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SRX2422796: GSM2428961: H2BK5Ac - TSWT; Mus musculus; ChIP-Seq
1 ILLUMINA (NextSeq 500) run: 103.5M spots, 7.9G bases, 1.7Gb downloads

Submitted by: NCBI (GEO)
Study: MAP3K4 Kinase Activity Controls Chromatin Remodelers for Transitions Between Epithelial and Mesenchymal Phenotypes in Trophoblast Stem Cells [ChIP-Seq]
show Abstracthide Abstract
MAP3K4 is a serine/threonine kinase that regulates epithelial to mesenchymal transition (EMT). Trophoblast stem (TS) cells lacking MAP3K4 kinase activity (TSKI4 cells) are in an intermediate state of EMT, having reduced epithelial and increased mesenchymal marker expression. Reduced epithelial gene expression in TSKI4 cells was due to loss of H2BK5 promoter acetylation catalyzed by the histone acetyltransferase CBP. Herein, we show that MAP3K4 also regulates the ubiquitination and degradation of the deacetylase HDAC6. Due to the loss of MAP3K4 kinase activity, TSKI4 cells have elevated HDAC6 expression and activity. Knockdown of HDAC6 in TSKI4 cells restores epithelial features, defining HDAC6 as a key regulator of EMT controlled by MAP3K4. HDAC6 promotes EMT by directly deacetylating H2BK5 on promoters of tight junction genes claudin6 and occludin, inhibiting their expression. Thus, MAP3K4 is a master regulator that coordinates chromatin modifiers, CBP and HDAC6, to regulate the transition between epithelial and mesenchymal states. Overall design: a-H2BK5Ac ChIP samples from TSWT, TSKI4, and TSKI4 HDAC6 sh2 cells and a TSWT input sample were analyzed.
Sample: H2BK5Ac - TSWT
SAMN06141629 • SRS1859864 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Cells were fixed in 1% paraformaldehyde for 10 minutes, harvested, and the nuclei were isolated and lysed. The nuclear lysate was sonicated and underwent immunoprecipitation using 50 µl of dynabeads (Invitrogen) coupled to 5 µl of Active Motif α-H2BK5Ac antibody per sample. DNA-protein crosslinks were reversed overnight at 65C, and samples were ribonuclease and proteinase treated before DNA was purified using Min Elute columns (Qiagen). Preparation of libraries was performed using 50 ng of ChIP or TSWT input DNA and the KAPA HyperPrep kit with Illumina TruSeq indexed adapters. Dual SPRI size selection was performed after 18 cycles of amplification according to the manufacturer’s protocol. The average library size was ~300 bp. 12-plex libraries were sequenced (1 X 75 bp) using an Illumina NextSeq500 ranging from 7.1-8.9 X 107 reads per sample.
Experiment attributes:
GEO Accession: GSM2428961
Links:
Runs: 1 run, 103.5M spots, 7.9G bases, 1.7Gb
Run# of Spots# of BasesSizePublished
SRR5110410103,532,0167.9G1.7Gb2017-03-09

ID:
3518550

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