Project description:Centromeres are a specialized chromatin domain that are required for the assembly of the mitotic kinetochore and the accurate segregation of chromosomes. Non-coding RNAs play essential roles in regulating genome organization including at the unique chromatin environment present at human centromeres. To identify RNAs that regulate centromeres we performed Chromatin-Associated RNA sequencing (ChAR-seq) in three different human cell lines to generate a comprehensive list of RNAs associated with centromeric chromatin at a repeat array and chromosome-specific resolution. Centromere enriched RNAs display distinct contact behaviors across repeat arrays and generally belong to three categories: centromere encoded, nucleolar localized, and highly abundant, broad-binding RNAs. Most centromere encoded RNAs remain locally associated with their transcription locus with the exception of a subset of human satellite RNAs. These findings highlight the localized nature of higher order repeat derived RNAs and the diversity of RNA-DNA contact patterns at human centromeres that may reflect or contribute to local chromatin differences.
Project description:RNA has been suggested to play a major role in the regulation of higher-order structures of chromatin. This study investigated chromatin-associated RNA (caRNA) in Drosophila melanogaster by applying high-throughput sequencing to RNA molecules that co-fractionate with chromatin. Using a cell-free in vitro chromatin assembly system (DREX), we demonstrated that caRNAs mainly comprise snoRNAs, snoRNA hosts and miRNAs.
Project description: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.
Project description: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.