Role and regulation of convergent antisense transcription by RNA polymerase II
Final Report Abstract
The human genome is pervasively transcribed by RNA polymerase II (Pol II) producing all protein-coding RNAs in the nucleus and a large set of non-coding RNAs. Gene transcription by Pol II is not a unidirectional process. Transcription in the sense direction is usually accompanied by antisense transcription in the opposite orientation. Antisense transcription is emerging as a new layer in regulating gene expression and represents a main source for noncoding RNAs in human cells. Misregulation of gene expression is a hallmark of human diseases. We have recently developed native elongating transcript sequencing (NET-seq) as a quantitative genome-wide approach for studying the full spectrum of sense and antisense transcription with nucleotide precision in human cells. Application of this high-resolution method has revealed a new antisense transcriptional activity of Pol II in the promoter-proximal region of protein-coding and long noncoding RNA genes, called convergent antisense transcription (CAT). However, key aspects of convergent antisense transcription remained undefined. In this project, we developed new improved protocols for performing NET-seq in mammalian cells along with computational methods to provide new insights into the causes and putative functions of convergent antisense transcription. We uncovered that CAT is widespread occurring at a large set of human genes. Importantly, we provide evidence that CAT indicate intragenic transcribed enhancers which allowed the identification of thousands of new putative enhancers within active genes. This project also uncovered that enhancer transcription, including CAT, is directly regulated by the BET family protein BRD4 emerging as a general regulator of Pol II transcription elongation. Finally, we have applied the integrative transcriptomics analysis pipeline that we have developed in this project to elucidate the cause and the mechanism of a rare human Mendelian progeroid syndrome. The key findings of this project provided a more complete view on the gene regulatory landscape in human cells and led to a prenatal diagnosis for a rare Mendelian progeroid syndrome. In future, we will extend the application of the developed genome-wide approaches and computational methods to human disease models to continue elucidating disease mechanisms.
Publications
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A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination. Molecular Cell, 81(17), 3589-3603.e13.
Arnold, Mirjam; Bressin, Annkatrin; Jasnovidova, Olga; Meierhofer, David & Mayer, Andreas
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Conserved DNA sequence features underlie pervasive RNA polymerase pausing. Nucleic Acids Research, 49(8), 4402-4420.
Gajos, Martyna; Jasnovidova, Olga; van Bömmel, Alena; Freier, Susanne; Vingron, Martin & Mayer, Andreas
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Emerging roles of BET proteins in transcription and co‐transcriptional RNA processing. WIREs RNA, 14(1).
Eischer, Nicole; Arnold, Mirjam & Mayer, Andreas
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Neue Einblicke in die Genregulation mittels funktioneller Multiomik. BIOspektrum, 28(3), 276-278.
Bressin, Annkatrin & Mayer, Andreas
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A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI‐NET sequencing. EMBO Molecular Medicine, 15(2).
Nabavizadeh, Nasrinsadat; Bressin, Annkatrin; Shboul, Mohammad; Moreno, Traspas Ricardo; Chia, Poh Hui; Bonnard, Carine; Szenker‐Ravi, Emmanuelle; Sarıbaş, Burak; Beillard, Emmanuel; Altunoglu, Umut; Hojati, Zohreh; Drutman, Scott; Freier, Susanne; El‐Khateeb, Mohammad; Fathallah, Rajaa; Casanova, Jean‐Laurent; Soror, Wesam; Arafat, Alaa; Escande‐Beillard, Nathalie ... & Reversade, Bruno
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High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. Nature Communications, 14(1).
Bressin, Annkatrin; Jasnovidova, Olga; Arnold, Mirjam; Altendorfer, Elisabeth; Trajkovski, Filip; Kratz, Thomas A.; Handzlik, Joanna E.; Hnisz, Denes & Mayer, Andreas
