The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis (ATAC-Seq)

Eukaryotic genomes produce a large variety of RNAs some of which are present in the chromatin and may affect important processes such as chromatin packaging and gene expression. The RNA exosome controls the levels of chromatin-associated RNAs (caRNAs), but little is known about its role in the regulation of chromatin packaging. The project aims at characterizing the role of the RNA exosome in the maintenance of chromatin packaging in Drosophila melanogaster S2 cells. We have used RNA interference to knock down the exosome catalytic subunits RRP6 and DIS3 (individually or simultaneously) and we have analyzed the effects of the depletions on chromatin accessibility by ATAC-seq. Nuclei from control (GFP-Control) and RNA exosome knockdown (dsRrp6, dsDis3, dsDouble) S2 cells were harvested for ATAC preparaton. All conditions consist of 3 biological replicates