Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila

Abstract

Chromatin insulators are functionally conserved DNA–protein complexes situated throughout the genome that organize independent transcriptional domains. Previous work implicated RNA as an important cofactor in chromatin insulator activity, although the precise mechanisms are not yet understood. Here we identify the exosome, the highly conserved major cellular 3′ to 5′ RNA degradation machinery, as a physical interactor of CP190-dependent chromatin insulator complexes in Drosophila. Genome-wide profiling of exosome by ChIP-seq in two different embryonic cell lines reveals extensive and specific overlap with the CP190, BEAF-32 and CTCF insulator proteins. Colocalization occurs mainly at promoters but also boundary elements such as Mcp, Fab-8, scs and scs′, which overlaps with a promoter. Surprisingly, exosome associates primarily with promoters but not gene bodies of active genes, arguing against simple cotranscriptional recruitment to RNA substrates. Similar to insulator proteins, exosome is also significantly enriched at divergently transcribed promoters. Directed ChIP of exosome in cell lines depleted of insulator proteins shows that CTCF is required specifically for exosome association at Mcp and Fab-8 but not other sites, suggesting that alternate mechanisms must also contribute to exosome chromatin recruitment. Taken together, our results reveal a novel positive relationship between exosome and chromatin insulators throughout the genome.

Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

“…Depending on the insulator studied, three different situations can be envisaged: (1) Depletion of a single DNA bound factor has no consequences on CP190 binding, as the remaining insulator proteins are sufficient for CP190 binding. This has been observed for BEAF-32 depletion, which does not affect CP190 recruitment to chromatin (Schwartz et al 2012;Lim et al 2013). (2) At other sites, CP190 may require the cooperation with at least two DNA-bound IBPs.…”

The exosome complex establishes a barricade to erythroid maturation

“…In Drosophila, exosome complex components colocalize with chromatin insulator factors at boundary elements and also localize to promoters. 23 In yeast, the exosome complex localizes to nucleoli and subnuclear regions enriched in actively transcribed genes. [57][58][59] The exosome complex regulates alternative transcription start site selection and may directly affect heterochromatin formation and gene silencing through posttranscriptional regulation.…”

Maintenance of a <em>Drosophila melanogaster</em> Population Cage

“…The ability to combine genetic and biochemical approaches has made Drosophila a particularly suitable organism for biochemistry and molecular biology studies [1][2][3] . These studies often require large amounts of biological material, not only from adult flies, but also from larvae 4 , pupae 5 and embryos [6][7][8] .…”