%0 Journal Article %A Emily J. Brown %A Doris Bachtrog %T The Drosophila Y chromosome affects heterochromatin integrity genome-wide %D 2017 %R 10.1101/156000 %J bioRxiv %P 156000 %X The Drosophila Y chromosome is gene poor and mainly consists of silenced, repetitive DNA. Nonetheless, the Y influences expression of hundreds of genes genome-wide, possibly by sequestering key components of the heterochromatin machinery away from other positions in the genome. To directly test the influence of the Y chromosome on the genome-wide chromatin landscape, we assayed the genomic distribution of histone modifications associated with gene activation (H3K4me3), or heterochromatin (H3K9me2 and H3K9me3) in fruit flies with varying sex chromosome complements (X0, XY and XYY males; XX and XXY females). Consistent with the general deficiency of active chromatin modifications on the Y, we find that Y gene dose has little influence on the genomic distribution of H3K4me3. In contrast, both the presence and the number of Y chromosomes strongly influence genomewide enrichment patterns of repressive chromatin modifications. Highly repetitive regions such as the pericentromeres, the dot, and the Y chromosome (if present) are enriched for heterochromatic modifications in wildtype males and females, and even more strongly in X0 flies. In contrast, the additional Y chromosome in XYY males and XXY females diminishes the heterochromatic signal in these normally silenced, repeat-rich regions, which is accompanied by an increase in expression of Y-linked repeats. We find hundreds of genes that are expressed differentially between individuals with aberrant sex chromosome karyotypes, many of which also show sex-biased expression in wildtype Drosophila. Thus, Y chromosomes influence heterochromatin integrity genome-wide, and differences in the chromatin landscape of males and females may also contribute to sex-biased gene expression and sexual dimorphisms.Author summary The Drosophila Y chromosome is gene poor and mainly consists of epigenetically silenced, repetitive junk DNA, yet the Y influences expression of thousands of genes genome-wide. Here we study the genome-wide chromatin landscape in flies with varying sex chromosome complements (X0, XY and XYY males; XX and XXY females), and show that the Y indirectly influences the epigenetic landscapes between sexes, by sequestering repressive chromatin marks. Differences in the sex-specific epigenome can have broad functional consequences: Increased amounts of repetitive DNA result in insufficient silencing of transposable elements and their remobilization in XXY and XYY flies. Hundreds of genes change their expression patterns in flies with different sex chromosome karyotypes, thereby contributing to sex-biased gene expression patterns and sexual dimorphism. %U https://www.biorxiv.org/content/biorxiv/early/2017/06/26/156000.full.pdf