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. Overall design: 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

真核基因组可产生种类繁多的RNA，其中部分RNA存在于染色质（chromatin）中，并可影响染色质包装（chromatin packaging）、基因表达等关键生物学过程。
RNA外切酶体（RNA exosome）能够调控染色质相关RNA（chromatin-associated RNAs，caRNAs）的丰度，但目前对于其在染色质包装调控中的作用仍知之甚少。
本项目旨在阐明RNA外切酶体在黑腹果蝇（Drosophila melanogaster）S2细胞的染色质包装维持过程中的功能。
我们采用RNA干扰（RNA interference）技术，分别或同时敲低RNA外切酶体的催化亚基RRP6与DIS3，并通过ATAC-seq分析了上述基因耗竭对染色质可及性的影响。
实验整体设计：收集对照组（GFP-Control）与RNA外切酶体敲低组（dsRrp6、dsDis3、dsDouble）的S2细胞核，用于ATAC测序样品制备。所有实验条件均设置3次生物学重复。