Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.
Yeast Npl3 is a highly abundant, nuclear-cytoplasmic shuttling, RNA-binding protein, related to metazoan SR proteins. Reported functions of Npl3 include transcription elongation, splicing and RNA 3' end processing. We used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding s...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-12-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1005735 |
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| author | Rebecca K Holmes Alex C Tuck Chenchen Zhu Hywel R Dunn-Davies Grzegorz Kudla Sandra Clauder-Munster Sander Granneman Lars M Steinmetz Christine Guthrie David Tollervey |
| author_facet | Rebecca K Holmes Alex C Tuck Chenchen Zhu Hywel R Dunn-Davies Grzegorz Kudla Sandra Clauder-Munster Sander Granneman Lars M Steinmetz Christine Guthrie David Tollervey |
| author_sort | Rebecca K Holmes |
| collection | DOAJ |
| description | Yeast Npl3 is a highly abundant, nuclear-cytoplasmic shuttling, RNA-binding protein, related to metazoan SR proteins. Reported functions of Npl3 include transcription elongation, splicing and RNA 3' end processing. We used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites, and strand-specific tiling arrays to look at the effects of loss of Npl3 on all transcripts across the genome. We found that Npl3 binds diverse RNA species, both coding and non-coding, at sites indicative of roles in both early pre-mRNA processing and 3' end formation. Tiling arrays and RNAPII mapping data revealed 3' extended RNAPII-transcribed RNAs in the absence of Npl3, suggesting that defects in pre-mRNA packaging events result in termination readthrough. Transcription readthrough was widespread and frequently resulted in down-regulation of neighboring genes. We conclude that the absence of Npl3 results in widespread 3' extension of transcripts with pervasive effects on gene expression. |
| format | Article |
| id | doaj-art-e24c2b5e4ec94d2a8f9c71541404b6f0 |
| institution | OA Journals |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2015-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-e24c2b5e4ec94d2a8f9c71541404b6f02025-08-20T02:34:12ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042015-12-011112e100573510.1371/journal.pgen.1005735Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough.Rebecca K HolmesAlex C TuckChenchen ZhuHywel R Dunn-DaviesGrzegorz KudlaSandra Clauder-MunsterSander GrannemanLars M SteinmetzChristine GuthrieDavid TollerveyYeast Npl3 is a highly abundant, nuclear-cytoplasmic shuttling, RNA-binding protein, related to metazoan SR proteins. Reported functions of Npl3 include transcription elongation, splicing and RNA 3' end processing. We used UV crosslinking and analysis of cDNA (CRAC) to map precise RNA binding sites, and strand-specific tiling arrays to look at the effects of loss of Npl3 on all transcripts across the genome. We found that Npl3 binds diverse RNA species, both coding and non-coding, at sites indicative of roles in both early pre-mRNA processing and 3' end formation. Tiling arrays and RNAPII mapping data revealed 3' extended RNAPII-transcribed RNAs in the absence of Npl3, suggesting that defects in pre-mRNA packaging events result in termination readthrough. Transcription readthrough was widespread and frequently resulted in down-regulation of neighboring genes. We conclude that the absence of Npl3 results in widespread 3' extension of transcripts with pervasive effects on gene expression.https://doi.org/10.1371/journal.pgen.1005735 |
| spellingShingle | Rebecca K Holmes Alex C Tuck Chenchen Zhu Hywel R Dunn-Davies Grzegorz Kudla Sandra Clauder-Munster Sander Granneman Lars M Steinmetz Christine Guthrie David Tollervey Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough. PLoS Genetics |
| title | Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough. |
| title_full | Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough. |
| title_fullStr | Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough. |
| title_full_unstemmed | Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough. |
| title_short | Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough. |
| title_sort | loss of the yeast sr protein npl3 alters gene expression due to transcription readthrough |
| url | https://doi.org/10.1371/journal.pgen.1005735 |
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