Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation
The influenza polymerase cleaves host RNAs ~10–13 nucleotides downstream of their 5′ ends and uses this capped fragment to prime viral mRNA synthesis. To better understand this process of cap snatching, we used high-throughput sequencing to determine the 5′ ends of A/WSN/33 (H1N1) influenza mRNAs. T...
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| Format: | Article |
| Language: | en_US |
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Oxford University Press
2015
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| Online Access: | http://hdl.handle.net/1721.1/97103 https://orcid.org/0000-0002-3872-2856 |
| _version_ | 1826188367861121024 |
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| author | Koppstein, David Neal Pira Bartel, David Ashour, Joseph |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Koppstein, David Neal Pira Bartel, David Ashour, Joseph |
| author_sort | Koppstein, David Neal Pira |
| collection | MIT |
| description | The influenza polymerase cleaves host RNAs ~10–13 nucleotides downstream of their 5′ ends and uses this capped fragment to prime viral mRNA synthesis. To better understand this process of cap snatching, we used high-throughput sequencing to determine the 5′ ends of A/WSN/33 (H1N1) influenza mRNAs. The sequences provided clear evidence for nascent-chain realignment during transcription initiation and revealed a strong influence of the viral template on the frequency of realignment. After accounting for the extra nucleotides inserted through realignment, analysis of the capped fragments indicated that the different viral mRNAs were each prepended with a common set of sequences and that the polymerase often cleaved host RNAs after a purine and often primed transcription on a single base pair to either the terminal or penultimate residue of the viral template. We also developed a bioinformatic approach to identify the targeted host transcripts despite limited information content within snatched fragments and found that small nuclear RNAs and small nucleolar RNAs contributed the most abundant capped leaders. These results provide insight into the mechanism of viral transcription initiation and reveal the diversity of the cap-snatched repertoire, showing that noncoding transcripts as well as mRNAs are used to make influenza mRNAs. |
| first_indexed | 2024-09-23T07:58:34Z |
| format | Article |
| id | mit-1721.1/97103 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T07:58:34Z |
| publishDate | 2015 |
| publisher | Oxford University Press |
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| spelling | mit-1721.1/971032022-09-23T10:00:43Z Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation Koppstein, David Neal Pira Bartel, David Ashour, Joseph Massachusetts Institute of Technology. Department of Biology Whitehead Institute for Biomedical Research Koppstein, David Neal Pira Bartel, David Ashour, Joseph The influenza polymerase cleaves host RNAs ~10–13 nucleotides downstream of their 5′ ends and uses this capped fragment to prime viral mRNA synthesis. To better understand this process of cap snatching, we used high-throughput sequencing to determine the 5′ ends of A/WSN/33 (H1N1) influenza mRNAs. The sequences provided clear evidence for nascent-chain realignment during transcription initiation and revealed a strong influence of the viral template on the frequency of realignment. After accounting for the extra nucleotides inserted through realignment, analysis of the capped fragments indicated that the different viral mRNAs were each prepended with a common set of sequences and that the polymerase often cleaved host RNAs after a purine and often primed transcription on a single base pair to either the terminal or penultimate residue of the viral template. We also developed a bioinformatic approach to identify the targeted host transcripts despite limited information content within snatched fragments and found that small nuclear RNAs and small nucleolar RNAs contributed the most abundant capped leaders. These results provide insight into the mechanism of viral transcription initiation and reveal the diversity of the cap-snatched repertoire, showing that noncoding transcripts as well as mRNAs are used to make influenza mRNAs. 2015-05-29T12:37:01Z 2015-05-29T12:37:01Z 2015-04 2015-03 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/97103 Koppstein, D., J. Ashour, and D. P. Bartel. “Sequencing the Cap-Snatching Repertoire of H1N1 Influenza Provides Insight into the Mechanism of Viral Transcription Initiation.” Nucleic Acids Research (April 21, 2015). https://orcid.org/0000-0002-3872-2856 en_US http://dx.doi.org/10.1093/nar/gkv333 Nucleic Acids Research Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Koppstein, David Neal Pira Bartel, David Ashour, Joseph Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation |
| title | Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation |
| title_full | Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation |
| title_fullStr | Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation |
| title_full_unstemmed | Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation |
| title_short | Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation |
| title_sort | sequencing the cap snatching repertoire of h1n1 influenza provides insight into the mechanism of viral transcription initiation |
| url | http://hdl.handle.net/1721.1/97103 https://orcid.org/0000-0002-3872-2856 |
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