Comment[ArrayExpressAccession]	E-GEOD-44119
MAGE-TAB Version	1.1				
Public Release Date	2013-04-01
Investigation Title	The histone chaperone Spt6 coordinates histone H3K27 demethylation to regulate gene expression and myogenesis				
Comment[Submitted Name]	The histone chaperone Spt6 coordinates histone H3K27 demethylation to regulate gene expression and myogenesis
Experiment Description	Histone chaperones affect chromatin structure and gene expression through interaction with histones and RNA polymerase II (PolII). Here, we report that the histone chaperone Spt6 counteracts H3K27me3, an epigenetic mark deposited by the Polycomb Repressive Complex 2 (PRC2) and associated with transcriptional repression. We found that Spt6 is required for proper engagement and function of the H3K27 demethylase KDM6A (UTX) on muscle genes and regulates muscle gene expression and cell differentiation. ChIP-Seq experiments revealed an extensive genome-wide overlap of Spt6, PolII and KDM6A at transcribed regions that are devoid of H3K27me3. Mammalian cells and zebrafish embryos with reduced Spt6 display increased H3K27me3 and diminished expression of the master regulator MyoD, resulting in myogenic differentiation defects. As a confirmation for an antagonistic relationship between Spt6 and H3K27me3, inhibition of PRC2 permits MyoD re-expression in myogenic cells with reduced Spt6. Our data indicate that, through cooperation with PolII and KDM6A, Spt6 orchestrates removal of H3K27me3, thus effectively controlling developmental gene expression and cell differentiation. Examination of Spt6 and KDM6A levels in a skeletal muscle cells at various developmental stages				
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl			
Person Last Name	Zare	Wang	Zare	Mousavi	Sartorelli
Person First Name	Hossein	A	Hossein	Kambiz	Vittorio
Person Mid Initials		H			
Person Email	hzare@mail.nih.gov				
Person Affiliation	NIH				
Person Address	NIH, 5o South Dr #1347, Bethesda, USA				
Person Roles	submitter				
Protocol Name	P-GSE44119-4	P-GSE44119-1	P-GSE44119-3	P-GSE44119-2	
Protocol Description	Illumina Casava1.8 software used for basecalling. Sequenced reads were mapped to mm9 whole genome using illumina pipline (Eland) Peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05 Genome_build: mm9 Supplementary_files_format_and_content: mapped reads in bed format, peak files in bed formats and wig files were generated using filtered reads residing in enriched regions	For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.	Lysates were clarified from sonicated nuclei and Spt6-DNA or KDM6A-DNA complexes were isolated with antibody Libraries were prepared according to NuGEN's instructions using Ovation SP Ultralow Library System (Part# 8033-32) on a Mondrian™ SP+ System. Libraries were sequenced on Illumina HiSeq following the manufacturer's protocols.	C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 20% fetal bovine serum (FBS) and penicillin/streptomycin.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol	
Experimental Factor Name	DEVELOPMENTAL STAGE	CHIP ANTIBODY			
Experimental Factor Type	developmental stage	chip antibody			
Comment[SecondaryAccession]	GSE44119				
Comment[GEOReleaseDate]	2013-04-01				
Comment[ArrayExpressSubmissionDate]	2013-02-06				
Comment[GEOLastUpdateDate]	2013-04-18				
Comment[AEExperimentType]	ChIP-seq				
Comment[SecondaryAccession]	SRP018432				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR680164-SRR680168				
SDRF File	E-GEOD-44119.sdrf.txt