Kiselev
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alternative splicing ,post-transcriptional regulation ,plant growth and development ,abiotic stress ,biotic stress ,Plant culture ,SB1-1110 - Published
- 2023
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6. Editorial: Alternative Splicing Regulation in Plants
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Ezequiel Petrillo, Maria Kalyna, Kranthi K. Mandadi, Shih-Long Tu, and Craig G. Simpson
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splicing factor ,development ,stress ,adaptation ,evolution ,environment ,Plant culture ,SB1-1110 - Published
- 2020
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7. Alternative Splicing Regulation During Light-Induced Germination of Arabidopsis thaliana Seeds
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Rocío Soledad Tognacca, Lucas Servi, Carlos Esteban Hernando, Maite Saura-Sanchez, Marcelo Javier Yanovsky, Ezequiel Petrillo, and Javier Francisco Botto
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dormancy ,germination ,light ,phytochrome B (phyB) ,alternative splicing (AS) ,Arabidopsis ,Plant culture ,SB1-1110 - Abstract
Seed dormancy and germination are relevant processes for a successful seedling establishment in the field. Light is one of the most important environmental factors involved in the relief of dormancy to promote seed germination. In Arabidopsis thaliana seeds, phytochrome photoreceptors tightly regulate gene expression at different levels. The contribution of alternative splicing (AS) regulation in the photocontrol of seed germination is still unknown. The aim of this work is to study gene expression modulated by light during germination of A. thaliana seeds, with focus on AS changes. Hence, we evaluated transcriptome-wide changes in stratified seeds irradiated with a pulse of red (Rp) or far-red (FRp) by RNA sequencing (RNA-seq). Our results show that the Rp changes the expression of ∼20% of the transcriptome and modifies the AS pattern of 226 genes associated with mRNA processing, RNA splicing, and mRNA metabolic processes. We further confirmed these effects for some of the affected AS events. Interestingly, the reverse transcriptase–polymerase chain reaction (RT–PCR) analyses show that the Rp modulates the AS of splicing-related factors (At-SR30, At-RS31a, At-RS31, and At-U2AF65A), a light-signaling component (At-PIF6), and a dormancy-related gene (At-DRM1). Furthermore, while the phytochrome B (phyB) is responsible for the AS pattern changes of At-U2AF65A and At-PIF6, the regulation of the other AS events is independent of this photoreceptor. We conclude that (i) Rp triggers AS changes in some splicing factors, light-signaling components, and dormancy/germination regulators; (ii) phyB modulates only some of these AS events; and (iii) AS events are regulated by R and FR light, but this regulation is not directly associated with the intensity of germination response. These data will help in boosting research in the splicing field and our understanding about the role of this mechanism during the photocontrol of seed germination.
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- 2019
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8. New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies
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Renesh Bedre, Sonia Irigoyen, Ezequiel Petrillo, and Kranthi K. Mandadi
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alternative splicing ,high-throughput sequencing ,bioinformatics ,RNA-seq ,PCR ,non-sense-mediated decay ,Plant culture ,SB1-1110 - Published
- 2019
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9. Do not panic: An intron-centric guide to alternative splicing
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Ezequiel Petrillo
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Cell Biology ,Plant Science - Abstract
This review is an attempt to establish concepts of splicing and alternative splicing giving proper relevance to introns, the key actors in this mechanism. It might also work as a guide for those who found their favorite gene undergoes alternative splicing and could benefit from gaining a theoretical framework to understand the possible impacts of this process. This is not a thorough review of all the work in the field, but rather a critical review of some of the most relevant work done to understand the underlying mechanisms of splicing and the key questions that remain unanswered such as: What is the physiological relevance of alternative splicing? What are the functions of the different outcomes? To what extent do different alternative splicing types contribute to the proteome? Intron retention is the most frequent alternative splicing event in plants and, although scientifically neglected, it is also common in animals. This is a heterogeneous type of alternative splicing that includes different sub-types with features that have distinctive consequences in the resulting transcripts. Remarkably, intron retention can be a dead end for a transcript, but it could also be a stable intermediate whose processing is resumed upon a particular signal or change in the cell status. New sequencing technologies combined with the study of intron lariats in different conditions might help to answer key questions and could help us to understand the actual relevance of introns in gene expression regulation.
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- 2023
10. Thinking out loud: how science faces crises
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Anabella Srebrow, Federico Fuchs Wightman, and Ezequiel Petrillo
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History ,General Biochemistry, Genetics and Molecular Biology - Published
- 2021
11. Alternative splicing in plants: current knowledge and future directions for assessing the biological relevance of splice variants
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Rocío S Tognacca, Florencia S Rodríguez, Federico E Aballay, Carla M Cartagena, Lucas Servi, and Ezequiel Petrillo
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Physiology ,Plant Science - Abstract
Alternative splicing is an important regulatory process that produces multiple transcripts from a single gene, significantly modulating the transcriptome and potentially the proteome, during development and in response to environmental cues. In the first part of this review, we summarize recent advances and highlight the accumulated knowledge on the biological roles of alternative splicing isoforms that are key for different plant responses and during development. Remarkably, we found that many of the studies in this area use similar methodological approaches that need to be improved to gain more accurate conclusions, since they generally presume that stable isoforms undoubtedly have coding capacities. This is mostly done without data indicating that a particular RNA isoform is in fact translated. So, in the latter part of the review, we propose a thorough strategy to analyze, evaluate, and characterize putative functions for alternative splicing isoforms of interest.
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- 2022
12. A DNA intercalating dye-based RT-qPCR alternative to diagnose SARS-CoV-2
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Juan C. Muñoz, Gonzalo Cabrerizo, Marcos Palavecino, Manuel J. Muñoz, José N. Stigliano, Nicolás Nieto Moreno, Anabella Srebrow, Ignacio E Schor, Fabian Rudolf, Micaela A. Godoy Herz, Martín Avaro, Cybele C. García, Elsa Baumeister, Valeria Buggiano, Lucas Servi, Estefanía Benedetti, Federico Remes Lenicov, Alberto R. Kornblihtt, Laureano Bragado, Ezequiel Petrillo, Federico Fuchs Wightman, Andrea Pontoriero, José Clemente, and Manuel de la Mata
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2019-20 coronavirus outbreak ,RDRP ,Diagnostic methods ,Coronavirus disease 2019 (COVID-19) ,Computer science ,diagnosis ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,TaqMan ,Early detection ,SARS-COV-2 ,Computational biology ,Diamines ,Biology ,DIAGNOSIS ,Real-Time Polymerase Chain Reaction ,Sensitivity and Specificity ,SYBR GREEN ,Limited access ,purl.org/becyt/ford/3.3 [https] ,03 medical and health sciences ,Technical Report ,0302 clinical medicine ,Nasopharynx ,TAQMAN ,RT-QPCR ,Humans ,SYBR Green ,Benzothiazoles ,Molecular Biology ,DNA Primers ,030304 developmental biology ,RdRP ,0303 health sciences ,Technical Paper ,SARS-CoV-2 ,RT-qPCR ,COVID-19 ,DNA ,Cell Biology ,Gold standard (test) ,Intercalating Agents ,COVID-19 Nucleic Acid Testing ,030220 oncology & carcinogenesis ,Quinolines ,RNA ,RNA, Viral ,purl.org/becyt/ford/3 [https] ,Alternative strategy - Abstract
Early detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been proven crucial during the efforts to mitigate the effects of the COVID-19 pandemic. Several diagnostic methods have emerged in the past few months, each with different shortcomings and limitations. The current gold standard, RT-qPCR using fluorescent probes, relies on demanding equipment requirements plus the high costs of the probes and specific reaction mixes. To broaden the possibilities of reagents and thermocyclers that could be allocated towards this task, we have optimized an alternative strategy for RT-qPCR diagnosis. This is based on a widely used DNA-intercalating dye and can be implemented with several different qPCR reagents and instruments. Remarkably, the proposed qPCR method performs similarly to the broadly used TaqMan-based detection, in terms of specificity and sensitivity, thus representing a reliable tool. We think that, through enabling the use of vast range of thermocycler models and laboratory facilities for SARS-CoV-2 diagnosis, the alternative proposed here can increase dramatically the testing capability, especially in countries with limited access to costly technology and reagents. Fil: Fuchs Wightman, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Godoy Herz, Micaela Amalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Muñoz, Juan Cristóbal. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Stigliano, Jose Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Bragado, Laureano Fabian Tomas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Nieto Moreno, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Palavecino Ruiz, Marcos Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Servi, Lucas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Cabrerizo, Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina Fil: Clemente, Jose Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Avaro, Martín. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas; Argentina Fil: Pontoriero, Andrea. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas; Argentina Fil: Benedetti, Estefanía. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas; Argentina Fil: Baumeister, Elsa. Dirección Nacional de Institutos de Investigación. Administración Nacional de Laboratorios e Institutos de Salud. Instituto Nacional de Enfermedades Infecciosas; Argentina Fil: Rudolf, Fabian. Eidgenössische Technische Hochschule Zürich; Suiza Fil: Remes Lenicov, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; Argentina Fil: Garcia, Cybele. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Buggiano, Valeria Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Srebrow, Anabella. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: de la Mata, Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Muñoz, Manuel Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Schor, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
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- 2021
13. Cotranscriptional RNA processing and modification in plants
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Sebastian Marquardt, Ezequiel Petrillo, and Pablo A Manavella
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Cell Biology ,Plant Science - Abstract
The activities of RNA polymerases shape the epigenetic landscape of genomes with profound consequences for genome integrity and gene expression. A fundamental event during the regulation of eukaryotic gene expression is the coordination between transcription and RNA processing. Most primary RNAs mature through various RNA processing and modification events to become fully functional. While pioneering results positioned RNA maturation steps after transcription ends, the coupling between the maturation of diverse RNA species and their transcription is becoming increasingly evident in plants. In this review, we discuss recent advances in our understanding of the crosstalk between RNA Polymerase II, IV, and V transcription and nascent RNA processing of both coding and noncoding RNAs.
