The exosome degrades chromatin-associated RNAs genome-wide and maintains chromatin homeostasis (RNA-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. Little is known about the role of the RNA exosome in the regulation of such chromatin-associated RNAs (caRNAs). The project aims at 1) identifying caRNAs produced from unique and repetitive sequences in the genome of Drosophila melanogaster S2 cells, and 2) characterize the role of the RNA exosome in controlling caRNA levels. To answer these questions, 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 the chromatin-associated transcriptome by sequencing RNAs purified from a chromatin fraction isolated from S2 cells. Overall design: RNA from GFP-Control, Rrp6-kd, Dis3-kd and Double-kd (Rrp6+Dis3) was extracted from D. melanogaster S2 cells. Total RNA samples consist of pooled biological triplicates. Chromatin samples consist of 3 biological triplicates sequenced independently.