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3. New insight into the catalytic -dependent and -independent roles of METTL3 in sustaining aberrant translation in chronic myeloid leukemia

Author

Ianniello, Zaira, Sorci, Melissa, Ceci Ginistrelli, Lavinia, Iaiza, Alessia, Marchioni, Marcella, Tito, Claudia, Capuano, Ernestina, Masciarelli, Silvia, Ottone, Tiziana, Attrotto, Cristina, Rizzo, Manuela, Franceschini, Luca, de Pretis, Stefano, Voso, Maria Teresa, Pelizzola, Mattia, Fazi, Francesco, and Fatica, Alessandro

Published
2021
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7. Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity

Author

Martins, Luis F., primary, Brambilla, Ilaria, additional, Motta, Alessia, additional, de Pretis, Stefano, additional, Bhat, Ganesh Parameshwar, additional, Badaloni, Aurora, additional, Malpighi, Chiara, additional, Amin, Neal D., additional, Imai, Fumiyasu, additional, Almeida, Ramiro D., additional, Yoshida, Yutaka, additional, Pfaff, Samuel L., additional, and Bonanomi, Dario, additional

Published
2022
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14. An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation

Author

Tesi, A, de Pretis, S, Furlan, M, Filipuzzi, M, Morelli, M, Andronache, A, Doni, M, Verrecchia, A, Pelizzola, M, Amati, B, Sabò, A, Tesi, Alessandra, de Pretis, Stefano, Furlan, Mattia, Filipuzzi, Marco, Morelli, Marco J, Andronache, Adrian, Doni, Mirko, Verrecchia, Alessandro, Pelizzola, Mattia, Amati, Bruno, Sabò, Arianna, Tesi, A, de Pretis, S, Furlan, M, Filipuzzi, M, Morelli, M, Andronache, A, Doni, M, Verrecchia, A, Pelizzola, M, Amati, B, Sabò, A, Tesi, Alessandra, de Pretis, Stefano, Furlan, Mattia, Filipuzzi, Marco, Morelli, Marco J, Andronache, Adrian, Doni, Mirko, Verrecchia, Alessandro, Pelizzola, Mattia, Amati, Bruno, and Sabò, Arianna

Abstract

Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy-producing and anabolic pathways, widespread chromatin decompaction, and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue by profiling the response to LPS stimulation in wild-type and c-myc-deleted primary mouse B-cells. Myc is rapidly induced, becomes detectable on virtually all active promoters and enhancers, but has no direct impact on global transcriptional activity. Instead, Myc contributes to the swift up- and down-regulation of several hundred genes, including many known regulators of the aforementioned cellular processes. Myc-activated promoters are enriched for E-box consensus motifs, bind Myc at the highest levels, and show enhanced RNA Polymerase II recruitment, the opposite being true at down-regulated loci. Remarkably, the Myc-dependent signature identified in activated B-cells is also enriched in Myc-driven B-cell lymphomas: hence, besides modulation of new cancer-specific programs, the oncogenic action of Myc may largely rely on sustained deregulation of its normal physiological targets.

Published
2019

19. Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

Author

Bianchi, Valerio, primary, Ceol, Arnaud, additional, Ogier, Alessandro G. E., additional, de Pretis, Stefano, additional, Galeota, Eugenia, additional, Kishore, Kamal, additional, Bora, Pranami, additional, Croci, Ottavio, additional, Campaner, Stefano, additional, Amati, Bruno, additional, Morelli, Marco J., additional, and Pelizzola, Mattia, additional

Published
2016
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21. Degradation dynamics of microRNAs revealed by a novel pulse-chase approach

Author

Marzi, Matteo J., primary, Ghini, Francesco, additional, Cerruti, Benedetta, additional, de Pretis, Stefano, additional, Bonetti, Paola, additional, Giacomelli, Chiara, additional, Gorski, Marcin M., additional, Kress, Theresia, additional, Pelizzola, Mattia, additional, Muller, Heiko, additional, Amati, Bruno, additional, and Nicassio, Francesco, additional

