Defining the landscape of chromatin-associated RNAs at human centromeric repeats

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. We performed chromatin-associated RNA sequencing (ChAR-seq) of human K562 cells to identify and map RNAs assoicated with centromeric chromatin. We generated two replicates split across multiple sequencing runs and combined for analysis. We also performed the same analysis on previously generated ChAR-seq data in human embryonic stem cells and differentiated definitive endoderm cells (see "Data table" below). *************************************************************** The table below lists GEO accessions reused/reanalyzed for this study. ***************************************************************