Trithorax-group protein ASH1 defines novel H3K36me3/H3K9me3 bivalent domains

A Trithorax-group (TrxG) protein ASH1 selectively dimethylates histone H3 lysine 36 (H3K36) and is required for expression of Hox genes. Genome-wide targets and molecular functions of ASH1, however, have remained elusive. Here we report ChIP-seq analysis of ASH1 targets in the human genome using a leukemia cell line K562. We identified 4,596 ASH1 binding sites, 2,502 of which are in the coding region, mostly in a proximity of promoters. Remaining half of the ASH1 binding sites are in the intergenic region. Analysis of histone methyation patterns revealed that a majority of ASH1 bidning sites are closely associated not only with trimethylated H3K36 (H3K36me3) but also with H3K9me3, shedding light for the first time to H3K36/H3K9 double methylation domains. Of note, an H3K9 methyltransferase SETDB1 is enriched in the ASH1 bidning sites, whereas EZH2 but not SUZ12 of the Polycomb Repression Complex 2 (PRC2) is present in bivalent domains. In addition, a small subset of ASH1 targets bear H3K4me3 and colocalize with RNA polymerase II. These select targets are highly enriched for regulators of gene expression, such as CXXC1, WHSC2/NELFA, and a battery of zinc finger proteins, suggesting that ASH1 might acts as a master regulator of gene expression. Overall design: Two biological replicates using different batches of affinity purified rabbit polyclonal antibodies against the C-terminal 18 amino acids of human/mouse ASH1. Anti-ASH1 antibodies were made in-house: batch #1 (Tanaka et al. Gene 397:161-168, 2007) and batch #3.