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

Cell Rep. 2017 Aug 1;20(5):1173-1186. doi: 10.1016/j.celrep.2017.07.021.

Authors

Affiliations

¹ Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA; Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
² Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
³ Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA.
⁴ BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA.
⁵ Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
⁶ Department of Biochemistry & Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
⁷ Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA.
⁸ Department of Molecular, Cell, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO 80045, USA.
⁹ Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: [email protected].
¹⁰ Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80303, USA. Electronic address: [email protected].

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.

MeSH terms

Cell Line
Chromatin / genetics
Chromatin / metabolism*
Cyclin-Dependent Kinase-Activating Kinase
Cyclin-Dependent Kinases / genetics
Cyclin-Dependent Kinases / metabolism*
Histone-Lysine N-Methyltransferase / genetics
Histone-Lysine N-Methyltransferase / metabolism
Humans
Phosphorylation
Positive Transcriptional Elongation Factor B / genetics
Positive Transcriptional Elongation Factor B / metabolism
RNA Polymerase II / genetics
RNA Polymerase II / metabolism
Transcription Factor TFIIH / genetics
Transcription Factor TFIIH / metabolism*
Transcription, Genetic*

Substances

Chromatin
Transcription Factor TFIIH
Histone-Lysine N-Methyltransferase
SETD1B protein, human
SETD2 protein, human
Setd1A protein, human
Positive Transcriptional Elongation Factor B
Cyclin-Dependent Kinases
RNA Polymerase II
Cyclin-Dependent Kinase-Activating Kinase
CDK7 protein, human

Abstract

MeSH terms

Substances

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