TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

Heeyoun Bunch; Xiaofeng Zheng; Adam Burkholder; Simon T Dillon; Shmulik Motola; Gabriel Birrane; Christopher C Ebmeier; Stuart Levine; David Fargo; Guang Hu; Dylan J Taatjes; Stuart K Calderwood

doi:10.1038/nsmb.2878

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

Nat Struct Mol Biol. 2014 Oct;21(10):876-83. doi: 10.1038/nsmb.2878. Epub 2014 Aug 31.

Authors

Affiliations

¹ Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
² 1] Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA. [2].
³ 1] Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA. [2].
⁴ 1] Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA. [2] Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
⁵ BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
⁶ 1] Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA. [2] Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
⁷ Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, Colorado, USA.
⁸ Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
⁹ Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.

Abstract

Promoter-proximal pausing of RNA polymerase II (Pol II) is a major checkpoint in transcription. An unbiased search for new human proteins that could regulate paused Pol II at the HSPA1B gene identified TRIM28. In vitro analyses indicated HSF1-dependent attenuation of Pol II pausing upon TRIM28 depletion, whereas in vivo data revealed de novo expression of HSPA1B and other known genes regulated by paused Pol II upon TRIM28 knockdown. These results were supported by genome-wide ChIP-sequencing analyses of Pol II occupancy that revealed a global role for TRIM28 in regulating Pol II pausing and pause release. Furthermore, in vivo and in vitro mechanistic studies suggest that transcription-coupled phosphorylation regulates Pol II pause release by TRIM28. Collectively, our findings identify TRIM28 as a new factor that modulates Pol II pausing and transcriptional elongation at a large number of mammalian genes.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

MeSH terms

Ataxia Telangiectasia Mutated Proteins / antagonists & inhibitors
Cell Line, Tumor
DNA-Activated Protein Kinase / antagonists & inhibitors
DNA-Binding Proteins / antagonists & inhibitors
DNA-Binding Proteins / genetics
HEK293 Cells
HSP70 Heat-Shock Proteins / biosynthesis
HSP70 Heat-Shock Proteins / genetics*
HeLa Cells
Heat Shock Transcription Factors
Humans
Phosphorylation
Promoter Regions, Genetic / genetics*
RNA Polymerase II / genetics*
Repressor Proteins / genetics
Repressor Proteins / metabolism*
Transcription Factors / antagonists & inhibitors
Transcription Factors / genetics
Transcription, Genetic / genetics
Tripartite Motif-Containing Protein 28

Substances

DNA-Binding Proteins
HSF1 protein, human
HSP70 Heat-Shock Proteins
HSPA1B protein, human
Heat Shock Transcription Factors
Repressor Proteins
Transcription Factors
TRIM28 protein, human
Tripartite Motif-Containing Protein 28
ATM protein, human
Ataxia Telangiectasia Mutated Proteins
DNA-Activated Protein Kinase
RNA Polymerase II

Associated data

GEO/GSE48253

Abstract

Publication types

MeSH terms

Substances

Associated data

Grants and funding