Repeat RNAs associate with replication forks and post-replicative DNA [short]

Non-coding RNA has a proven ability to direct and regulate chromatin modifications by acting as scaffolds between DNA and histone-modifying complexes. However, it is unknown if ncRNA plays any role in DNA replication and epigenome maintenance, including histone eviction and re-instalment of histone-modifications after genome duplication. Isolation of nascent chromatin has identified a large number of RNA-binding proteins in addition to unknown components of the replication and epigenetic maintenance machinery. Here, we isolated and characterized long and short RNAs associated with nascent chromatin at active replication forks and track RNA composition during chromatin maturation across the cell cycle. Shortly after fork passage, GA-rich-, Alpha repeats and TERRA RNA are associated with replicated DNA. These repeat RNAs arise from loci undergoing replication, suggesting an interaction in cis. Post-replication during chromatin maturation, and even after mitosis in G1, the repeats remain enriched on DNA. This argues that specific types of repeat RNAs are transcribed shortly after DNA replication and stably associates with their loci of origin throughout cell cycle. Our rich data set provides a resource to understand how repeat RNAs and their engagement with chromatin are regulated with respect to DNA replication and across the cell cycle. Cells were synchronized, released and harvested at 3 different time points (0, 2 and 10h) measured from 3 hours post cell release into S-phase. Input samples were taken at each time-point and every sample was produced in biological triplicates. 3/4 of samples were labeled with biotin dUTP (b-dUTP) each of which was harvested at different time points and 1 sample was harvested at t=0 and used for Histone3 and Streptavedin pull-down.