Sex-specific histone modification ChIP-seq in Drosophila miranda. Drosophila miranda strain:MSH22

The chromatin landscape is key for gene regulation, but little is known about how it differs between the sexes or between species. Here, we study the sex-specific chromatin landscape of Drosophila miranda, a species with young sex chromosomes, and compare it to the model organism D. melanogaster. We analyze six histone modifications in male and female larvae of D. miranda (H3K4me1, H3K4me3, H3K36me3, H4K16ac, H3K27me3 and H3K9me2), and define seven biologically meaningful chromatin states that show different enrichment for transcribed and silent genes, repetitive elements, housekeeping and tissue-specific genes. The genome-wide distribution of both active and repressive chromatin states differs between males and females. In males, active chromatin is enriched on the X, relative to females, due to dosage compensation of the hemizygous X. Furthermore, a smaller fraction of the euchromatic portion of the genome is in a repressive chromatin state in males relative to females. However, sex-specific chromatin states appear not to explain sex-biased expression of genes. Overall, our data are consistent with the hypothesis that heteromorphic sex chromosomes in males (that is, a hypertranscribed X and an inactivated Y) may contribute to globally redistribute active and repressive chromatin marks between chromosomes and sexes.