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Series GSE98367 Query DataSets for GSE98367
Status Public on Jul 01, 2017
Title IFN-γ Represses M2 Gene Expression in Human Macrophages by Suppressing and Disassembling MAF-binding Enhancers [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Mechanisms by which IFN-γ activates genes to promote macrophage activation are well studied, but little is known about mechanisms and functions of IFN-γ-mediated gene repression. We used an integrated transcriptomic and epigenomic approach to analyze chromatin accessibility, histone modifications, transcription factor binding, and gene expression in IFN-γ-primed human macrophages. IFN-γ suppressed basal expression of genes corresponding to an ‘M2’-like homeostatic/reparative phenotype. IFN-γ repressed genes by suppressing the function of enhancers enriched for binding by transcription factor MAF. Mechanistically, IFN-γ ‘disassembled’ a subset of enhancers by inducing coordinate suppression of binding by MAF, lineage-determining transcription factors, and chromatin accessibility. Genes associated with MAF-binding disassembled enhancers were suppressed in rheumatoid arthritis macrophages, revealing a disease-associated ‘negative IFN-γ signature’. These results identify enhancer inactivation and disassembly as a mechanism of IFN-γ-mediated gene repression, and MAF as a regulator of the macrophage enhancer landscape that is suppressed by IFN-γ to augment macrophage activation.
 
Overall design ChIP-seq analysis of epigenomic changes in human macrophages stimulated with or without IFN-γ.
 
Contributor(s) Ivashkiv L, Kang K, Kang K, Giannopoulou E, Qiao Y
Citation(s) 28813657
Submission date Apr 30, 2017
Last update date May 15, 2019
Contact name Lionel B. Ivashkiv
Organization name Hospital for Special Surgery
Street address 535 East 70th Street
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (17)
GSM2592797 C/EBPB_IFN-γ_rep1
GSM2592798 C/EBPB_IFN-γ_rep2
GSM2592799 C/EBPB_Resting_rep1
This SubSeries is part of SuperSeries:
GSE98369 Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF
Relations
BioProject PRJNA384909
SRA SRP105693

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE98367_RAW.tar 10.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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