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- 2022
14. PICLN modulates alternative splicing and ensures adaptation to light and temperature changes in plants
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Julieta L. Mateos, Sabrina E Sanchez, Martina Legris, David Esteve-Bruna, Jeanette C. Torchio, Ezequiel Petrillo, Daniela Goretti, Noel Blanco-Touriñán, Danelle K. Seymour, Markus Schmid, Detlef Weigel, David Alabadí, and Marcelo J. Yanovsky
- Abstract
Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. PICLN is part of the methylosome complex in both humans and Arabidopsis thaliana, and we show here that the human PICLN ortholog rescues phenotypes of A. thaliana picln mutants. Altered photomorphogenic and photoperiodic responses in A. thaliana picln mutants are associated with changes in pre-mRNA splicing, which partially overlap with those in prmt5 mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PROTEIN-ARGININE METHYL TRANSFERASE 5 (PRMT5), the main protein of the methylosome, are controlled by A. thaliana GEMIN2. As with GEMIN2 and SME1/PCP, low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.
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- 2022
15. PICLN modulates alternative splicing and light/temperature responses in plants
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Julieta L Mateos, Sabrina E Sanchez, Martina Legris, David Esteve-Bruna, Jeanette C Torchio, Ezequiel Petrillo, Daniela Goretti, Noel Blanco-Touriñán, Danelle K Seymour, Markus Schmid, Detlef Weigel, David Alabadí, and Marcelo J Yanovsky
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Physiology ,Genetics ,Plant Science - Abstract
Plants undergo transcriptome reprograming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.
- Published
- 2022
16. Canonical ErbB-2 isoform and ErbB-2 variant c located in the nucleus drive triple negative breast cancer growth
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Nicolás Bellora, Franco Izzo, Rosalia Ines Cordo Russo, Pablo Guzmán, Juan Carlos Roa, Matías G. Pereyra, Mara De Martino, Mauro E. Cenciarini, Ezequiel Petrillo, Silvina Figurelli, Jose L. Daniotti, Daniel Lopez Della Vecchia, Osvaldo L. Podhajcer, Sabrina Barchuk, Lucía Santa María de la Parra, Patricia V. Elizalde, Violeta A. Chiauzzi, Cecilia J. Proietti, Leandro N. Guttlein, Roxana Schillaci, María F. Chervo, and Agustina Dupont
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0301 basic medicine ,Gene isoform ,Cancer Research ,Receptor, ErbB-2 ,Otras Ciencias Biológicas ,Triple Negative Breast Neoplasms ,Receptor tyrosine kinase ,Ciencias Biológicas ,Transcriptome ,03 medical and health sciences ,ErbB-2 ,Breast cancer ,0302 clinical medicine ,ErbB ,RNA interference ,Cell Line, Tumor ,Genetics ,Humans ,Protein Isoforms ,Molecular Biology ,Transcription factor ,Mitogen-Activated Protein Kinase 7 ,Triple-negative breast cancer ,Cell Proliferation ,Cell Nucleus ,Paraffin Embedding ,biology ,Alternative splicing ,030104 developmental biology ,030220 oncology & carcinogenesis ,Cancer research ,biology.protein ,Female ,TNBC ,CIENCIAS NATURALES Y EXACTAS - Abstract
Triple negative breast cancer (TNBC) refers to tumors that do not express clinically significant levels of estrogen and progesterone receptors, and lack membrane overexpression or gene amplification of ErbB-2/HER2, a receptor tyrosine kinase. Transcriptome and proteome heterogeneity of TNBC poses a major challenge to precision medicine. Clinical biomarkers and targeted therapies for this disease remain elusive, so chemotherapy has been the standard of care for early and metastatic TNBC. Our present findings placed ErbB-2 in an unanticipated scenario: the nucleus of TNBC (NErbB-2). Our study on ErbB-2 alternative splicing events, using a PCR-sequencing approach combined with an RNA interference strategy, revealed that TNBC cells express either the canonical (wild-type) ErbB-2, encoded by transcript variant 1, or the non-canonical ErbB-2 isoform c, encoded by alternative variant 3 (RefSeq), or both. These ErbB-2 isoforms function in the nucleus as transcription factors. Evicting both from the nucleus or silencing isoform c only, blocks TN cell and tumor growth. This reveals not only NErbB-2 canonical and alternative isoforms role as targets of therapy in TNBC, but also isoform c dominant oncogenic potential. Furthermore, we validated our findings in the clinic and observed that NErbB-2 correlates with poor prognosis in primary TN tumors, disclosing NErbB-2 as a novel biomarker for TNBC. Our discoveries challenge the present scenario of drug development for personalized BC medicine that focuses on wild-type RefSeq proteins, which conserve the canonical domains and are located in their classical cellular compartments. Fil: Chervo, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Cordo Russo, Rosalia Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Izzo, Franco. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: de Martino, Mara. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Bellora, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales. Universidad Nacional del Comahue. Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales; Argentina Fil: Cenciarini, Mauro Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Chiauzzi, Violeta Alicia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Santa María de la Parra, Lucía. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Pereyra Matías G.. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Güttlein, Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Podhajcer, Osvaldo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Daniotti, Jose Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; Argentina Fil: Dupont, Agustina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Juan A. Fernández"; Argentina Fil: Barchuk, Sabrina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Juan A. Fernández"; Argentina Fil: Figurelli, Silvina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Juan A. Fernández"; Argentina Fil: Lopez Della Vecchia, Daniel Edgardo. Gobierno de la Ciudad de Buenos Aires. Hospital General de Agudos "Juan A. Fernández"; Argentina Fil: Roa, Juan Carlos. Universidad de La Frontera. Núcleo Científico y Tecnológico en Recursos Naturales; Chile. Pontificia Universidad Católica de Chile; Chile Fil: Guzmán, Pablo. Universidad de La Frontera. Núcleo Científico y Tecnológico en Recursos Naturales; Chile Fil: Proietti Anastasi, Cecilia Jazmín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Schillaci, Roxana. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Elizalde, Patricia Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina
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- 2020
17. Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana’s life cycle
- Author
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M. Guillermina Kubaczka, Florencia S Rodríguez, Lucas Servi, Micaela A. Godoy Herz, Rocío Soledad Tognacca, and Ezequiel Petrillo
- Subjects
biology ,Alternative splicing ,food and beverages ,RNA polymerase II ,Biochemistry ,Chromatin ,Cell biology ,Transcription (biology) ,RNA splicing ,Gene expression ,Genetics ,biology.protein ,Developmental plasticity ,Reprogramming ,Biotechnology - Abstract
Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.
