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The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors
In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3′- and 5′-ends of 261 yeast genes by run-on. The results obtained indicate that the 3′/5′ run-on ratio varies among the genes studied by over 12 log(2) uni...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919717/ https://www.ncbi.nlm.nih.gov/pubmed/20385590 http://dx.doi.org/10.1093/nar/gkq215 |
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author | Rodríguez-Gil, Alfonso García-Martínez, José Pelechano, Vicent Muñoz-Centeno, María de la Cruz Geli, Vincent Pérez-Ortín, José E. Chávez, Sebastián |
author_facet | Rodríguez-Gil, Alfonso García-Martínez, José Pelechano, Vicent Muñoz-Centeno, María de la Cruz Geli, Vincent Pérez-Ortín, José E. Chávez, Sebastián |
author_sort | Rodríguez-Gil, Alfonso |
collection | PubMed |
description | In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3′- and 5′-ends of 261 yeast genes by run-on. The results obtained indicate that the 3′/5′ run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3′/5′ RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in both cases. We detected a subset of elongation-related factors that are important for maintaining the wild-type profiles of active transcription, including DSIF, Mediator, factors related to the methylation of histone H3-lysine 4, the Bur CDK and the RNA polymerase II subunit Rpb9. We conducted a more detailed investigation of the alterations caused by rpb9Δ to find that Rpb9 contributes to the intragenic profiles of active transcription by influencing the probability of arrest of RNA polymerase II. |
format | Text |
id | pubmed-2919717 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-29197172010-08-11 The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors Rodríguez-Gil, Alfonso García-Martínez, José Pelechano, Vicent Muñoz-Centeno, María de la Cruz Geli, Vincent Pérez-Ortín, José E. Chávez, Sebastián Nucleic Acids Res Gene Regulation, Chromatin and Epigenetics In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3′- and 5′-ends of 261 yeast genes by run-on. The results obtained indicate that the 3′/5′ run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3′/5′ RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in both cases. We detected a subset of elongation-related factors that are important for maintaining the wild-type profiles of active transcription, including DSIF, Mediator, factors related to the methylation of histone H3-lysine 4, the Bur CDK and the RNA polymerase II subunit Rpb9. We conducted a more detailed investigation of the alterations caused by rpb9Δ to find that Rpb9 contributes to the intragenic profiles of active transcription by influencing the probability of arrest of RNA polymerase II. Oxford University Press 2010-08 2010-04-12 /pmc/articles/PMC2919717/ /pubmed/20385590 http://dx.doi.org/10.1093/nar/gkq215 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Gene Regulation, Chromatin and Epigenetics Rodríguez-Gil, Alfonso García-Martínez, José Pelechano, Vicent Muñoz-Centeno, María de la Cruz Geli, Vincent Pérez-Ortín, José E. Chávez, Sebastián The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors |
title | The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors |
title_full | The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors |
title_fullStr | The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors |
title_full_unstemmed | The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors |
title_short | The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors |
title_sort | distribution of active rna polymerase ii along the transcribed region is gene-specific and controlled by elongation factors |
topic | Gene Regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919717/ https://www.ncbi.nlm.nih.gov/pubmed/20385590 http://dx.doi.org/10.1093/nar/gkq215 |
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