H3K4me3 ChIP chips

In yeast and other eukaryotes, the histone methyltransferase Set1 mediates methylation of lysine 4 on histone H3 (H3K4me). This modification marks the 5' end of transcribed genes in a 5' to 3' tri- to di- to monomethyl gradient, and promotes association of chromatin remodeling enzymes that regulate transcription. In a screen to identify factors that control the distinct H3K4 methylation states, we identified Ctk1, the serine 2 C-terminal domain (CTD) kinase for RNA polymerase II (RNAP II). We found that CTK1 deletion nearly abolished H3K4 monomethylation, yet caused a significant increase in H3K4 di- and trimethylation. Both on individual genes and genome-wide, the loss of CTK1 disrupted the H3K4 methylation patterns normally observed. H3K4me2 and H3K4me3 spread 3' into the body of genes, while H3K4 monomethylation was diminished. These effects were dependent on the catalytic activity of Ctk1, but are independent of Set2-mediated H3K36 methylation. Furthermore, these effects are not due to spurious transcription initiation in the body of genes, changes in RNAP II occupancy, changes in serine 5 CTD phosphorylation patterns, or to ‘transcriptional stress’. These data show that Ctk1 acts to restrict the spread of H3K4 methylation through a mechanism that is independent of a general transcription defect. The evidence presented indicates that Ctk1 controls the maintenance of suppressive chromatin in the coding regions of genes by both promoting H3K36 methylation, which leads to histone hypoacetylation, and by preventing the 3' spread of H3K4 trimethylation, a mark associated with chromatin remodeling at the 5' end of genes. Keywords: ChIP-chip Studying genome-wide distribution of H3K4me3 in ctk1del strains in Saccharomyces cerevisae