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Start Over Author "Conn, Simon J." Topic alternative splicing
7 results on '"Conn, Simon J."'

1. ESRP1 controls biogenesis and function of a large abundant multiexon circRNA.

Author

Liu D, Dredge BK, Bert AG, Pillman KA, Toubia J, Guo W, Dyakov BJA, Migault MM, Conn VM, Conn SJ, Gregory PA, Gingras AC, Patel D, Wu B, and Goodall GJ

Subjects
RNA genetics, RNA metabolism, RNA Splicing, Humans, Cell Line, Tumor, Alternative Splicing, RNA, Circular genetics, RNA-Binding Proteins metabolism, rac GTP-Binding Proteins genetics, rac GTP-Binding Proteins metabolism
Abstract

While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2-27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal transition (EMT) and whose formation depends on the epithelial splicing regulator ESRP1. CircDOCK1(2-27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis and CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2-27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 may modify the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2024
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2. miR-200/375 control epithelial plasticity-associated alternative splicing by repressing the RNA-binding protein Quaking.

Author

Pillman KA, Phillips CA, Roslan S, Toubia J, Dredge BK, Bert AG, Lumb R, Neumann DP, Li X, Conn SJ, Liu D, Bracken CP, Lawrence DM, Stylianou N, Schreiber AW, Tilley WD, Hollier BG, Khew-Goodall Y, Selth LA, Goodall GJ, and Gregory PA

Subjects
Animals, Cell Line, Tumor, Cell Movement, Dogs, Humans, Madin Darby Canine Kidney Cells, Mice, SCID, Alternative Splicing physiology, Cell Plasticity physiology, Epithelial-Mesenchymal Transition physiology, MicroRNAs physiology, RNA-Binding Proteins physiology
Abstract

Members of the miR-200 family are critical gatekeepers of the epithelial state, restraining expression of pro-mesenchymal genes that drive epithelial-mesenchymal transition (EMT) and contribute to metastatic cancer progression. Here, we show that miR-200c and another epithelial-enriched miRNA, miR-375, exert widespread control of alternative splicing in cancer cells by suppressing the RNA-binding protein Quaking (QKI). During EMT, QKI-5 directly binds to and regulates hundreds of alternative splicing targets and exerts pleiotropic effects, such as increasing cell migration and invasion and restraining tumour growth, without appreciably affecting mRNA levels. QKI-5 is both necessary and sufficient to direct EMT-associated alternative splicing changes, and this splicing signature is broadly conserved across many epithelial-derived cancer types. Importantly, several actin cytoskeleton-associated genes are directly targeted by both QKI and miR-200c, revealing coordinated control of alternative splicing and mRNA abundance during EMT These findings demonstrate the existence of a miR-200/miR-375/QKI axis that impacts cancer-associated epithelial cell plasticity through widespread control of alternative splicing., (© 2018 The Authors. Published under the terms of the CC BY 4.0 license.)

Published
2018
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3. SRRM4 Expands the Repertoire of Circular RNAs by Regulating Microexon Inclusion.

Author

Conn, Vanessa M., Gabryelska, Marta, Marri, Shashikanth, Stringer, Brett W., Ormsby, Rebecca J., Penn, Timothy, Poonnoose, Santosh, Kichenadasse, Ganessan, and Conn, Simon J.

Subjects
NUCLEOTIDE sequence, NON-coding RNA, MESSENGER RNA, TUMOR markers, RNA sequencing, CIRCULAR RNA, WNT proteins
Abstract

High-throughput RNA sequencing (RNA-seq) and dedicated bioinformatics pipelines have synergized to identify an expansive repertoire of unique circular RNAs (circRNAs), exceeding 100,000 variants. While the vast majority of these circRNAs comprise canonical exonic and intronic sequences, microexons (MEs)—which occur in 30% of functional mRNA transcripts—have been entirely overlooked. CircRNAs which contain these known MEs (ME-circRNAs) could be identified with commonly utilized circRNA prediction pipelines, CIRCexplorer2 and CIRI2, but were not previously recognized as ME-circRNAs. In addition, when employing a bespoke bioinformatics pipeline for identifying RNA chimeras, called Hyb, we could also identify over 2000 ME-circRNAs which contain novel MEs at their backsplice junctions, that are uncalled by either CIRCexplorer2 or CIRI2. Analysis of circRNA-seq datasets from gliomas of varying clinical grades compared with matched control tissue has shown circRNAs have potential as prognostic markers for stratifying tumor from healthy tissue. Furthermore, the abundance of microexon-containing circRNAs (ME-circRNAs) between tumor and normal tissues is correlated with the expression of a splicing associated factor, Serine/arginine repetitive matrix 4 (SRRM4). Overexpressing SRRM4, known for regulating ME inclusion in mRNAs critical for neural differentiation, in human HEK293 cells resulted in the biogenesis of over 2000 novel ME-circRNAs, including ME-circEIF4G3, and changes in the abundance of many canonical circRNAs, including circSETDB2 and circLRBA. This shows SRRM4, in which its expression is correlated with poor prognosis in gliomas, acts as a bona fide circRNA biogenesis factor. Given the known roles of MEs and circRNAs in oncogenesis, the identification of these previously unrecognized ME-circRNAs further increases the complexity and functional purview of this non-coding RNA family. [ABSTRACT FROM AUTHOR]

