Genomics

Dataset Information

26

ChIP-chip with antibodies for histone 3 lysine 4 trimethylation and histone 3 in Mll1+/+ and Mll1-/- MEFs


ABSTRACT: Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions. The Set1/COMPASS was the founding member and the only H3K4 methylases in S. cerevisiae, however, in mammals at least six H3K4 methylases Set1A/B and MLL1-4 are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation pattern in wild-type Mll1+/+ and Mll1-/- mouse fibroblasts (MEFs). We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters carrying this modification. Many of these genes, which include developmental regulators such as Hox genes show decreased levels of RNA polymerase II recruitment and expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, Menin, a component of the Mll1 and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci. However, the loss of MLL3/4 and/or the Set1 complexes have little to no effect on the Hox loci H3K4 methylation or expression levels in these MEFs. Together these data provide insight into redundancy and specialization of COMPASS-like complexes in mammals and provide evidence on a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation. Overall design: Chromatin Immunoprecipitation was performed with antibodies for histone 3 lysine 4 trimethylation and histone 3 in Mll1+/+ and Mll1-/- mouse embryonic fibroblasts. Two biological replicates were done. DNA for all four samples was hybridized to the commercially available Agilent Mouse Promoter array, a two-array set that tiles mouse promoters genome-wide.

INSTRUMENT(S): Agilent-014716 Mouse Promoter ChIP-on-Chip Set 244K, Microarray 1 of 2 (G4490A) (Feature Number version)

SUBMITTER: Pengfei Wang 

PROVIDER: GSE18262 | GEO | 2009-10-20

SECONDARY ACCESSION(S): PRJNA123517

REPOSITORIES: GEO

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Publications

Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II.

Wang Pengfei P   Lin Chengqi C   Smith Edwin R ER   Guo Hong H   Sanderson Brian W BW   Wu Min M   Gogol Madelaine M   Alexander Tara T   Seidel Christopher C   Wiedemann Leanne M LM   Ge Kai K   Krumlauf Robb R   Shilatifard Ali A  

Molecular and cellular biology 20090824 22


A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions. Set1/COMPASS was the founding member and is the only H3K4 methylase in Saccharomyces cerevisiae; however, in mammals, at least six H3K4 methylases, Set1A and Set1B and MLL1 to MLL4, are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wid  ...[more]

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