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A unified view of the sequence and functional organization of the human RNA polymerase II promoter
To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641323/ https://www.ncbi.nlm.nih.gov/pubmed/32597978 http://dx.doi.org/10.1093/nar/gkaa531 |
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author | Luse, Donal S Parida, Mrutyunjaya Spector, Benjamin M Nilson, Kyle A Price, David H |
author_facet | Luse, Donal S Parida, Mrutyunjaya Spector, Benjamin M Nilson, Kyle A Price, David H |
author_sort | Luse, Donal S |
collection | PubMed |
description | To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location. |
format | Online Article Text |
id | pubmed-7641323 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-76413232020-11-10 A unified view of the sequence and functional organization of the human RNA polymerase II promoter Luse, Donal S Parida, Mrutyunjaya Spector, Benjamin M Nilson, Kyle A Price, David H Nucleic Acids Res Gene regulation, Chromatin and Epigenetics To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location. Oxford University Press 2020-06-29 /pmc/articles/PMC7641323/ /pubmed/32597978 http://dx.doi.org/10.1093/nar/gkaa531 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Gene regulation, Chromatin and Epigenetics Luse, Donal S Parida, Mrutyunjaya Spector, Benjamin M Nilson, Kyle A Price, David H A unified view of the sequence and functional organization of the human RNA polymerase II promoter |
title | A unified view of the sequence and functional organization of the human RNA polymerase II promoter |
title_full | A unified view of the sequence and functional organization of the human RNA polymerase II promoter |
title_fullStr | A unified view of the sequence and functional organization of the human RNA polymerase II promoter |
title_full_unstemmed | A unified view of the sequence and functional organization of the human RNA polymerase II promoter |
title_short | A unified view of the sequence and functional organization of the human RNA polymerase II promoter |
title_sort | unified view of the sequence and functional organization of the human rna polymerase ii promoter |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641323/ https://www.ncbi.nlm.nih.gov/pubmed/32597978 http://dx.doi.org/10.1093/nar/gkaa531 |
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