The role of H3K36 methylation and associated methyl transferases in chromosome-specific gene regulation

In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X chromosome and Painting of fourth targeting chromosome 4. Here, we explore the role of histone H3 methylated at lysine-36 (H3K36) and the associated methyltransferases—Set2, NSD, and Ash1—in these two chromosome-specific systems. We show that the loss of Set2 impairs the MSL complex–mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the fourth chromosome requires intact H3K36 and depends on the additive functions of NSD and Ash1. We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X chromosome and the fourth chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes. RNA-seq in male third instar larvae brains. 5 brains per sample and between 4 and 7 replicates per condition (Oregon R, Set21 , ash122/ash19011, NSDds46, ash122 NSDds46/ash19011 NSD ds46, ΔHisC; 12xH3K36R, ΔHisC; 12xH3K36K and ΔH3.3B; ΔH3.3A). The sequencing was performed in two rounds and Oregon R was used as wild type control in both sequencing runs.