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DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts
Human DIS3, the nuclear catalytic subunit of the exosome complex, contains exonucleolytic and endonucleolytic active domains. To identify DIS3 targets genome-wide, we combined comprehensive transcriptomic analyses of engineered HEK293 cells that expressed mutant DIS3, with Photoactivatable Ribonucle...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617959/ https://www.ncbi.nlm.nih.gov/pubmed/26294688 http://dx.doi.org/10.1101/gr.189597.115 |
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author | Szczepińska, Teresa Kalisiak, Katarzyna Tomecki, Rafal Labno, Anna Borowski, Lukasz S. Kulinski, Tomasz M. Adamska, Dorota Kosinska, Joanna Dziembowski, Andrzej |
author_facet | Szczepińska, Teresa Kalisiak, Katarzyna Tomecki, Rafal Labno, Anna Borowski, Lukasz S. Kulinski, Tomasz M. Adamska, Dorota Kosinska, Joanna Dziembowski, Andrzej |
author_sort | Szczepińska, Teresa |
collection | PubMed |
description | Human DIS3, the nuclear catalytic subunit of the exosome complex, contains exonucleolytic and endonucleolytic active domains. To identify DIS3 targets genome-wide, we combined comprehensive transcriptomic analyses of engineered HEK293 cells that expressed mutant DIS3, with Photoactivatable Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP) experiments. In cells expressing DIS3 with both catalytic sites mutated, RNAs originating from unannotated genomic regions increased ∼2.5-fold, covering ∼70% of the genome and allowing for thousands of novel transcripts to be discovered. Previously described pervasive transcription products, such as Promoter Upstream Transcripts (PROMPTs), accumulated robustly upon DIS3 dysfunction, representing a significant fraction of PAR-CLIP reads. We have also detected relatively long putative premature RNA polymerase II termination products of protein-coding genes whose levels in DIS3 mutant cells can exceed the mature mRNAs, indicating that production of such truncated RNA is a common phenomenon. In addition, we found DIS3 to be involved in controlling the formation of paraspeckles, nuclear bodies that are organized around NEAT1 lncRNA, whose short form was overexpressed in cells with mutated DIS3. Moreover, the DIS3 mutations resulted in misregulation of expression of ∼50% of transcribed protein-coding genes, probably as a secondary effect of accumulation of various noncoding RNA species. Finally, cells expressing mutant DIS3 accumulated snoRNA precursors, which correlated with a strong PAR-CLIP signal, indicating that DIS3 is the main snoRNA-processing enzyme. EXOSC10 (RRP6) instead controls the levels of the mature snoRNAs. Overall, we show that DIS3 has a major nucleoplasmic function in shaping the human RNA polymerase II transcriptome. |
format | Online Article Text |
id | pubmed-4617959 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-46179592016-05-01 DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts Szczepińska, Teresa Kalisiak, Katarzyna Tomecki, Rafal Labno, Anna Borowski, Lukasz S. Kulinski, Tomasz M. Adamska, Dorota Kosinska, Joanna Dziembowski, Andrzej Genome Res Research Human DIS3, the nuclear catalytic subunit of the exosome complex, contains exonucleolytic and endonucleolytic active domains. To identify DIS3 targets genome-wide, we combined comprehensive transcriptomic analyses of engineered HEK293 cells that expressed mutant DIS3, with Photoactivatable Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP) experiments. In cells expressing DIS3 with both catalytic sites mutated, RNAs originating from unannotated genomic regions increased ∼2.5-fold, covering ∼70% of the genome and allowing for thousands of novel transcripts to be discovered. Previously described pervasive transcription products, such as Promoter Upstream Transcripts (PROMPTs), accumulated robustly upon DIS3 dysfunction, representing a significant fraction of PAR-CLIP reads. We have also detected relatively long putative premature RNA polymerase II termination products of protein-coding genes whose levels in DIS3 mutant cells can exceed the mature mRNAs, indicating that production of such truncated RNA is a common phenomenon. In addition, we found DIS3 to be involved in controlling the formation of paraspeckles, nuclear bodies that are organized around NEAT1 lncRNA, whose short form was overexpressed in cells with mutated DIS3. Moreover, the DIS3 mutations resulted in misregulation of expression of ∼50% of transcribed protein-coding genes, probably as a secondary effect of accumulation of various noncoding RNA species. Finally, cells expressing mutant DIS3 accumulated snoRNA precursors, which correlated with a strong PAR-CLIP signal, indicating that DIS3 is the main snoRNA-processing enzyme. EXOSC10 (RRP6) instead controls the levels of the mature snoRNAs. Overall, we show that DIS3 has a major nucleoplasmic function in shaping the human RNA polymerase II transcriptome. Cold Spring Harbor Laboratory Press 2015-11 /pmc/articles/PMC4617959/ /pubmed/26294688 http://dx.doi.org/10.1101/gr.189597.115 Text en © 2015 Szczepińska et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Research Szczepińska, Teresa Kalisiak, Katarzyna Tomecki, Rafal Labno, Anna Borowski, Lukasz S. Kulinski, Tomasz M. Adamska, Dorota Kosinska, Joanna Dziembowski, Andrzej DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts |
title | DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts |
title_full | DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts |
title_fullStr | DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts |
title_full_unstemmed | DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts |
title_short | DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts |
title_sort | dis3 shapes the rna polymerase ii transcriptome in humans by degrading a variety of unwanted transcripts |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617959/ https://www.ncbi.nlm.nih.gov/pubmed/26294688 http://dx.doi.org/10.1101/gr.189597.115 |
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