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Series GSE53090 Query DataSets for GSE53090
Status Public on Jan 27, 2014
Title KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Pluripotency of embryonic stem (ES) cells is controlled in part by chromatin-modifying factors that regulate histone H3 lysine 4 (H3K4) methylation. However, it remains unclear how H3K4 demethylation contributes to ES cell function. Here, we show that KDM5B, which demethylates lysine 4 of histone H3, co-localizes with H3K4me3 near promoters and enhancers of active genes in ES cells; its depletion leads to spreading of H3K4 methylation into gene bodies and enhancer shores, indicating that KDM5B functions to focus H3K4 methylation at promoters and enhancers. Spreading of H3K4 methylation to gene bodies and enhancer shores is linked to defects in gene expression programs and enhancer activity, respectively, during self-renewal and differentiation of KDM5B-depleted ES cells. KDM5B critically regulates H3K4 methylation at bivalent genes during differentiation in the absence of LIF or Oct4. We also show that KDM5B and LSD1, another H3K4 demethylase, co-regulate H3K4 methylation at active promoters but they retain distinct roles in demethylating gene body regions and bivalent genes. Our results provide global and functional insight into the role of KDM5B in regulating H3K4 methylation marks near promoters, gene bodies, and enhancers in ES cells and during differentiation.
 
Overall design RNA-Seq of murine shLuc and shKdm5b ES cells differentiated for 72h in the absence of LIF.
 
Contributor(s) Kidder BL, Hu G, Zhao K
Citation(s) 24495580
Submission date Dec 06, 2013
Last update date May 15, 2019
Contact name Benjamin L Kidder
E-mail(s) benjamin.kidder@wayne.edu
Organization name Wayne State University
Department Oncology
Lab Laboratory of Epigenomics
Street address 4100 John R St
City Detroit
State/province MI
ZIP/Postal code 48201
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (2)
GSM1282302 mES_shLuc_ctrl
GSM1282304 mES_shKdm5b
This SubSeries is part of SuperSeries:
GSE53093 KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation
Relations
BioProject PRJNA230823
SRA SRP033568

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Supplementary file Size Download File type/resource
GSE53090_RAW.tar 1.4 Gb (http)(custom) TAR (of BED, BEDGRAPH, RPKM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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