Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome
Divergent transcription occurs at the majority of RNA polymerase II (RNAPII) promoters in mouse embryonic stem cells (mESCs), and this activity correlates with CpG islands. Here we report the characterization of upstream antisense transcription in regions encoding transcription start site associated...
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| Format: | Article |
| Language: | en_US |
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National Academy of Sciences (U.S.)
2014
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| Online Access: | http://hdl.handle.net/1721.1/85106 https://orcid.org/0000-0003-1465-1691 https://orcid.org/0000-0001-5013-0442 |
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| author | Flynn, Ryan A. Almada, Albert Ernesto Zamudio, Jesse Ray Sharp, Phillip A. |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Flynn, Ryan A. Almada, Albert Ernesto Zamudio, Jesse Ray Sharp, Phillip A. |
| author_sort | Flynn, Ryan A. |
| collection | MIT |
| description | Divergent transcription occurs at the majority of RNA polymerase II (RNAPII) promoters in mouse embryonic stem cells (mESCs), and this activity correlates with CpG islands. Here we report the characterization of upstream antisense transcription in regions encoding transcription start site associated RNAs (TSSa-RNAs) at four divergent CpG island promoters: Isg20l1, Tcea1, Txn1, and Sf3b1. We find that upstream antisense RNAs (uaRNAs) have distinct capped 5′ termini and heterogeneous nonpolyadenylated 3′ ends. uaRNAs are short-lived with average half-lives of 18 minutes and are present at 1–4 copies per cell, approximately one RNA per DNA template. Exosome depletion stabilizes uaRNAs. These uaRNAs are probably initiation products because their capped termini correlate with peaks of paused RNAPII. The pausing factors NELF and DSIF are associated with these antisense polymerases and their sense partners. Knockdown of either NELF or DSIF results in an increase in the levels of uaRNAs. Consistent with P-TEFb controlling release from pausing, treatment with its inhibitor, flavopiridol, decreases uaRNA and nascent mRNA transcripts with similar kinetics. Finally, Isg20l1 induction reveals equivalent increases in transcriptional activity in sense and antisense directions. Together these data show divergent polymerases are regulated after P-TEFb recruitment with uaRNA levels controlled by the exosome. |
| first_indexed | 2024-09-23T11:52:10Z |
| format | Article |
| id | mit-1721.1/85106 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:52:10Z |
| publishDate | 2014 |
| publisher | National Academy of Sciences (U.S.) |
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| spelling | mit-1721.1/851062022-10-01T06:33:53Z Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome Flynn, Ryan A. Almada, Albert Ernesto Zamudio, Jesse Ray Sharp, Phillip A. Massachusetts Institute of Technology. Department of Biology Koch Institute for Integrative Cancer Research at MIT Flynn, Ryan A. Almada, Albert Ernesto Zamudio, Jesse Ray Sharp, Phillip A. Divergent transcription occurs at the majority of RNA polymerase II (RNAPII) promoters in mouse embryonic stem cells (mESCs), and this activity correlates with CpG islands. Here we report the characterization of upstream antisense transcription in regions encoding transcription start site associated RNAs (TSSa-RNAs) at four divergent CpG island promoters: Isg20l1, Tcea1, Txn1, and Sf3b1. We find that upstream antisense RNAs (uaRNAs) have distinct capped 5′ termini and heterogeneous nonpolyadenylated 3′ ends. uaRNAs are short-lived with average half-lives of 18 minutes and are present at 1–4 copies per cell, approximately one RNA per DNA template. Exosome depletion stabilizes uaRNAs. These uaRNAs are probably initiation products because their capped termini correlate with peaks of paused RNAPII. The pausing factors NELF and DSIF are associated with these antisense polymerases and their sense partners. Knockdown of either NELF or DSIF results in an increase in the levels of uaRNAs. Consistent with P-TEFb controlling release from pausing, treatment with its inhibitor, flavopiridol, decreases uaRNA and nascent mRNA transcripts with similar kinetics. Finally, Isg20l1 induction reveals equivalent increases in transcriptional activity in sense and antisense directions. Together these data show divergent polymerases are regulated after P-TEFb recruitment with uaRNA levels controlled by the exosome. United States. Public Health Service (NIH grant R01-GM34277) National Cancer Institute (U.S.) (Cancer Center Support (core) Grant P30-CA14051) National Institutes of Health (U.S.) (NIH/NIGMS Pre-Doctoral Training in Biological Sciences Grant GM007287) 2014-02-27T16:09:56Z 2014-02-27T16:09:56Z 2011-06 2011-05 Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/85106 Flynn, Ryan A., Albert E. Almada, Jesse R. Zamudio, and Phillip A. Sharp. "Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome." PNAS 2011 108 (26) 10460-10465. https://orcid.org/0000-0003-1465-1691 https://orcid.org/0000-0001-5013-0442 en_US http://dx.doi.org/10.1073/pnas.1106630108 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Flynn, Ryan A. Almada, Albert Ernesto Zamudio, Jesse Ray Sharp, Phillip A. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome |
| title | Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome |
| title_full | Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome |
| title_fullStr | Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome |
| title_full_unstemmed | Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome |
| title_short | Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome |
| title_sort | antisense rna polymerase ii divergent transcripts are p tefb dependent and substrates for the rna exosome |
| url | http://hdl.handle.net/1721.1/85106 https://orcid.org/0000-0003-1465-1691 https://orcid.org/0000-0001-5013-0442 |
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