Comment[ArrayExpressAccession]	E-GEOD-50465
MAGE-TAB Version	1.1					
Public Release Date	2013-12-17
Investigation Title	Genome-wide maps of MyoD, MLL4 and histone modifications during MyoD-induced myogenesis in WT and MLL4-/- brown preadipocytes					
Comment[Submitted Name]	Genome-wide maps of MyoD, MLL4 and histone modifications during MyoD-induced myogenesis in WT and MLL4-/- brown preadipocytes
Experiment Description	Enhancers play a central role in cell-type-specific gene expression and are marked by H3K4me1/2. Active enhancers are further marked by H3K27ac. However, the methyltransferases responsible for the deposition of H3K4me1/2 on enhancers remain elusive. Furthermore, the functions of these methyltransferases on enhancers and associated cell-type-specific gene expression are poorly understood. Here, we identify MLL4 (KMT2D) as a major H3K4 mono- and di-methyltransferase in mammalian cells. Using adipogenesis and myogenesis as model systems, we show that MLL4 exhibits cell-type- and differentiation-stage-specific genomic binding and is predominantly localized on enhancers. MLL4 co-localizes with lineage-determining transcription factors (TFs) on active enhancers during differentiation. Deletion of MLL4 dramatically decreases H3K4me1/2 and H3K27ac on enhancers and leads to severe defects in cell-type-specific gene expression and cell differentiation. Finally, we provide evidence that lineage-determining TFs recruit and require MLL4 to establish enhancers critical for cell-type-specific gene expression. Together, these results identify MLL4 as an H3K4 mono-/di-methyltransferase required for enhancer activation during cell differentiation. ChIP-Seq of MyoD, MLL4 and histone modifications (H3K4me1, H3K4me3, and H3K27ac) in adenoviral GFP- or Cre-infected MLL3-/-;MLL4-flox/flox cells. Preadipocytes: brown preadipocytes before differentiation. D5 myocytes: 5 days after MyoD-induced myogenesis of brown preadipocytes.					
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	Ge	Lee	Wang	Xu	Peng	Ge
Person First Name	Kai	Ji-Eun	Chaochen	Shiliyang	Weiqun	Kai
Person Email	kai.ge@nih.gov					
Person Affiliation	NIH					
Person Phone	301-451-1998					
Person Address	NIDDK, NIH, 10 Center Dr Rm 8N307, Bethesda, MD, USA					
Person Roles	submitter					
Protocol Name	P-GSE50465-1	P-GSE50465-3	P-GSE50465-2			
Protocol Description	2% horse serum.	Lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibody (MyoD: Santa Cruz Biotechnology, sc-760 (lot: H2107); H3K4me1: abcam, ab8895 (lot: GR61280-1); H3K4me3: Millipore, 17-614 (lot: 2109590); H3K27ac: abcam, ab4729 (lot: GR81163-1); homemade MLL4). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.	E18.5 mouse embryo-derived MLL3-/-;MLL4flox/flox brown preadipocytes were immortalized by SV40T. Cells were infected with retroviral plasmid expressing MyoD, followed by infection with adenoviral Cre to delete the MLL4 gene. Cells were changed to myogenic medium (2% horse serum) when 70% confluent.			
Protocol Type	sample treatment protocol	nucleic acid library construction protocol	growth protocol			
Experimental Factor Name	CHIP ANTIBODY	CELL TYPE	GENOTYPE			
Experimental Factor Type	chip antibody	cell type	genotype			
Comment[SecondaryAccession]	GSE50465					
Comment[GEOReleaseDate]	2013-12-17					
Comment[ArrayExpressSubmissionDate]	2013-08-29					
Comment[GEOLastUpdateDate]	2013-12-19					
Comment[AEExperimentType]	ChIP-seq					
Comment[SecondaryAccession]	SRP029355					
SDRF File	E-GEOD-50465.sdrf.txt