Cargando…

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-...

Descripción completa

Detalles Bibliográficos
Autores principales: Luse, Donal S, Parida, Mrutyunjaya, Spector, Benjamin M, Nilson, Kyle A, Price, David H
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
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
_version_ 1783605892551278592
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
work_keys_str_mv AT lusedonals aunifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT paridamrutyunjaya aunifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT spectorbenjaminm aunifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT nilsonkylea aunifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT pricedavidh aunifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT lusedonals unifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT paridamrutyunjaya unifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT spectorbenjaminm unifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT nilsonkylea unifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter
AT pricedavidh unifiedviewofthesequenceandfunctionalorganizationofthehumanrnapolymeraseiipromoter