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Dey P, Mattick JS. High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs. Epigenetics Chromatin. 2021;14(1):45doi: 10.1186/s13072-021-00419-2.
Dey, P., & Mattick, J. S. (2021). High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs. Epigenetics & chromatin, 14(1), 45. https://doi.org/10.1186/s13072-021-00419-2
Dey, Pinki, and Mattick, John S. "High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs." Epigenetics & chromatin vol. 14,1 (2021): 45. doi: https://doi.org/10.1186/s13072-021-00419-2
Dey P, Mattick JS. High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs. Epigenetics Chromatin. 2021 Sep 27;14(1):45. doi: 10.1186/s13072-021-00419-2. PMID: 34579770; PMCID: PMC8477579.
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Epigenetics Chromatin. 2021 Sep 27;14(1):45. doi: 10.1186/s13072-021-00419-2.

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

Epigenetics & chromatin

Pinki Dey, John S Mattick

Affiliations

  1. School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Sydney, Australia.
  2. School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Sydney, Australia. [email protected].

PMID: 34579770 PMCID: PMC8477579 DOI: 10.1186/s13072-021-00419-2

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 over 50% of lncRNAs examined and are mostly first introns with an average length of just 354 bp, compared to the average length of all human introns of 6355 and 7987 bp in mRNAs and lncRNAs, respectively. Removal of short introns from the dataset abrogated the high upstream H3K4me3 signal, confirming that the association of slabs and short lncRNA introns with intron retention holds genome-wide. The high upstream H3K4me3 signal is also associated with alternatively spliced exons, known to be prominent in lncRNAs. This phenomenon was not observed with mRNAs.

CONCLUSIONS: There is widespread intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs, which raises intriguing questions about the relationship of IR to lncRNA function and chromatin organization.

© 2021. The Author(s).

Keywords: Exons; Histone modifications; Introns; Long non-coding RNAs; Nucleosomes

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