Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications

Christopher C. Ebmeier; Benjamin Erickson; Benjamin L. Allen; Mary A. Allen; Hyunmin Kim; Nova Fong; Jeremy R. Jacobsen; Kaiwei Liang; Ali Shilatifard; Robin D. Dowell; William M. Old; David L. Bentley; Dylan J. Taatjes

doi:10.1016/j.celrep.2017.07.021

Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications

Christopher C. Ebmeier, Benjamin Erickson, Benjamin L. Allen, Mary A. Allen, Hyunmin Kim, Nova Fong, Jeremy R. Jacobsen, Kaiwei Liang, Ali Shilatifard, Robin D. Dowell, William M. Old, David L. Bentley^*, Dylan J. Taatjes

^*Corresponding author for this work

Biochemistry and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

108 Scopus citations

Abstract

CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3′ ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5′ ends and H3K36me3 was displaced toward gene 3′ ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated versus P-TEFb-phosphorylated CTD (versus unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD, and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent “CTD code” that regulates chromatin marks in addition to RNA processing and pol II pausing.

Original language	English (US)
Pages (from-to)	1173-1186
Number of pages	14
Journal	Cell reports
Volume	20
Issue number	5
DOIs	https://doi.org/10.1016/j.celrep.2017.07.021
State	Published - Aug 1 2017

Funding

We thank R. Fisher for HCT116 CDK7as cells, R. Tjian for ERCC3 antibodies, and J. Goodrich for critical reading of the manuscript. We thank the UC Cancer Center for STR analysis and K. Diener and B. Gao at the UC Denver sequencing facility. We thank K. Luger and U. Muthurajan for providing purified nucleosome templates. This work was supported by the National Science Foundation (grant MCB-1244175 to D.J.T.) and NIH (grants GM063873 and R35GM118051 to D.L.B., grant GM110064 to D.J.T., grant T32 GM07135 to C.C.E., and grant T32 GM08759 to B.L.A.).

Keywords

H3K36me3
H3K4me3
Mediator
P-TEFb
RNA-seq
TFIIH
THZ1
chromatin
epigenetic
proteomics

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.celrep.2017.07.021

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@article{38d2d399f56a4d8b96d9fe447d769d55,

title = "Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications",

abstract = "CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3′ ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5′ ends and H3K36me3 was displaced toward gene 3′ ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated versus P-TEFb-phosphorylated CTD (versus unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD, and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent “CTD code” that regulates chromatin marks in addition to RNA processing and pol II pausing.",

keywords = "H3K36me3, H3K4me3, Mediator, P-TEFb, RNA-seq, TFIIH, THZ1, chromatin, epigenetic, proteomics",

author = "Ebmeier, {Christopher C.} and Benjamin Erickson and Allen, {Benjamin L.} and Allen, {Mary A.} and Hyunmin Kim and Nova Fong and Jacobsen, {Jeremy R.} and Kaiwei Liang and Ali Shilatifard and Dowell, {Robin D.} and Old, {William M.} and Bentley, {David L.} and Taatjes, {Dylan J.}",

note = "Publisher Copyright: {\textcopyright} 2017 The Author(s)",

year = "2017",

month = aug,

day = "1",

doi = "10.1016/j.celrep.2017.07.021",

language = "English (US)",

volume = "20",

pages = "1173--1186",

journal = "Cell reports",

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T1 - Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications

AU - Ebmeier, Christopher C.

AU - Erickson, Benjamin

AU - Allen, Benjamin L.

AU - Allen, Mary A.

AU - Kim, Hyunmin

AU - Fong, Nova

AU - Jacobsen, Jeremy R.

AU - Liang, Kaiwei

AU - Shilatifard, Ali

AU - Dowell, Robin D.

AU - Old, William M.

AU - Bentley, David L.

AU - Taatjes, Dylan J.

PY - 2017/8/1

Y1 - 2017/8/1

N2 - CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3′ ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5′ ends and H3K36me3 was displaced toward gene 3′ ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated versus P-TEFb-phosphorylated CTD (versus unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD, and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent “CTD code” that regulates chromatin marks in addition to RNA processing and pol II pausing.

AB - CDK7 phosphorylates the RNA polymerase II (pol II) C-terminal domain CTD and activates the P-TEFb-associated kinase CDK9, but its regulatory roles remain obscure. Here, using human CDK7 analog-sensitive (CDK7as) cells, we observed reduced capping enzyme recruitment, increased pol II promoter-proximal pausing, and defective termination at gene 3′ ends upon CDK7 inhibition. We also noted that CDK7 regulates chromatin modifications downstream of transcription start sites. H3K4me3 spreading was restricted at gene 5′ ends and H3K36me3 was displaced toward gene 3′ ends in CDK7as cells. Mass spectrometry identified factors that bound TFIIH-phosphorylated versus P-TEFb-phosphorylated CTD (versus unmodified); capping enzymes and H3K4 methyltransferase complexes, SETD1A/B, selectively bound phosphorylated CTD, and the H3K36 methyltransferase SETD2 specifically bound P-TEFb-phosphorylated CTD. Moreover, TFIIH-phosphorylated CTD stimulated SETD1A/B activity toward nucleosomes, revealing a mechanistic basis for CDK7 regulation of H3K4me3 spreading. Collectively, these results implicate a CDK7-dependent “CTD code” that regulates chromatin marks in addition to RNA processing and pol II pausing.

KW - H3K36me3

KW - H3K4me3

KW - Mediator

KW - P-TEFb

KW - RNA-seq

KW - TFIIH

KW - THZ1

KW - chromatin

KW - epigenetic

KW - proteomics

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UR - http://www.scopus.com/inward/citedby.url?scp=85026856368&partnerID=8YFLogxK

U2 - 10.1016/j.celrep.2017.07.021

DO - 10.1016/j.celrep.2017.07.021

M3 - Article

C2 - 28768201

AN - SCOPUS:85026856368

SN - 2211-1247

VL - 20

SP - 1173

EP - 1186

JO - Cell reports

JF - Cell reports

IS - 5

ER -

Human TFIIH Kinase CDK7 Regulates Transcription-Associated Chromatin Modifications

Abstract

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Keywords

ASJC Scopus subject areas

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