Insulator proteins contribute to expression of gene loci repositioned into heterochromatin in the course ofDrosophilaevolution

Abstract

AbstractPericentric heterochromatin inDrosophilais generally composed of repetitive DNA forming a transcriptionally repressive environment. Nevertheless, dozens of genes were embedded into pericentric genome regions during evolution ofDrosophilidaelineage and retained functional activity. However, factors that contribute to “immunity” of these gene loci to transcriptional silencing remain unknown. Here, we investigated molecular evolution of the essentialMybandRanbp16genes. These protein-coding genes reside in euchromatic loci of chromosome X inD. melanogasterand related species, while in other studiedDrosophilaspecies, including evolutionary distant ones, they are located in genomic regions highly enriched with the remnants of transposable elements (TEs), suggesting their heterochromatic nature and location. The promoter region ofMybexhibits a conserved structure throughout theDrosophilaphylogeny and carries motifs for binding of chromatin remodeling factors, including insulator BEAF-32, regardless of eu- or heterochromatic surroundings. Importantly, BEAF-32 occupies not only the promoter region ofMybbut is also found in the vicinity of transcriptional start sites (TSS) ofRanbp16gene as well as in a wide range of genes located in the contrasting chromatin types inD. melanogasterandD. virilis,denoting the boundary of the nucleosome-free region available for RNA polymerase II recruitment and the surrounding heterochromatin. We also find that along with BEAF-32, insulators dCTCF and GAF are enriched at the TSS of heterochromatic genes inD. melanogaster. Thus, we propose that insulator proteins contribute to gene expression in the heterochromatic environment and, hence, facilitate the evolutionary repositioning of gene loci into heterochromatin.Author summaryHeterochromatin inDrosophilais generally associated with transcriptional silencing. Nevertheless, hundreds of essential genes have been identified in the pericentric heterochromatin ofDrosophila melanogaster. Interestingly, genes embedded in pericentric heterochromatin ofD. melanogastermay occupy different genomic loci, euchromatic or heterochromatic, due to repositioning in the course of evolution ofDrosophilaspecies. By surveying factors that contribute to the normal functioning of the relocated genes in distantDrosophilaspecies, i.e.D. melanogasterandD. virilis, we identify certain insulator proteins (e.g.BEAF-32) that facilitate the expression of heterochromatic genes in spite of the repressive environment.