Elucidating the landscape of genome-wide chromatin interaction sites of the lncRNA TUG1 in bovine cell lines and liver tissue.

Abstract

Long-noncoding RNA (lncRNA) interact with DNA, RNA and proteins to regulate the epigenome and fundamental biological processes. In the bovine genome, the nature and mechanisms of lncRNA interactions with specific chromatin regions are unexplored yet. Here, we aimed to unravel the chromatin interaction sites of the evolutionary conserved lncRNA TUG1 in the bovine genome using ChIRP-seq (chromatin isolation by RNA precipitation) in two popular bovine cell lines (MDBK, MAC-T) and liver tissue. About half of the genome-wide TUG1 chromatin occupancy in the genome (3225, 3587 and 3977 interaction sites in MDBK, MAC-T and liver, respectively) was associated with protein-coding genes. Observation of numerous concordant TUG1 chromatin interaction sites between MDBK and MAC-T cells and liver tissue was consistent with the known ubiquitous expression of TUG1. Analysis of overlaps between ChIRP-seq peaks and ATAC-seq peaks in MDBK and MAC-T cells pinpointed TUG1 chromatin interaction sites relevant for modulating chromatin accessibility.