- Published
- 2020
18. ODP551 Halting ErbB-2 Isoforms Retrograde Transport to the Nucleus as a New Theragnostic Approach for Triple Negative Breast Cancer
- Author
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Patricia Virginia Elizalde, Franco Izzo, Maria Florencia Chervo, Sharon Salma Merin, Agustina Dupont, Violeta Chiauzzi, Sofia Bruni, Ezequiel Petrillo, Diego Montero, Maria Florencia Mercogliano, Cecilia Jazmin Proietti, Roxana Schillaci, Santiago Madera, and Rosalia Ines Cordo Russo
- Subjects
Endocrinology, Diabetes and Metabolism - Abstract
Triple negative breast cancer (TNBC) is clinically defined by the absence of estrogen and progesterone receptors and the lack of membrane overexpression or gene amplification of the receptor tyrosine kinase ErbB-2/HER2. Due to its heterogeneity, clinical biomarkers and targeted therapies for this disease remain elusive, and chemotherapy has been the standard of care for TNBC. ErbB-2 is classically located at the membrane of BC cells, where it triggers signaling cascades and promotes oncogenesis. We previously demonstrated that ErbB-2 is also localized in the nucleus (NErbB-2) of TNBC cells, from where it drives growth (1). We also discovered that TNBC expresses both wild-type ErbB-2 (WTErbB-2) and alternative ErbB-2 isoform c (ErbB-2c) (1). ErbB-2 migrates to the nucleus via retrograde transport. Here, we revealed that Retro-2, an inhibitor of retrograde transport that protects cells form the deleterious effects of toxins and viruses, evicts both WTErbB-2 and ErbB-2c from the nucleus of BC cells. Using BC models from several molecular subtypes, as well as normal breast cells, we demonstrated that Retro-2 specifically halts the proliferation of cells expressing NErbB-2. Moreover, Retro-2 decreased the expression of genes induced by NErbB-2 (i. e. cyclin D1 and Erk5) and promoted cell cycle arrest at G0/G1 phase and apoptosis. In addition to R2 growth inhibitory activity in vitro, we here also demonstrated that its optimized cyclic derivative Retro-2.1 (in particular the (S)-enantiomer) showed improved efficacy both to evict ErbB-2 isoforms from the nucleus and to inhibit proliferation in vitro. Importantly, Retro-2 eviction of both ErbB-2 isoforms from the nucleus resulted in a striking growth abrogation in multiple TNBC preclinical models, including xenografts and tumor explants). Our mechanistic studies demonstrated that Retro-2 induces a differential accumulation of WTErbB-2 at the early endosomes and plasma membrane, and of ErbB-2c at the Golgi, shedding light both on Retro-2 action on endogenous protein cargoes undergoing retrograde transport and on the biology of ErbB-2 splicing variants. Compelling evidence demonstrated that mRNAs 5' and 3' untranslated regions (UTRs) mediate post-transcriptional regulation of gene expression and determine protein levels and fate. While both T1 and T3 have different 5' but the same 3' UTRs sequences, our in silico studies showed that T1 and T3 RNA secondary structures vary in the region containing both their 5' and 3' UTRs. These findings suggest that T3 secondary structure impacts in its cell specific localization. Together, our present discoveries identify R2 as a precision oncology tool to target NErbB-2 retrograde transport. This novel theragnostic approach could greatly improve the outcome of TNBC patients. (1) Chervo MF et al, Oncogene 2020: 39: 6245-62. Presentation: No date and time listed
- Published
- 2022
19. Apoplastic class III peroxidases PRX62 and PRX69 regulate ROS-homeostasis and cell wall associated extensins linked to root hair growth at low-temperature in Arabidopsis thaliana
- Author
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Diana Rosa Rodriguez Garcia, Javier Martínez Pacheco, Lucia Ferrero, Mariana Carignani Sardoy, Yossmayer del Carmen Rondon Guerrero, Javier Francisco Botto, Victoria Berdion Gabarain, Philippe Ranocha, Corina M. Fusari, Cecilia Borassi, Eliana Marzol, Lucas Servi, Ezequiel Petrillo, José M. Estevez, Luciana Kasulin, Federico Ariel, Claudio Meneses, Juan Manuel Peralta, and Christophe Dunand
- Subjects
biology ,ROOT HAIRS ,Ros homeostasis ,ARABIDOPSIS THALIANA ,Class iii ,Root hair ,PRX69 ,biology.organism_classification ,Apoplast ,Cell biology ,purl.org/becyt/ford/1 [https] ,Cell wall ,PRX62 ,biology.protein ,Arabidopsis thaliana ,purl.org/becyt/ford/1.6 [https] ,Extensin ,LOW TEMPERATURE ,Peroxidase - Abstract
Root hairs (RH) growth is highly influenced by endogenous as well as by external environmental signals that coordinately regulate its final cell size. RHs actively expand the root surface responsible for nutrient uptake and water absorption. We have recently determined that RH growth was unexpectedly boosted when Arabidopsis thaliana seedlings are cultivated at low temperatures. It was proposed that RH growth plasticity in response to cold was linked to a reduced nutrient availability in the media. Here, we explored the molecular basis of this strong RH growth response by using the Genome Wide Association Studies (GWAS) approach on Arabidopsis thaliana natural accessions. We identified the poorly characterized PEROXIDASE 62 (PRX62) as a key protein triggering this conditional growth under a moderate low-temperature stress. In addition, we identified the related protein PRX69 as an important factor in this developmental process. The prx62 prx69 double mutant and the PRX62 and PRX69 over-expressing lines showed contrasting RH phenotypes, peroxidase activities and cyt/apoReactive Oxygen Species (ROS) levels. Strikingly, a cell wall protein extensin (EXT) reporter revealed the effect of peroxidase activity on the EXT cell wall association at 10C in the RH apical zone. EXT cell wall insolubilization was enhanced at 10C, which was completely abolished under the PRX inhibitor salicylhydroxamic acid (SHAM) treatment. Finally, we demonstrated that the Root Hair defective 6 like 4 (RSL4) transcription factor directly controls the expression of PRX69 under low-temperature. Collectively, our results indicate that both PRX62 and PRX69 are key apoplastic PRXs that modulate ROS-homeostasis and cell wall EXT-insolubilization linked to RH elongation at low-temperature. Fil: Martinez Pacheco, Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Ranocha, Philippe. Université de Toulouse; Francia Fil: Kasulin, Luciana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Fusari, Corina Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro de Estudios Fotosintéticos y Bioquímicos. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Centro de Estudios Fotosintéticos y Bioquímicos; Argentina Fil: Servi, Lucas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Ferrero, Lucia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Berdion Gabarain, Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Peralta, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Borassi, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Marzol, Eliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Rodriguez Garcia, Diana Rosa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Rondon Guerrero, Yossmayer del Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Carignani Sardoy, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Botto, Javier Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina Fil: Meneses, Claudio. Universidad Andrés Bello; Chile Fil: Ariel, Federico Damian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Dunand, Christophe. Université de Toulouse; Francia Fil: Estevez, Jose Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Universidad Andrés Bello; Chile
- Published
- 2021
20. DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2
- Author
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Christian Beisel, Michael Spahr, Sarah Nadeau, Daniel Neumeier, Annette Oxenius, Roy A. Ehling, Ina Nissen, Ching-Hsiang Chang, Kai-Lin Hong, Fabian Rudolf, Miodrag Savic, Sai T. Reddy, Ezequiel Petrillo, Beichen Gao, Asli Azizoglu, Elodie Burcklen, Tanja Stadler, Alexander Yermanos, Andreas Dounas, Andreas Agrafiotis, Jiami Han, Cecilia Valenzuela, and Mirjam Feldkamp
- Subjects
Whole genome sequencing ,0303 health sciences ,Population level ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Diagnostic test ,Surveillance Methods ,Computational biology ,Limiting ,Biology ,Deep sequencing ,03 medical and health sciences ,0302 clinical medicine ,Viral evolution ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity.Abstract FigureGraphical abstractDeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.
- Published
- 2021
21. Abstract 344: Blockade of retrograde transport in triple negative breast cancer excludes ErbB-2 isoforms from the nucleus and abrogates tumor growth
- Author
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Santiago Madera, Franco Izzo, Maria F. Chervo, Agustina Dupont, Violeta A. Chiauzzi, Sofia Bruni, Ezequiel Petrillo, Diego Montero, Sharon Merin, Maria F. Mercogliano, Cecilia J. Proietti, Roxana Schillaci, Rosalia I. Cordo Russo, and Patricia V. Elizalde
- Subjects
Cancer Research ,Oncology - Abstract
Triple negative breast cancer (TNBC) is clinically defined by the absence of estrogen and progesterone receptors and the lack of membrane overexpression or gene amplification of the receptor tyrosine kinase ErbB-2/HER2. Due to its heterogeneity, clinical biomarkers and targeted therapies for this disease remain elusive, and chemotherapy has been the standard of care for early and metastatic TNBC. ErbB-2 is classically located at the membrane of BC cells, where it triggers signalling cascades and promotes oncogenesis. However, we have demonstrated that ErbB-2 is also localized in the nucleus (NErbB-2) of TNBC cells and primary tumors, from where it drives growth. We also discovered that TNBC expresses both wild-type ErbB-2 (WTErbB-2) and alternative ErbB-2 isoform c (ErbB-2c). ErbB-2 migrates to the nucleus via retrograde transport. The small molecule Retro-2 is a non-toxic inhibitor of the retrograde transport route that protects cells from the deleterious effects of toxins and viruses. Here, we revealed that Retro-2 evicts both WTErbB-2 and ErbB-2c from the nuclei. Using BC models from several molecular subtypes, we demonstrated that Retro-2 specifically halts the proliferation of cells expressing NErbB-2 in a dose-dependent manner, whilst did not inhibit cell proliferation in the ErbB-2-negative MCF10A normal breast cell line. Additionally, Retro-2 decreased the expression of genes induced by NErbB-2 (cyclin D1 and Erk5) and promoted cell cycle arrest at G0/G1 phase and apoptosis. Even more, in preclinical models (including xenografts and tumor explants), Retro-2 treatment resulted in the eviction of NErbB-2 and abrogation of tumor growth. Our mechanistic studies demonstrated that Retro-2 induces a differential accumulation of WTErbB-2 at the early endosomes and plasma membrane, and of ErbB-2c at the Golgi, further preventing its sorting to the endoplasmic reticulum. These findings shed light both on Retro-2 action on endogenous protein cargoes undergoing retrograde transport and on the biology of ErbB-2 splicing variants. Together, our present discoveries provide evidence for the rational repurposing of Retro-2 as a novel therapeutic agent for TNBC. Citation Format: Santiago Madera, Franco Izzo, Maria F. Chervo, Agustina Dupont, Violeta A. Chiauzzi, Sofia Bruni, Ezequiel Petrillo, Diego Montero, Sharon Merin, Maria F. Mercogliano, Cecilia J. Proietti, Roxana Schillaci, Rosalia I. Cordo Russo, Patricia V. Elizalde. Blockade of retrograde transport in triple negative breast cancer excludes ErbB-2 isoforms from the nucleus and abrogates tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 344.
- Published
- 2022
22. Nuclear ErbB-2-Induced Transcriptome Drives Triple Negative Breast Cancer Growth
- Author
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Nicolás Bellora, Tim H-M Huang, Agustina Roldán Deamicis, Rosalia Ines Cordo Russo, Patricia V. Elizalde, María F. Chervo, Santiago Madera, Micaela Parra, Cecilia J. Proietti, Kohzoh Mitsuya, Violeta A. Chiauzzi, Ezequiel Petrillo, and Roxana Schillaci
- Subjects
Transcriptome ,Text mining ,ErbB ,business.industry ,Endocrinology, Diabetes and Metabolism ,Cancer research ,Tumor Biology ,Biology ,business ,Triple-negative breast cancer ,Hormone Actions in Tumor Biology: From New Mechanisms to Therapy ,AcademicSubjects/MED00250 - Abstract
Triple negative breast cancer (TNBC) refers to tumors that do not express clinically significant levels of estrogen and progesterone receptors, and lack membrane overexpression or gene amplification of ErbB-2 tyrosine kinase receptor. Transcriptome and proteome heterogeneity of TNBC poses a major challenge to precision medicine. Gene expression analyses have categorized TNBC into distinct molecular subtypes. Up to 78% of clinical TNBCs belong to the basal-like (BL) subtype. Here we found ErbB-2 in an unanticipated scenario: the nucleus of TNBC (NErbB-2). Our study on ErbB-2 alternative splicing, using a PCR-sequencing approach combined with RNA interference, revealed that BL TNBC cells express the canonical ErbB-2 (WTErbB-2), encoded by transcript 1, and the non-canonical isoform c, encoded by alternative transcript 3 (T3). The latter was not previously reported in normal or malignant cells. To characterize the isoform c we designed siRNAs targeting T3 (T3 siRNAs), which silenced up to 93% of said isoform. Transfection of T3 siRNAs into BL cells expressing only isoform c or both isoform c and WTErbB-2 was sufficient to decrease cell proliferation. Intratumoral injections of T3 siRNAs into mice bearing BL TN tumors also blocked in vivo growth. To explore whether isoform c growth-promoting effect is due to its functions as a transcriptional regulator, we performed RNA-seq in BL cells expressing only this isoform. We identified a set of genes differentially regulated in BL cells where we evicted isoform c from the nucleus, as compared to control cells. In the up-regulated group, we found enrichment of pro-apoptotic and tumor suppressor genes and in the down-regulated one, genes involved in proliferation and stemness. We used gene set enrichment analysis (GSEA) to identify the biological processes associated with these isoform c-regulated genes. We found a pronounced enrichment of gene sets related to apoptosis, activation of DNA damage pathways and cell cycle arrest in response to eviction of nuclear isoform c. GSEA also revealed negative regulation of gene sets involved in cell motility, cellular differentiation and growth pathways in BL cells lacking nuclear isoform c expression. These results suggest that NErbB-2 function modulates tumor growth and promotes a metastatic phenotype in TNBC. Furthermore, our clinical findings identified NErbB-2 as an independent predictor of shorter OS (HR 2.54; 95% CI 1.22-5.28; P = 0.013), DFS (HR 2.91; 95% CI 1.44-5.87; P = 0.003), and DMFS (HR 2.59; 95% CI 1.20-5.60; P = 0.015) in 99 TN primary tumors. Our discoveries challenge the present scenario of drug development for personalized BC medicine that focuses on wild-type proteins, which conserve the canonical domains and are located in their classical cellular compartments, highlighting the potential of NErbB-2 isoforms as novel therapeutic targets and clinical biomarkers in TNBC.
- Published
- 2021
23. Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout
- Author
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Rocío S, Tognacca, M Guillermina, Kubaczka, Lucas, Servi, Florencia S, Rodríguez, Micaela A, Godoy Herz, and Ezequiel, Petrillo
- Subjects
Alternative Splicing ,Life Cycle Stages ,Light ,Transcription, Genetic ,Arabidopsis ,food and beverages ,RNA Polymerase II ,Review ,Chromatin - Abstract
Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana’s life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.
- Published
- 2020
24. Alternative Splicing Regulation During Light-Induced Germination of Arabidopsis thaliana Seeds
- Author
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Marcelo J. Yanovsky, Carlos Esteban Hernando, Maite Saura-Sanchez, Lucas Servi, Ezequiel Petrillo, Javier Francisco Botto, and Rocío Soledad Tognacca
- Subjects
0106 biological sciences ,0301 basic medicine ,dormancy ,alternative splicing (AS) ,Arabidopsis ,Plant Science ,lcsh:Plant culture ,01 natural sciences ,purl.org/becyt/ford/1 [https] ,Ciencias Biológicas ,03 medical and health sciences ,Gene expression ,lcsh:SB1-1110 ,purl.org/becyt/ford/1.6 [https] ,biology ,Phytochrome ,DORMANCY ,Alternative splicing ,Seed dormancy ,phytochrome B (phyB) ,Bioquímica y Biología Molecular ,biology.organism_classification ,ARABIDOPSIS ,Cell biology ,030104 developmental biology ,LIGHT ,germination ,Germination ,RNA splicing ,Dormancy ,ALTERNATIVE SPLICING (AS) ,light ,PHYTOCHROME B (PHYB) ,CIENCIAS NATURALES Y EXACTAS ,010606 plant biology & botany ,GERMINATION - Abstract
Seed dormancy and germination are relevant processes for a successful seedling establishment in the field. Light is one of the most important environmental factors involved in the relief of dormancy to promote seed germination. In Arabidopsis thaliana seeds, phytochrome photoreceptors tightly regulate gene expression at different levels. The contribution of alternative splicing (AS) regulation in the photocontrol of seed germination is still unknown. The aim of this work is to study gene expression modulated by light during germination of A. thaliana seeds, with focus on AS changes. Hence, we evaluated transcriptome-wide changes in stratified seeds irradiated with a pulse of red (Rp) or far-red (FRp) by RNA sequencing (RNA-seq). Our results show that the Rp changes the expression of ∼20% of the transcriptome and modifies the AS pattern of 226 genes associated with mRNA processing, RNA splicing, and mRNA metabolic processes. We further confirmed these effects for some of the affected AS events. Interestingly, the reverse transcriptase–polymerase chain reaction (RT–PCR) analyses show that the Rp modulates the AS of splicing-related factors (At-SR30, At-RS31a, At-RS31, and At-U2AF65A), a light-signaling component (At-PIF6), and a dormancy-related gene (At-DRM1). Furthermore, while the phytochrome B (phyB) is responsible for the AS pattern changes of At-U2AF65A and At-PIF6, the regulation of the other AS events is independent of this photoreceptor. We conclude that (i) Rp triggers AS changes in some splicing factors, light-signaling components, and dormancy/germination regulators; (ii) phyB modulates only some of these AS events; and (iii) AS events are regulated by R and FR light, but this regulation is not directly associated with the intensity of germination response. These data will help in boosting research in the splicing field and our understanding about the role of this mechanism during the photocontrol of seed germination. Fil: Tognacca, Rocío Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Servi, Lucas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Hernando, Carlos Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Saura Sanchez, Maite. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina Fil: Yanovsky, Marcelo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Botto, Javier Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina
- Published
- 2019
25. Light remote control of alternative splicing in roots through TOR kinase
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Lucas Servi, Alois Schweighofer, Peter Venhuizen, Craig G. Simpson, Armin Fuchs, Andrea Barta, Christian Meyer, John W. S. Brown, Maria Kalyna, Kubaczka Mg, Herz Mag, Ezequiel Petrillo, and Stefan Riegler
- Subjects
0106 biological sciences ,0303 health sciences ,Kinase ,Alternative splicing ,Regulator ,Mitochondrion ,Biology ,01 natural sciences ,Cell biology ,Chloroplast ,03 medical and health sciences ,Gene expression ,Kinase activity ,Function (biology) ,030304 developmental biology ,010606 plant biology & botany - Abstract
SummaryFor plants, light is the source of energy and the most relevant regulator of growth and adaptations to the environment by inducing changes in gene expression at various levels, including alternative splicing. Chloroplasts trigger retrograde signals that control alternative splicing in leaves and roots in response to light. Here we provide evidence suggesting that sugars, derived from photosynthesis, act as mobile signals controlling alternative splicing in roots. The inhibition of TOR kinase activity diminishes the alternative splicing response to light and/or sugars in roots, showing the relevance of the TOR pathway in this signaling mechanism. Furthermore, disrupting the function of the mitochondria abolishes alternative splicing changes supporting a key role for these organelles in this signaling axis. We conclude that sugars can act as mobile signals coordinating alternative splicing responses to light throughout the whole plant, exerting this function in roots by activating the TOR pathway.Graphical AbstractArt by Dr. Luciana Giono.
- Published
- 2018
- Full Text
- View/download PDF
26. Organelle Remote Control of Alternative Splicing Through TOR
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Maria Kalyna, Andrea Barta, Christian Meyer, Alberto R. Kornblihtt, Lucas Servi, Stefan Riegler, Armin Fuchs, and Ezequiel Petrillo
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Chloroplast ,Organelle ,Alternative splicing ,Gene expression ,Regulator ,Translation (biology) ,Signal transduction ,Mitochondrion ,Biology ,Cell biology - Abstract
Light makes the difference between life and death for plants, it is their source of energy and also a regulator of plant growth and adaptations to the environment. In plants, light regulates gene expression at various levels including alternative splicing. Chloroplasts are a key part in this process sensing light and providing retrograde signals which modulate alternative splicing in the leaves but also in the roots. We show here that sugars are the mobile signals responsible for the alternative splicing changes in the roots. We provide evidence for the involvement of mitochondria and the activation of TOR kinase in this light signaling pathway. Furthermore, translation activation seems to be of most relevance in order to properly adjust the alternative splicing patterns in response to light/dark transitions and might be a common node for cross-regulation by different pathways.
- Published
- 2018
27. Effects of airborne particulate matter on alternative pre-mRNA splicing in colon cancer cells
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Mariano Alló, Maria Ana Redal, Alberto R. Kornblihtt, Mamdouh I. Khoder, Manuel J. Muñoz, Valeria Buggiano, Mansour A. Alghamdi, Celina Lafaille, Ezequiel Petrillo, and Magdy Shamy
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Untranslated region ,Cellular differentiation ,Bone Morphogenetic Protein 4 ,Biology ,Bone morphogenetic protein ,Biochemistry ,Ciencias de la Tierra y relacionadas con el Medio Ambiente ,PARTICULATE MATTER ,Cell Line, Tumor ,RNA Precursors ,medicine ,Humans ,ALTERNATIVE SPLICING ,COLON CANCER CELLS ,RNA, Messenger ,DNA Primers ,General Environmental Science ,BONE MORPHOGENETIC PROTEIN ,Genetics ,Messenger RNA ,Base Sequence ,Reverse Transcriptase Polymerase Chain Reaction ,Cell growth ,Alternative splicing ,Cancer ,medicine.disease ,Cell biology ,Alternative Splicing ,AIR POLLUTION ,HEK293 Cells ,Colonic Neoplasms ,RNA splicing ,Particulate Matter ,Meteorología y Ciencias Atmosféricas ,CIENCIAS NATURALES Y EXACTAS - Abstract
Alternative pre-mRNA splicing plays key roles in determining tissue- and species-specific cell differentiation as well as in the onset of hereditary disease and cancer, being controlled by multiple post- and co-transcriptional regulatory mechanisms. We report here that airborne particulate matter, resulting from industrial pollution, inhibits expression and specifically affects alternative splicing at the 5' untranslated region of the mRNA encoding the bone morphogenetic protein BMP4 in human colon cells in culture. These effects are consistent with a previously reported role for BMP4 in preventing colon cancer development, suggesting that ingestion of particulate matter could contribute to the onset of colon cell proliferation. We also show that the underlying mechanism might involve changes in transcriptional elongation. This is the first study to demonstrate that particulate matter causes non-pleiotropic changes in alternative splicing. Fil: Buggiano, Valeria Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Alló, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Lafaille, Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Redal, María Ana. Instituto Universitario del Hospital Italiano de Buenos Aires; Argentina Fil: Alghamdi, Mansour A.. King Abdulaziz University; Arabia Saudita Fil: Khoder, Mamdouh I.. King Abdulaziz University; Arabia Saudita Fil: Shamy, Magdy. King Abdulaziz University; Arabia Saudita Fil: Muñoz, Manuel Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
- Published
- 2015
28. Light regulates alternative splicing outcomes via the TOR kinase pathway
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Stefan, Riegler, Lucas, Servi, M Regina, Scarpin, Micaela A, Godoy Herz, María G, Kubaczka, Peter, Venhuizen, Christian, Meyer, Jacob O, Brunkard, Maria, Kalyna, Andrea, Barta, and Ezequiel, Petrillo
- Subjects
Sirolimus ,Alternative Splicing ,Chloroplasts ,Light ,Arabidopsis Proteins ,Gene Expression Regulation, Plant ,TOR Serine-Threonine Kinases ,Arabidopsis ,Plants ,Article ,Signal Transduction - Abstract
SUMMARY For plants, light is the source of energy and the most relevant regulator of growth and adaptations to the environment by inducing changes in gene expression at various levels, including alternative splicing. Light-triggered chloroplast retrograde signals control alternative splicing in Arabidopsis thaliana. Here, we provide evidence that light regulates the expression of a core set of splicing-related factors in roots. Alternative splicing responses in roots are not directly caused by light but are instead most likely triggered by photo-synthesized sugars. The target of rapamycin (TOR) kinase plays a key role in this shoot-to-root signaling pathway. Knocking down TOR expression or pharmacologically inhibiting TOR activity disrupts the alternative splicing responses to light and exogenous sugars in roots. Consistently, splicing decisions are modulated by mitochondrial activity in roots. In conclusion, by activating the TOR pathway, sugars act as mobile signals to coordinate alternative splicing responses to light throughout the whole plant., Graphical Abstract, In brief Riegler et al. reveal a central role for TOR kinase paired with retrograde signaling in alternative splicing regulation by light in roots and, to a certain extent, in leaves. Activating the TOR pathway, sugars act as mobile signals to coordinate alternative splicing responses to light throughout the whole plant.
- Published
- 2017
29. Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation
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Michal Krzyszton, Lucas Servi, Szymon Swiezewski, John W. S. Brown, Micaela A. Godoy Herz, Grzegorz Brzyżek, M. Guillermina Kubaczka, Craig G. Simpson, Alberto R. Kornblihtt, and Ezequiel Petrillo
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Transcription Elongation, Genetic ,Light ,Transcription elongation ,Arabidopsis ,Biology ,Histones ,03 medical and health sciences ,0302 clinical medicine ,Gene Expression Regulation, Plant ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Arabidopsis Proteins ,Alternative splicing ,Acetylation ,Cell Biology ,Darkness ,Plants, Genetically Modified ,Molecular biology ,Alternative Splicing ,Kinetics ,RNA, Plant ,Mutation ,RNA Polymerase II ,Transcriptional Elongation Factors ,Transcriptional elongation ,030217 neurology & neurosurgery - Abstract
Light makes carbon fixation possible, allowing plant and animal life on Earth. We have previously shown that light regulates alternative splicing in plants. Light initiates a chloroplast retrograde signaling that regulates nuclear alternative splicing of a subset of Arabidopsis thaliana transcripts. Here, we show that light promotes RNA polymerase II (Pol II) elongation in the affected genes, whereas in darkness, elongation is lower. These changes in transcription are consistent with elongation causing the observed changes in alternative splicing, as revealed by different drug treatments and genetic evidence. The light control of splicing and elongation is abolished in an Arabidopsis mutant defective in the transcription factor IIS (TFIIS). We report that the chloroplast control of nuclear alternative splicing in plants responds to the kinetic coupling mechanism found in mammalian cells, providing unique evidence that coupling is important for a whole organism to respond to environmental cues.
