High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs.

ABSTRACT:

Background

It is established that protein-coding exons are preferentially localized in nucleosomes. To examine whether the same is true for non-coding exons, we analysed nucleosome occupancy in and adjacent to internal exons in genes encoding long non-coding RNAs (lncRNAs) in human CD4+ T cells and K562 cells.

Results

We confirmed that internal exons in lncRNAs are preferentially associated with nucleosomes, but also observed an elevated signal from H3K4me3-marked nucleosomes in the sequences upstream of these exons. Examination of 200 genomic lncRNA loci chosen at random across all chromosomes showed that high-density regions of H3K4me3-marked nucleosomes, which we term 'slabs', are associated with genomic regions exhibiting intron retention. These retained introns occur in

SUBMITTER: Dey P 

PROVIDER: S-EPMC8477579 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature