A chromatin activity-based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing

Cui Liu; Yanbao Yu; Feng Liu; Xin Wei; John A Wrobel; Harsha P Gunawardena; Li Zhou; Jian Jin; Xian Chen

doi:10.1038/ncomms6733

A chromatin activity-based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing

Nat Commun. 2014 Dec 15:5:5733. doi: 10.1038/ncomms6733.

Authors

Cui Liu¹, Yanbao Yu¹, Feng Liu², Xin Wei¹, John A Wrobel¹, Harsha P Gunawardena¹, Li Zhou¹, Jian Jin³, Xian Chen⁴

Affiliations

¹ Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
² Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
³ Department of Structural and Chemical Biology, Department of Oncological Sciences, and Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
⁴ 1] Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA [2] Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA [3] Department of Chemistry, Fudan University, Shanghai 200433, China.

Abstract

Immune cells develop endotoxin tolerance (ET) after prolonged stimulation. ET increases the level of a repression mark H3K9me2 in the transcriptionally silent chromatin specifically associated with pro-inflammatory genes. However, it is not clear what proteins are functionally involved in this process. Here we show that a novel chromatin activity-based chemoproteomic (ChaC) approach can dissect the functional chromatin protein complexes that regulate ET-associated inflammation. Using UNC0638 that binds the enzymatically active H3K9-specific methyltransferase G9a/GLP, ChaC reveals that G9a is constitutively active at a G9a-dependent mega-dalton repressome in primary endotoxin-tolerant macrophages. G9a/GLP broadly impacts the ET-specific reprogramming of the histone code landscape, chromatin remodelling and the activities of select transcription factors. We discover that the G9a-dependent epigenetic environment promotes the transcriptional repression activity of c-Myc for gene-specific co-regulation of chronic inflammation. ChaC may also be applicable to dissect other functional protein complexes in the context of phenotypic chromatin architectures.

Publication types

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

MeSH terms

Animals
Bone Marrow Cells / drug effects
Bone Marrow Cells / immunology
Bone Marrow Cells / pathology
Cell Differentiation
Cell Line
Chromatin / chemistry
Chromatin / drug effects
Chromatin / immunology*
Chromatin Assembly and Disassembly / drug effects
Epigenesis, Genetic / immunology*
Female
Histone-Lysine N-Methyltransferase / antagonists & inhibitors
Histone-Lysine N-Methyltransferase / genetics
Histone-Lysine N-Methyltransferase / immunology*
Histones / genetics
Histones / immunology*
Immune Tolerance / genetics*
Inflammation / genetics
Inflammation / immunology
Inflammation / pathology
Inflammation / prevention & control
Lipopolysaccharides / pharmacology
Macrophages / drug effects
Macrophages / immunology*
Macrophages / pathology
Male
Mice
Mice, Inbred C57BL
Primary Cell Culture
Proteomics / methods
Proto-Oncogene Proteins c-myc / genetics
Proto-Oncogene Proteins c-myc / immunology*
Quinazolines / pharmacology
RNA, Small Interfering / genetics
RNA, Small Interfering / immunology
Signal Transduction
Transcription, Genetic

Substances

Chromatin
Histones
Lipopolysaccharides
Myc protein, mouse
Proto-Oncogene Proteins c-myc
Quinazolines
RNA, Small Interfering
UNC 0638
G9a protein, mouse
Histone-Lysine N-Methyltransferase

Abstract

Publication types

MeSH terms

Substances

Grants and funding