- Published
- 2019
30. Transcriptional elongation and alternative splicing
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Ignacio E. Schor, Ezequiel Petrillo, Micaela A. Godoy Herz, Mariano Alló, Valeria Buggiano, Celina Lafaille, Manuel J. Muñoz, Nicolás Nieto Moreno, Gwendal Dujardin, Ana Fiszbein, Alberto R. Kornblihtt, and Luciana Inés Gómez Acuña
- Subjects
Transcription Elongation, Genetic ,Transcription elongation ,Biophysics ,RNA polymerase II ,Computational biology ,Models, Biological ,Biochemistry ,Ciencias Biológicas ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,Transcription (biology) ,Genetics ,Animals ,Humans ,ALTERNATIVE SPLICING ,TRANSCRIPTION ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,Alternative splicing ,Bioquímica y Biología Molecular ,Chromatin ,Alternative Splicing ,Kinetics ,Crosstalk (biology) ,RNA splicing ,Proteome ,biology.protein ,POL II ELONGATION ,RNA Polymerase II ,Transcriptional elongation ,CIENCIAS NATURALES Y EXACTAS ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Alternative splicing has emerged as a key contributor to proteome diversity, highlighting the importance of understanding its regulation. In recent years it became apparent that splicing is predominantly cotranscriptional, allowing for crosstalk between these two nuclear processes. We discuss some of the links between transcription and splicing, with special emphasis on the role played by transcription elongation in the regulation of alternative splicing events and in particular the kinetic model of alternative splicing regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation. Fil: Dujardin, Gwendal. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Lafaille, Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Buggiano, Valeria Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Gómez Acuña, Luciana Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Fiszbein, Ana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Godoy Herz, Micaela Amalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Nieto Moreno, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Muñoz, Manuel Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Alló, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Schor, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina
- Published
- 2013
31. A Polar Mechanism Coordinates Different Regions of Alternative Splicing within a Single Gene
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Sebastian Kadener, Alberto R. Kornblihtt, Alexei D. Neverov, Ezequiel Petrillo, Francisco E. Baralle, Federico Pelisch, Guadalupe Nogués, Andrés F. Muro, Mikhail S. Gelfand, and Juan Pablo Fededa
- Subjects
RNA Splicing ,Mutant ,Exonic splicing enhancer ,RNA-binding protein ,RNA polymerase II ,Biology ,Transfection ,Exon ,Mice ,Cell Line, Tumor ,Alpha-Globulins ,Chlorocebus aethiops ,Animals ,Humans ,Protein Isoforms ,Antigens, Viral, Tumor ,Promoter Regions, Genetic ,Gene ,Molecular Biology ,Alleles ,Genetics ,Mice, Knockout ,Models, Genetic ,Serine-Arginine Splicing Factors ,Alternative splicing ,Computational Biology ,Nuclear Proteins ,RNA-Binding Proteins ,Exons ,Cell Biology ,Fibroblasts ,Fibronectins ,DNA-Binding Proteins ,Alternative Splicing ,Genes ,RNA splicing ,COS Cells ,biology.protein ,RNA Polymerase II ,Dichlororibofuranosylbenzimidazole ,Transcription Factors - Abstract
Alternative splicing plays a key role in generating protein diversity. Transfections with minigenes revealed coordination between two distant, alternatively spliced exons in the same gene. Mutations that either inhibit or stimulate inclusion of the upstream alternative exon deeply affect inclusion of the downstream one. However, similar mutations at the downstream alternative exon have little effect on the upstream one. This polar effect is promoter specific and is enhanced by inhibition of transcriptional elongation. Consistently, cells from mutant mice with either constitutive or null inclusion of a fibronectin alternative exon revealed coordination with a second alternative splicing region, located far downstream. Using allele-specific RT-PCR, we demonstrate that this coordination occurs in cis and is also affected by transcriptional elongation rates. Bioinformatics supports the generality of these findings, indicating that 25% of human genes contain multiple alternative splicing regions and identifying several genes with nonrandom distribution of mRNA isoforms at two alternative regions.
- Published
- 2005
- Full Text
- View/download PDF
32. Let there be light: Regulation of gene expression in plants
- Author
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Alberto R. Kornblihtt, Andrea Barta, Maria Kalyna, Micaela A. Godoy Herz, and Ezequiel Petrillo
- Subjects
retrograde signaling ,0106 biological sciences ,Light ,Arabidopsis ,Points-of-View ,Biology ,01 natural sciences ,Ciencias Biológicas ,purl.org/becyt/ford/1 [https] ,alternative splicing ,03 medical and health sciences ,chloroplast ,Gene Expression Regulation, Plant ,Transcription (biology) ,Gene expression ,ALTERNATIVE SPLICING ,Photosynthesis ,RETROGRADE SIGNALING ,purl.org/becyt/ford/1.6 [https] ,Molecular Biology ,Gene ,030304 developmental biology ,2. Zero hunger ,Genetics ,Regulation of gene expression ,0303 health sciences ,Messenger RNA ,PHOTORECEPTORS ,Arabidopsis Proteins ,Alternative splicing ,CHLOROPLAST ,RNA ,photoreceptors ,Cell Biology ,Bioquímica y Biología Molecular ,Cell biology ,LIGHT ,RNA splicing ,CIENCIAS NATURALES Y EXACTAS ,010606 plant biology & botany - Abstract
Gene expression regulation relies on a variety of molecular mechanisms affecting different steps of a messenger RNA (mRNA) life: transcription, processing, splicing, alternative splicing, transport, translation, storage and decay. Light induces massive reprogramming of gene expression in plants. Differences in alternative splicing patterns in response to environmental stimuli suggest that alternative splicing plays an important role in plant adaptation to changing life conditions. In a recent publication, our laboratories showed that light regulates alternative splicing of a subset of Arabidopsis genes encoding proteins involved in RNA processing by chloroplast retrograde signals. The light effect on alternative splicing is also observed in roots when the communication with the photosynthetic tissues is not interrupted, suggesting that a signaling molecule travels through the plant. These results point at alternative splicing regulation by retrograde signals as an important mechanism for plant adaptation to their environment. Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Medical University of Vienna; Austria Fil: Godoy Herz, Micaela Amalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina Fil: Barta, Andrea. Medical University of Vienna; Austria Fil: Kalyna, Maria. University of Natural Resources and Life Sciences; Austria Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular. Laboratorio de Fisiología y Biología Molecular; Argentina
- Published
- 2014
33. Shedding light on the chloroplast as a remote control of nuclear gene expression
- Author
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Alberto R. Kornblihtt, Andrea Barta, Maria Kalyna, Micaela A. Godoy Herz, and Ezequiel Petrillo
- Subjects
0106 biological sciences ,Photoreceptors, Plant ,Phototropin ,Nuclear gene ,Chloroplasts ,Light Signal Transduction ,Light ,Otras Ciencias Biológicas ,Plant Science ,Biology ,Chloroplast ,01 natural sciences ,Ciencias Biológicas ,03 medical and health sciences ,alternative splicing ,retrograde signal ,Cryptochrome ,chloroplast ,Gene Expression Regulation, Plant ,030304 developmental biology ,Cell Nucleus ,0303 health sciences ,Phytochrome ,Alternative splicing ,Photoreceptor protein ,food and beverages ,Mini-Review ,Molecular biology ,Cell biology ,Retrograde signaling ,RNA ,sense organs ,Retrograde signal ,CIENCIAS NATURALES Y EXACTAS ,010606 plant biology & botany - Abstract
Plants rely on a sophisticated light sensing and signaling system that allows them to respond to environmental changes. Photosensory protein systems -phytochromes, cryptochromes, phototropins, and ultraviolet (UV)-B photoreceptors- have evolved to let plants monitor light conditions and regulate different levels of gene expression and developmental processes. However, even though photoreceptor proteins are best characterized and deeply studied, it is also known that chloroplasts are able to sense light conditions and communicate the variations to the nucleus that adjust its transcriptome to the changing environment. The redox state of components of the photosynthetic electron transport chain works as a sensor of photosynthetic activity and can affect nuclear gene expression by a retrograde signaling pathway. Recently, our groups showed that a retrograde signaling pathway can modulate the alternative splicing process, revealing a novel layer of gene expression control by chloroplast retrograde signaling. Fil: Godoy Herz, Micaela Amalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Barta, Andrea. Medical University of Vienna; Austria Fil: Kalyna, Maria. University of Natural Resources and Life Sciences; Austria Fil: Petrillo, Ezequiel. Medical University of Vienna; Austria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
- Published
- 2014
34. Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation
- Author
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Alberto R. Kornblihtt, Ignacio E. Schor, Ezequiel Petrillo, and Ana Fiszbein
- Subjects
