A unified view of the sequence and functional organization of the human RNA polymerase II promoter

Donal S Luse; Mrutyunjaya Parida; Benjamin M Spector; Kyle A Nilson; David H Price

doi:10.1093/nar/gkaa531

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A unified view of the sequence and functional organization of the human RNA polymerase II promoter

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A unified view of the sequence and functional organization of the human RNA polymerase II promoter

Donal S Luse, Mrutyunjaya Parida, Benjamin M Spector, Kyle A Nilson and David H Price

Nucleic acids research, Vol.48(14), pp.7767-7785

06/29/2020

DOI: 10.1093/nar/gkaa531

PMCID: PMC7641323

PMID: 32597978

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Abstract

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.

AcademicSubjects

Gene regulation, Chromatin and Epigenetics

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Details

Title: Subtitle: A unified view of the sequence and functional organization of the human RNA polymerase II promoter
Creators: Donal S Luse - Cleveland Clinic
Mrutyunjaya Parida - University of Iowa
Benjamin M Spector - University of Iowa
Kyle A Nilson - University of Iowa
David H Price - , Iowa City, IA 52242
Resource Type: Journal article
Publication Details: Nucleic acids research, Vol.48(14), pp.7767-7785
DOI: 10.1093/nar/gkaa531
PMID: 32597978
PMCID: PMC7641323
NLM abbreviation: Nucleic Acids Res
ISSN: 0305-1048
eISSN: 1362-4962
Publisher: Oxford University Press
Grant note: GM113935; GM35500; GM126908; GM121428 / ;
Language: English
Date published: 06/29/2020
Academic Unit: Pathology; Biochemistry and Molecular Biology
Record Identifier: 9984293075202771

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