Published
2016
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22. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Author

Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, Natoli, Gioacchino, Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, and Natoli, Gioacchino

Published
2015

23. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Author

Hubrecht Institute with UMC, Divisie Biomedische Genetica, Cancer, Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, Natoli, Gioacchino, Hubrecht Institute with UMC, Divisie Biomedische Genetica, Cancer, Austenaa, Liv M I, Barozzi, Iros, Simonatto, Marta, Masella, Silvia, Della Chiara, Giulia, Ghisletti, Serena, Curina, Alessia, de Wit, Elzo, Bouwman, Britta A M, de Pretis, Stefano, Piccolo, Viviana, Termanini, Alberto, Prosperini, Elena, Pelizzola, Mattia, de Laat, Wouter, and Natoli, Gioacchino

Published
2015

24. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination

Author

Austenaa, Liv M.I., primary, Barozzi, Iros, additional, Simonatto, Marta, additional, Masella, Silvia, additional, Della Chiara, Giulia, additional, Ghisletti, Serena, additional, Curina, Alessia, additional, de Wit, Elzo, additional, Bouwman, Britta A.M., additional, de Pretis, Stefano, additional, Piccolo, Viviana, additional, Termanini, Alberto, additional, Prosperini, Elena, additional, Pelizzola, Mattia, additional, de Laat, Wouter, additional, and Natoli, Gioacchino, additional

Published
2015
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29. Integrative classification of human coding and noncoding genes through RNA metabolism profiles

Author

Mukherjee, Neelanjan, Calviello, Lorenzo, Hirsekorn, Antje, de Pretis, Stefano, Pelizzola, Mattia, and Ohler, Uwe

Abstract

Pervasive transcription of the human genome results in a heterogeneous mix of coding RNAs and long noncoding RNAs (lncRNAs). Only a small fraction of lncRNAs have demonstrated regulatory functions, thus making functional lncRNAs difficult to distinguish from nonfunctional transcriptional byproducts. This difficulty has resulted in numerous competing human lncRNA classifications that are complicated by a steady increase in the number of annotated lncRNAs. To address these challenges, we quantitatively examined transcription, splicing, degradation, localization and translation for coding and noncoding human genes. We observed that annotated lncRNAs had lower synthesis and higher degradation rates than mRNAs and discovered mechanistic differences explaining slower lncRNA splicing. We grouped genes into classes with similar RNA metabolism profiles, containing both mRNAs and lncRNAs to varying extents. These classes exhibited distinct RNA metabolism, different evolutionary patterns and differential sensitivity to cellular RNA-regulatory pathways. Our classification provides an alternative to genomic context-driven annotations of lncRNAs.

Published
2017
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30. Dynamics of transcriptional and post-transcriptional regulation.

Author

Furlan M, de Pretis S, and Pelizzola M

Subjects
Animals, Humans, Models, Genetic, RNA biosynthesis, RNA genetics, RNA Processing, Post-Transcriptional, Transcription, Genetic
Abstract

Despite gene expression programs being notoriously complex, RNA abundance is usually assumed as a proxy for transcriptional activity. Recently developed approaches, able to disentangle transcriptional and post-transcriptional regulatory processes, have revealed a more complex scenario. It is now possible to work out how synthesis, processing and degradation kinetic rates collectively determine the abundance of each gene's RNA. It has become clear that the same transcriptional output can correspond to different combinations of the kinetic rates. This underscores the fact that markedly different modes of gene expression regulation exist, each with profound effects on a gene's ability to modulate its own expression. This review describes the development of the experimental and computational approaches, including RNA metabolic labeling and mathematical modeling, that have been disclosing the mechanisms underlying complex transcriptional programs. Current limitations and future perspectives in the field are also discussed., (© The Author(s) 2020. Published by Oxford University Press.)

Published
2021
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