CHROMATIN ,Chromatin Immunoprecipitation ,Cellular differentiation ,Biology ,Real-Time Polymerase Chain Reaction ,General Biochemistry, Genetics and Molecular Biology ,Article ,Epigenesis, Genetic ,Ciencias Biológicas ,Exon ,Mice ,Cell Line, Tumor ,Animals ,ALTERNATIVE SPLICING ,Epigenetics ,RNA, Small Interfering ,Molecular Biology ,Neural Cell Adhesion Molecules ,DNA Primers ,Neurons ,General Immunology and Microbiology ,Reverse Transcriptase Polymerase Chain Reaction ,General Neuroscience ,Alternative splicing ,Intron ,Cell Differentiation ,Azepines ,Exons ,Sequence Analysis, DNA ,Bioquímica y Biología Molecular ,respiratory system ,DNA Methylation ,Molecular biology ,Chromatin ,Alternative Splicing ,DIFFERENTIATION ,nervous system ,RNA splicing ,Azacitidine ,Quinazolines ,Neural cell adhesion molecule ,POL II ELONGATION ,CIENCIAS NATURALES Y EXACTAS - Abstract
Alternative splicing contributes to cell type-specific transcriptomes. Here, we show that changes in intragenic chromatin marks affect NCAM (neural cell adhesion molecule) exon 18 (E18) alternative splicing during neuronal differentiation. An increase in the repressive marks H3K9me2 and H3K27me3 along the gene body correlated with inhibition of polymerase II elongation in the E18 region, but without significantly affecting total mRNA levels. Treatment with the general DNA methylation inhibitor 5-azacytidine and BIX 01294, a specific inhibitor of H3K9 dimethylation, inhibited the differentiation-induced E18 inclusion, pointing to a role for repressive marks in sustaining NCAM splicing patterns typical of mature neurons. We demonstrate that intragenic deployment of repressive chromatin marks, induced by intronic small interfering RNAs targeting NCAM intron 18, promotes E18 inclusion in undifferentiated N2a cells, confirming the chromatin changes observed upon differentiation to be sufficient to induce alternative splicing. Combined with previous evidence that neuronal depolarization causes H3K9 acetylation and subsequent E18 skipping, our results show how two alternative epigenetic marks regulate NCAM alternative splicing and E18 levels in different cellular contexts. Fil: Schor, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina Fil: Fiszbein, Ana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina
- Published
- 2013
35. Alternative splicing: a pivotal step between eukaryotic transcription and translation
- Author
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Mariano Alló, Gwendal Dujardin, Manuel J. Muñoz, Ezequiel Petrillo, Alberto R. Kornblihtt, and Ignacio E. Schor
- Subjects
Transcription, Genetic ,Computational biology ,Biology ,Ciencias Biológicas ,Transcription (biology) ,RNA Precursors ,Animals ,Humans ,Molecular Biology ,Transcription factor ,Gene ,Genetics ,Alternative splicing ,Eukaryotic transcription ,Eukaryota ,Cell Biology ,Bioquímica y Biología Molecular ,Chromatin ,Alternative Splicing ,Multicellular organism ,SPLICING ALTERNATIVO ,Protein Biosynthesis ,RNA splicing ,Spliceosomes ,SPLICING ,CIENCIAS NATURALES Y EXACTAS ,Signal Transduction ,Transcription Factors - Abstract
Alternative splicing was discovered simultaneously with splicing over three decades ago. Since then, an enormous body of evidence has demonstrated the prevalence of alternative splicing in multicellular eukaryotes, its key roles in determining tissue- and species-specific differentiation patterns, the multiple post- and co-transcriptional regulatory mechanisms that control it, and its causal role in hereditary disease and cancer. The emerging evidence places alternative splicing in a central position in the flow of eukaryotic genetic information, between transcription and translation, in that it can respond not only to various signalling pathways that target the splicing machinery but also to transcription factors and chromatin structure. Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Schor, Ignacio Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Alló, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Dujardin, Gwendal. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Muñoz, Manuel Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina
- Published
- 2013
36. The control of root growth by reactive oxygen species in Salix nigra Marsh. seedlings
- Author
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Sara I. Maldonado, Gonzalo Roqueiro, Verónica Láinez, Humberto F. Causin, Ezequiel Petrillo, Liliana B. Pena, Cintia F. Marchetti, and Susana M. Gallego
- Subjects
Blotting, Western ,Plant Science ,Root hair ,Salix nigra ,Plant Roots ,chemistry.chemical_compound ,Superoxides ,Botany ,Genetics ,Hydrogen peroxide ,Peroxidase ,Plant Proteins ,chemistry.chemical_classification ,Budding ,Reactive oxygen species ,NADPH oxidase ,biology ,NADPH Oxidases ,Salix ,General Medicine ,Hydrogen Peroxide ,Meristem ,biology.organism_classification ,chemistry ,Seedlings ,biology.protein ,Electrophoresis, Polyacrylamide Gel ,Reactive Oxygen Species ,Agronomy and Crop Science - Abstract
The production of reactive oxygen species (ROS) in specific regions of Salix seedlings roots seems essential for the normal growth of this organ. We examined the role of different ROS in the control of root development in Salix nigra seedlings, and explored possible mechanisms involved in the regulation of ROS generation and action. Root growth was not significantly affected by OH quenchers, while it was either partially or completely inhibited in the presence of H2O2 or O2 − scavengers, respectively. O2 − production was elevated in the root apex, particularly in the subapical meristem and protodermal zones. Apical O2 − generation activity was correlated to a high level of either Cu/Zn superoxide dismutase protein as well as carbonylated proteins. While NADPH-oxidase (NOX) was probably the main source of O2 − generation, the existence of other sources should not be discarded. O2 − production was also high in root hairs during budding, but it markedly decreased when the hair began to actively elongate. Root hair formation increased in the presence of H2O2 scavengers, and was suppressed when H2O2 or peroxidase inhibitors were supplied. The negative effect of H2O2 was partially counteracted by a MAPKK inhibitor. Possible mechanisms of action of the different ROS in comparison with other plant model systems are discussed.
- Published
- 2011
37. Alternative splicing adds a new loop to the circadian clock
- Author
-
Alberto R. Kornblihtt, Ezequiel Petrillo, Marcelo J. Yanovsky, and Sabrina E. Sanchez
- Subjects
Ciencias Biológicas ,Genetics ,purl.org/becyt/ford/1 [https] ,Bioquímica y Biología Molecular ,Arginine methyltransferase ,Biology ,General Agricultural and Biological Sciences ,Splicing ,purl.org/becyt/ford/1.6 [https] ,Humanities ,CIENCIAS NATURALES Y EXACTAS ,Plantas ,Article Addendum - Abstract
Circadian clocks allow organisms to adjust multiple physiological and developmental processes in anticipation of daily and seasonal changes in the environment. At the molecular level these clocks consist of interlocked feedback loops, involving transcriptional activation and repression, but also post-translational modifications. In a recently published work we provided evidence that PRMT5, a protein arginine methyl transferase, is part of a novel loop within the circadian clock of the plant Arabidopsis thaliana by regulating alternative splicing of key clock mRNAs. We also found evidence indicating that PRMT5 has a role in the regulation of alternative splicing and the circadian network in Drosophila melanogaster, although the clock connection in the latter is more elusive and seems to be at the output level. We conclude that alternative precursor messenger RNA (pre-mRNA) splicing is part of the circadian program and could be a main actor in the fine-tuning of biological clocks. Here, we embrace the alternative splicing process as part of the circadian program and discuss the possibility that this mechanism is of fundamental relevance for the fine-tuning of biological clocks. Fil: Petrillo, Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Sanchez, Sabrina Elena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Kornblihtt, Alberto Rodolfo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Fisiología, Biología Molecular y Neurociencias. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Fisiología, Biología Molecular y Neurociencias; Argentina Fil: Yanovsky, Marcelo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina
- Published
- 2011
38. Alternative splicing at the right time
- Author
-
Ezequiel Petrillo, Alberto R. Kornblihtt, Marcelo J. Yanovsky, and Sabrina E. Sanchez
- Subjects
Genetics ,Protein-Arginine N-Methyltransferases ,Models, Genetic ,Arabidopsis Proteins ,Protein arginine methyltransferase 5 ,Circadian clock ,Alternative splicing ,Arabidopsis ,Context (language use) ,Cell Biology ,Computational biology ,Biology ,Alternative Splicing ,Drosophila melanogaster ,Circadian Clocks ,RNA splicing ,Proteome ,Animals ,Drosophila Proteins ,Epigenetics ,Circadian rhythm ,Protein Methyltransferases ,Molecular Biology ,Point of View - Abstract
Alternative splicing (AS) allows the production of multiple mRNA variants from a single gene, which contributes to increase the complexity of the proteome. There is evidence that AS is regulated not only by auxiliary splicing factors, but also by components of the core spliceosomal machinery, as well as through epigenetic modifications. However, to what extent these different mechanisms contribute to the regulation of AS in response to endogenous or environmental stimuli is still unclear. Circadian clocks allow organisms to adjust physiological processes to daily changes in environmental conditions. Here we review recent evidence linking circadian clock and AS, and discuss the role of Protein Arginine Methyltransferase 5 (PRMT5) in these processes. We propose that the interactions between daily oscillations in AS and circadian rhythms in the expression of splicing factors and epigenetic regulators offer a great opportunity to dissect the contribution of these mechanisms to the regulation of AS in a physiologically relevant context.
