Sex Differences in <i>Drosophila melanogaster</i> Heterochromatin Are Regulated by Non-Sex Specific Factors

<div><p>The eukaryotic genome is assembled into distinct types of chromatin. Gene-rich euchromatin has active chromatin marks, while heterochromatin is gene-poor and enriched for silencing marks. In spite of this, genes native to heterochromatic regions are dependent on their normal environment for full expression. Expression of genes in autosomal heterochromatin is reduced in male flies mutated for the noncoding <i>roX</i> RNAs, but not in females. <i>roX</i> mutations also disrupt silencing of reporter genes in male, but not female, heterochromatin, revealing a sex difference in heterochromatin. We adopted a genetic approach to determine how this difference is regulated, and found no evidence that known X chromosome counting elements, or the sex determination pathway that these control, are involved. This suggested that the sex chromosome karyotype regulates autosomal heterochromatin by a different mechanism. To address this, candidate genes that regulate chromosome organization were examined. In XX flies mutation of <i>Topoisomerase II (Top2)</i>, a gene involved in chromatin organization and homolog pairing, made heterochromatic silencing dependent on <i>roX</i>, and thus male-like. Interestingly, Top2 also binds to a large block of pericentromeric satellite repeats (359 bp repeats) that are unique to the X chromosome. Deletion of X heterochromatin also makes autosomal heterochromatin in XX flies dependent on <i>roX</i> and enhances the effect of <i>Top2 mutations</i>, suggesting a combinatorial action. We postulate that Top2 and X heterochromatin in <i>Drosophila</i> comprise a novel karyotype-sensing pathway that determines the sensitivity of autosomal heterochromatin to loss of <i>roX</i> RNA.</p>