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

ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE222260 | GEO | 2025/01/01

REPOSITORIES: GEO

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

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Project description:RNA molecules can attach to chromatin and thus provide a type of epigenomic information. It remains difficult to know what RNAs are associated with chromatin and where are the genomic target loci of these RNAs. Here, we present MARGI (Mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNA (caRNA) with their target genomic sequence by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for human embryonic stem (ES) cells and HEK cells. MARGI revealed hundreds of chromatin-associated RNAs (caRNA), including previously known XIST, SNHG1, NEAT1, and MALAT1, as well as each caRNA's genomic interaction loci. Using a cross-species experiment, we estimated that approximately 2.2% of MARGI identified interactions are false positives. MARGI data suggested that 80-95% of interactions are proximal, where a caRNA is connected to its nearby genomic regions, 1-2% are distal, and 5-15% are inter-chromosomal. The majority of TSSs are associated with distal or inter-chromosomal caRNAs. ChIP-seq reported H3K27ac and H3K4me3 levels are positively correlated while H3K9me is negatively correlated with MARGI reported RNA attachment levels. The MARGI technology should facilitate revealing novel RNA functions and epigenomic events.

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2021-03-18 | GSE160368 | GEO

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