- Published
- 2011
39. The serine/arginine-rich protein SF2/ASF regulates protein sumoylation
- Author
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Federico Pelisch, Eduardo Arzt, Belinda J. Westman, Guillermo Risso, Jimena Druker, Anabella Srebrow, Ezequiel Petrillo, Juan Gerez, Angus I. Lamond, Ignacio E. Schor, and Manuel Javier Muñoz
- Subjects
RNA splicing ,protein p53 ,SUMO protein ,protein binding ,Heterogeneous ribonucleoprotein particle ,environment and public health ,Substrate Specificity ,nuclear protein ,Transcriptional regulation ,genetics ,RNA, Small Interfering ,E3 ligase ,serine-arginine-rich splicing proteins ,Multidisciplinary ,protein asf ,biology ,Serine-Arginine Splicing Factors ,sumoylation ,article ,protein processing ,Nuclear Proteins ,RNA-Binding Proteins ,ubiquitin-conjugating enzyme UBC9 ,cell line ,protein function ,Biological Sciences ,heat shock ,unclassified drug ,enzyme activity ,Ubiquitin ligase ,ubiquitin conjugating enzyme ,regulator protein ,priority journal ,Biochemistry ,protein protein interaction ,ubiquitin protein ligase E3 ,signal transduction ,conjugation ,Protein Binding ,Protein sumoylation ,regulatory mechanism ,SUMO-1 Protein ,protein Ubc9 ,SUMO enzymes ,Cell Line ,heat shock response ,SR protein ,Humans ,controlled study ,human ,enzyme specificity ,protein expression ,protein inhibitor of activated STAT1 ,RNA metabolism ,Splicing factor ,protein inhibitor of activated STAT ,human cell ,SUMO E3 ligase ,RNA binding protein ,small interfering RNA ,Sumoylation Pathway ,RNA processing ,protein sf2 ,Ubiquitin-Conjugating Enzymes ,biology.protein ,RNA ,Posttranslational modification ,molecular recognition ,Tumor Suppressor Protein p53 ,metabolism ,SUMO 1 protein ,Heat-Shock Response - Abstract
Protein modification by conjugation of small ubiquitin-related modifier (SUMO) is involved in diverse biological functions, such as transcription regulation, subcellular partitioning, stress response, DNA damage repair, and chromatin remodeling. Here, we show that the serine/arginine-rich protein SF2/ASF, a factor involved in splicing regulation and other RNA metabolism-related processes, is a regulator of the sumoylation pathway. The overexpression of this protein stimulates, but its knockdown inhibits SUMO conjugation. SF2/ASF interacts with Ubc9 and enhances sumoylation of specific substrates, sharing characteristics with already described SUMO E3 ligases. In addition, SF2/ASF interacts with the SUMO E3 ligase PIAS1 (protein inhibitor of activated STAT-1), regulating PIAS1-induced overall protein sumoylation. The RNA recognition motif 2 of SF2/ASF is necessary and sufficient for sumoylation enhancement. Moreover, SF2/ASF has a role in heat shock-induced sumoylation and promotes SUMO conjugation to RNA processing factors. These results add a component to the sumoylation pathway and a previously unexplored role for the multifunctional SR protein SF2/ASF. Fil:Pelisch, F. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Gerez, J. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Druker, J. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Schor, I.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Muñoz, M.J. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Risso, G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Petrillo, E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Srebrow, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.
- Published
- 2010
40. A methyl transferase links the circadian clock to the regulation of alternative splicing
- Author
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Esteban J. Beckwith, Craig G. Simpson, Fernanda M. Ceriani, Mathias L. Rugnone, Alberto R. Kornblihtt, Paloma Mas, C. Esteban Hernando, Micaela A. Godoy Herz, Sabrina E. Sanchez, Marcelo J. Yanovsky, Pablo D. Cerdán, Xu Zhang, Ana Depetris-Chauvin, Juan C. Cuevas, Justin O. Borevitz, Ezequiel Petrillo, John W. S. Brown, Yanovsky, Marcelo J., Fundación Antorchas, Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina), Universidad de Buenos Aires, European Commission, Howard Hughes Medical Institute, Ministerio de Educación y Ciencia (España), and EMBO
- Subjects
Protein-Arginine N-Methyltransferases ,Light ,Period (gene) ,Circadian clock ,Arabidopsis ,Biology ,Methylation ,RAR-related orphan receptor alpha ,Gene Expression Regulation, Plant ,Circadian Clocks ,RNA Precursors ,Animals ,Drosophila Proteins ,Protein Methyltransferases ,RNA, Messenger ,Circadian rhythm ,Hardware_REGISTER-TRANSFER-LEVELIMPLEMENTATION ,Genetics ,Multidisciplinary ,Base Sequence ,Arabidopsis Proteins ,Gene Expression Profiling ,ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS ,Alternative splicing ,Neurosciences ,Period Circadian Proteins ,Darkness ,Bacterial circadian rhythms ,Circadian Rhythm ,CLOCK ,ComputingMilieux_MANAGEMENTOFCOMPUTINGANDINFORMATIONSYSTEMS ,Alternative Splicing ,Drosophila melanogaster ,Phenotype ,Neurons and Cognition ,Mutation ,RNA splicing ,Spliceosomes ,RNA Splice Sites ,InformationSystems_MISCELLANEOUS ,Transcription Factors ,Autre (Sciences du Vivant) - Abstract
HAL Id: hal-01218274, Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day–night cycle. Post-transcriptional regulation is emerging as an important component of circadian networks, but the molecular mechanisms linking the circadian clock to the control of RNA processing are largely unknown. Here we show that PROTEIN ARGININE METHYL TRANSFERASE 5 (PRMT5), which transfers methyl groups to arginine residues present in histones and Sm spliceosomal proteins, links the circadian clock to the control of alternative splicing in plants. Mutations in PRMT5 impair several circadian rhythms in Arabidopsis thaliana and this phenotype is caused, at least in part, by a strong alteration in alternative splicing of the core-clock gene PSEUDO RESPONSE REGULATOR 9 (PRR9). Furthermore, genome-wide studies show that PRMT5 contributes to the regulation of many pre-messenger-RNA splicing events, probably by modulating 5′-splice-site recognition. PRMT5 expression shows daily and circadian oscillations, and this contributes to the mediation of the circadian regulation of expression and alternative splicing of a subset of genes. Circadian rhythms in locomotor activity are also disrupted in dart5-1, a mutant affected in the Drosophila melanogaster PRMT5 homologue, and this is associated with alterations in splicing of the core-clock gene period and several clock-associated genes. Our results demonstrate a key role for PRMT5 in the regulation of alternative splicing and indicate that the interplay between the circadian clock and the regulation of alternative splicing by PRMT5 constitutes a common mechanism that helps organisms to synchronize physiological processes with daily changes in environmental conditions., This work was supported by grants from the Fundación Antorchas, the Agencia Nacional de Promoción de Ciencia y Tecnología of Argentina, the Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina and the University of Buenos Aires to M.J.Y. and A.R.K., and from the European Union Network of Excellence on Alternative Splicing (EURASNET) to A.R.K. and J.W.S.B. M.J.Y. and A.R.K. are Howard Hughes Medical Institute international research scholars. P.M.’s laboratory is supported by a Ministerio de Educación y Ciencia grant, the European Young Investigator Awards and the EMBO Young Investigator Awards; M.F.C.’s laboratory is supported by Proyecto de Investigación Científica y Tecnológica 2006-1249.
- Published
- 2010
41. Control of alternative splicing through siRNA-mediated transcriptional gene silencing
- Author
-
Eduardo Eyras, Manuel de la Mata, Alberto R. Kornblihtt, Mariano Alló, Valeria Buggiano, Mireya Plass, Benoit Chabot, Juan Pablo Fededa, Roscoe Klinck, Ignacio E. Schor, Ezequiel Petrillo, Eneritz Agirre, and Sherif Abou Elela
- Subjects
Male ,Ribonuclease III ,Small interfering RNA ,Carcinoma, Hepatocellular ,Transcription, Genetic ,Exonic splicing enhancer ,Biology ,Methylation ,Epigenesis, Genetic ,Histones ,Exon ,Mice ,Structural Biology ,RNA interference ,Heterochromatin ,Animals ,Humans ,Eukaryotic Initiation Factors ,RNA, Small Interfering ,Promoter Regions, Genetic ,Molecular Biology ,Base Sequence ,Lysine ,Alternative splicing ,Liver Neoplasms ,TAF9 ,Exons ,Argonaute ,Oligonucleotides, Antisense ,Molecular biology ,Fibronectins ,Alternative Splicing ,Chromobox Protein Homolog 5 ,Gene Knockdown Techniques ,RNA splicing ,Argonaute Proteins ,RNA Interference ,RNA Polymerase II ,HeLa Cells - Abstract
When targeting promoter regions, small interfering RNAs (siRNAs) trigger a previously proposed pathway known as transcriptional gene silencing by promoting heterochromatin formation. Here we show that siRNAs targeting intronic or exonic sequences close to an alternative exon regulate the splicing of that exon. The effect occurred in hepatoma and HeLa cells with siRNA antisense strands designed to enter the silencing pathway, suggesting hybridization with nascent pre-mRNA. Unexpectedly, in HeLa cells the sense strands were also effective, suggesting that an endogenous antisense transcript, detectable in HeLa but not in hepatoma cells, acts as a target. The effect depends on Argonaute-1 and is counterbalanced by factors favoring chromatin opening or transcriptional elongation. The increase in heterochromatin marks (dimethylation at Lys9 and trimethylation at Lys27 of histone H3) at the target site, the need for the heterochromatin-associated protein HP1alpha and the reduction in RNA polymerase II processivity suggest a mechanism involving the kinetic coupling of transcription and alternative splicing.
- Published
- 2008
42. Erratum: Alternative splicing: a pivotal step between eukaryotic transcription and translation
- Author
-
Alberto R. Kornblihtt, Ignacio E. Schor, Mariano Alló, Gwendal Dujardin, Ezequiel Petrillo, and Manuel J. Muñoz
- Subjects
Cell Biology ,Molecular Biology - Published
- 2013
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