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Series GSE72886 Query DataSets for GSE72886
Status Public on Feb 25, 2016
Title Histone acetylation H2BK20ac marks cell-state specific active regulatory elements
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Characterisation of different histone modifications is crucial to understand gene regulation. In order to study the most predictive histone modification for active enhancers we created unbiased set of enhancers and used machine learning approach. Our approach revealed an unconventional histone modification H2BK20ac as most efficient marker of active enhancers. H2BK20ac also showed superior coverage of tissue specific active enhancers in complex invivo samples. Adding H2BK20ac to set of conventional histone modifications lead to identification of new chromatin state which could be active enhancers. H2BK20ac tends to occur only at cell-type specific active promoters and showed higher specificity for related disease mutations than H3K27ac and other histone modifications. Using transient state of BV2 microglia cells after lipopolysaccharide based activation, we found that H2BK20ac also marks cell-state specific cis-regulatory elements. Further analysis using inhibition of TGF-beta pathway in BV2 cells and LPS stimulation, revealed differential patterns of H2BK20ac and H3K27ac at genome locations associated with opposite roles response to stmulation. Our study about H2BK20ac hints about a new mechanism of regulation of cell-type specificity and a distinct mode of action of pathways to maintain balance between cell-responses.
 
Overall design Chip-seq of H2BK20ac and other histone modifcation was performed in 3 cell types and embryonic mouse forebrain. The sensitivity for active enhancers was compared for different histone modification ChIP-seq.The level of H2BK20ac at promoters and enhancers was assesed for relationship to cell-type specific expression. H2BK20ac signals were also analysed during cell-state transition when microgila are stimulated by LPS
 
Contributor(s) Kumar V, Masafumi M, Prabhakar S
Citation(s) 26957309
Submission date Sep 10, 2015
Last update date Mar 19, 2019
Contact name Vibhor Kumar
E-mail kumarv1@gis.a-star.edu.sg
Organization name Genome Institute of Singapore
Department CMB-6
Street address 60 Biopolis Street, Genome, #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platforms (3)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (23)
GSM1874085 Forebrain_H3K4me2_ChIPSeq
GSM1874086 Forebrain_H3K4me1_ChIPSeq
GSM1874087 Forebrain_H3K27ac_ChIPSeq
Relations
BioProject PRJNA295265
SRA SRP063554

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

Supplementary file Size Download File type/resource
GSE72886_RAW.tar 193.9 Mb (http)(custom) TAR (of TXT, WIG)
Raw data are available in SRA
Processed data provided as supplementary file

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