Published
2020
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4. SplintQuant: a method for accurately quantifying circular RNA transcript abundance without reverse transcription bias

Author

Simon J. Conn, Vanessa M. Conn, Conn, Vanessa, and Conn, Simon J

Subjects
splint ligation, Method, Computational biology, Biology, Real-Time Polymerase Chain Reaction, Cell Line, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Bias, Circular RNA, Humans, Molecular Biology, Gene, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, DNA ligase, Oligonucleotide, Sequence Analysis, RNA, RNA, circular RNA, RNA, Circular, Reverse Transcription, reverse transcription, Reverse transcriptase, qPCR, Alternative Splicing, Real-time polymerase chain reaction, chemistry, 030220 oncology & carcinogenesis, DNA
Abstract

Reverse transcription of RNA is fallible, introducing biases and confounding the quantification of transcript abundance. We demonstrate that circular RNAs (circRNAs) are more subjective to overestimation of transcript abundance than cognate linear RNAs due to their covalently closed, circular form, producing multiple concatameric products from a single priming of reverse transcriptase. We developed SplintQuant, where custom DNA oligonucleotides are ligated by PBCV-1 DNA ligase only when bound to their target RNA. These circRNA-specific DNA oligonucleotides are terminally tagged with universal primers, allowing SplintQuant to accurately quantify even lowly abundant circRNAs through highly specific quantitative PCR (qPCR) in the absence of reverse transcription. SplintQuant is sensitive, specific, highly reproducible, and applicable to the quantification of canonical and noncanonical RNA transcripts including alternative splice variants, gene fusions, and offers a gold-standard approach for accurately quantifying circRNAs. Refereed/Peer-reviewed

Published
2019

5. CircRNAs in Plants

Author

Xuelei Lai, Chloe Zubieta, Stuart Webb, Martin Crespi, Simon J. Conn, Jérémie Bazin, Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Flinders University of South Australia, J. Xiao, Univ Groningen, Lab Biophys Chem, Nijenborgh 7, NL-9747 AG Groningen, Netherlands, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), European Molecular Biology Laboratory, European Molecular Biology Laboratory [Grenoble] (EMBL), Unit for Virus Host-Cell Interactions [Grenoble] (UVHCI), Université Joseph Fourier - Grenoble 1 (UJF)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Lai, Xuelei, Bazin, Jérémie, Webb, Stuart, Crespi, Martin, Zubieta, Chloe, and Conn, Simon J

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Computational biology, Biology, Transcriptome, transcriptomics, 03 medical and health sciences, Transcription (biology), Arabidopsis, microRNA, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Transcriptomics, ComputingMilieux_MISCELLANEOUS, plants, Alternative splicing, food and beverages, Plants, biology.organism_classification, Genome-wide profiling, Phenotype, genome-wide profiling, 030104 developmental biology, RNA splicing, circRNAs, Biogenesis
Abstract

International audience; Circular RNAs (circRNAs) are covalently closed, single-stranded transcripts that are ubiquitously expressed in all eukaryotes and even prokaryotic archaea. Although once regarded as splicing artifacts, circRNAs are a novel class of regulatory molecules with diverse biological functions, including regulation of transcription, modulation of alternative splicing, and binding of miRNAs and proteins. The majority of studies of circRNAs have been performed in animals with a focus on the biogenesis, function, and mechanistic characterization of these molecules. In contrast, the study of circRNAs in plants is just emerging. Interestingly, recent circRNA profiling studies in model plant systems show distinct features of plant circRNAs compared with those from animals, including putative roles in stress response, differences in expression patterns, and novel biogenesis mechanisms. This provides a great opportunity to broaden our knowledge of circRNAs using plant model systems, such as Arabidopsis and rice, which are ideal for phenotypic characterization and genetic studies. In this review, we summarize current knowledge of plant circRNAs, discuss their identification and biogenesis, describe potential functions, and propose future perspectives for plant circRNA study.

