title: A chromatin activity-based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing.
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.
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Cui
authors.initials: C
authors.lastname: Liu
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Yanbao
authors.initials: Y
authors.lastname: Yu
authors.affiliation: 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.
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Wei
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Wrobel
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Harsha P
authors.initials: HP
authors.lastname: Gunawardena
authors.affiliation: Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Zhou
authors.affiliation: 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.
authors.forename: Jian
authors.initials: J
authors.lastname: Jin
authors.affiliation: 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.
authors.forename: Xian
authors.initials: X
authors.lastname: Chen
mesh_terms: D000818:Animals; D001854:Bone Marrow Cells / Q000187:drug effects / Q000276:immunology / Q000473:pathology; D002454:Cell Differentiation; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry / Q000187:drug effects / Q000276:immunology*; D042002:Chromatin Assembly and Disassembly / Q000187:drug effects; D044127:Epigenesis, Genetic / Q000276:immunology*; D005260:Female; D011495:Histone-Lysine N-Methyltransferase / Q000037:antagonists & inhibitors / Q000235:genetics / Q000276:immunology*; D006657:Histones / Q000235:genetics / Q000276:immunology*; D007108:Immune Tolerance / Q000235:genetics*; D007249:Inflammation / Q000235:genetics / Q000276:immunology / Q000473:pathology / Q000517:prevention & control; D008070:Lipopolysaccharides / Q000494:pharmacology; D008264:Macrophages / Q000187:drug effects / Q000276:immunology* / Q000473:pathology; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D061251:Primary Cell Culture; D040901:Proteomics / Q000379:methods; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics / Q000276:immunology*; D011799:Quinazolines / Q000494:pharmacology; D034741:RNA, Small Interfering / Q000235:genetics / Q000276:immunology; D015398:Signal Transduction; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D006657:Histones; D008070:Lipopolysaccharides; C489428:Myc protein, mouse; D016271:Proto-Oncogene Proteins c-myc; D011799:Quinazolines; D034741:RNA, Small Interfering; C561310:UNC 0638; C533711:G9a protein, mouse; D011495:Histone-Lysine N-Methyltransferase