Published
2018
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6. miR-200/375 control epithelial plasticity-associated alternative splicing by repressing the RNA-binding protein Quaking

Author

David M. Lawrence, Caroline A Phillips, Andreas W. Schreiber, Xiaochun Li, Wayne D. Tilley, Katherine A. Pillman, Luke A. Selth, John Toubia, Gregory J. Goodall, Daniel P. Neumann, Philip A. Gregory, Simon J. Conn, Suraya Roslan, Brett G. Hollier, Nataly Stylianou, B. Kate Dredge, Cameron P. Bracken, Dawei Liu, Rachael Lumb, Yeesim Khew-Goodall, Andrew G. Bert, Pillman, Katherine A, Phillips, Caroline A, Roslan, Suraya, Toubia, John, Dredge, B Kate, Bert, Andrew G, Lumb, Rachael, Neumann, Daniel P, Li, Xiaochun, Conn, Simon J, Liu, Dawei, Bracken, Cameron P, Lawrence, David M, Schreiber, Andreas W, Khew-Goodall, Yeesim, Goodall, Greogory J, and Gregory, Philip A

Subjects
0301 basic medicine, Epithelial-Mesenchymal Transition, Cell Plasticity, epithelial-mesenchymal transition, RNA-binding protein, Mice, SCID, Biology, epithelial–mesenchymal transition, General Biochemistry, Genetics and Molecular Biology, Article, Madin Darby Canine Kidney Cells, 03 medical and health sciences, alternative splicing, Quaking, Dogs, miR‐375, Cell Movement, Cell Line, Tumor, microRNA, Animals, Humans, Epithelial–mesenchymal transition, Molecular Biology, Gene, Cancer, Messenger RNA, General Immunology and Microbiology, General Neuroscience, Alternative splicing, RNA-Binding Proteins, Articles, miR-200, miR-375, RNA Biology, Protein Quaking, Cell biology, MicroRNAs, 030104 developmental biology, miR‐200, RNA splicing, Cell Adhesion, Polarity & Cytoskeleton
Abstract

Members of the miR-200 family are critical gatekeepers of the epithelial state, restraining expression of pro-mesenchymal genes that drive epithelial-mesenchymal transition (EMT) and contribute to metastatic cancer progression. Here, we show that miR-200cand another epithelial-enriched miRNA, miR-375, exert wide spread control of alternative splicing in cancer cells by suppressing the RNA-binding protein Quaking (QKI). During EMT, QKI-5 directly binds to and regulates hundreds of alternative splicing targets and exerts pleiotropic effects, such as increasing cell migration and invasion and restraining tumour growth, without appreciably affecting mRNA levels. QKI-5 is both necessary and sufficient to direct EMT-associated alternative splicing changes, and this splicing signature is broadly conserved across many epithelial-derived cancer types. Importantly, several actin cytoskeleton-associated genes are directly targeted by both QKI and miR-200c, revealing coordinated control of alternative splicing and mRNA abundance during EMT. These findings demonstrate the existence of a miR200/miR-375/QKI axis that impacts cancer-associated epithelial cell plasticity through widespread control of alternative splicing. Refereed/Peer-reviewed

Published
2018

7. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation

Author

Chloe Zubieta, Markus Schmid, Vanessa M. Conn, Aditya Nayak, Véronique Hugouvieux, Agnès Jourdain, Simon J. Conn, Gökhan Cildir, Giovanna Capovilla, Vinay Tergaonkar, Stephanie A. Conos, Centre for Cancer Biology, Hanson Institute, Adelaide, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Biochemistry, Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore (NUS), Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, ANR (FLOPINET), CNRS, NHMRC [GNT1089167], Australian Research Council [FT160100318], ATIP-Avenir, LabEx GRAL [ANR-10-LABX-49-01], South Australian Government Department of State Development, CEA Irtelis fellowship, ANR-16-CE92-0023,FLOPINET,Floral Pioneer Factors(2016), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Conn, Vanessa M, Hugouvieux, Véronique, Nayak, Aditya, Conos, Stephanie A, Capovilla, Giovanna, Cildir, Gökhan, Jourdain, Agnés, Tergaonkar, Vinay, Schmid, Markus, Zubieta, Chloe, Conn, Simon J, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), ANR-16-CE92-0023,FLOPINET,Floral Pioneer Factors, and ANR-10-LABX-49-01,Labex GRAL

Subjects
0106 biological sciences, 0301 basic medicine, circular RNAs (circRNAs), DNA, Plant, RNA Splicing, SEP3, Arabidopsis, Plant Science, Biology, 01 natural sciences, Flowering, 03 medical and health sciences, Splicing factor, Exon, alternative splicing, Circular RNA, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Gene, SEPALLATA3, Homeodomain Proteins, Genetics, Arabidopsis Proteins, Alternative splicing, RNA, Plant, Gene regulation, 030104 developmental biology, back-splicing, RNA splicing, DNA, Circular, Transcription factor, Homeotic gene, Transcription Factors, 010606 plant biology & botany
Abstract

Simon J. Conn (simon.conn@unisa.edu.au); International audience; Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life(1), yet their functions have remained elusive. Here, we report that circRNAs can be used as $bona\ fide$ biomarkers of functional, exon-skipped AS variants in $Arabidopsis$, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA:DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS(2-4). This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.

Published
2017
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