Chromatin accessibility determines intron retention in a cell type-specific manner

Abstract

Background: The phenomenon of widespread and dynamic intron retention (IR) programs in cells of vertebrate species has recently gained increasing attention. It has been shown that IR is involved in a multitude of cell-physiological processes, while aberrant IR profiles have been associated with numerous human diseases including several cancers. Gap: Despite consistent reports about intrinsic sequence features that predispose introns to become retained, conflicting findings about cell type or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. Methods: We integrated matched mRNA sequencing (RNA-seq), whole genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq), and chromatin immunoprecipitation sequencing (ChIP-seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. Results: Our results show that intrinsic characteristics are key for introns to evade splicing and that some epigenetic marks are associated with IR. However, cell type-specific IR profiles are largely marked by changes in chromatin accessibility, whereby predisposed introns in permissive chromatin regions are more likely to be retained. Conclusion: This study demonstrates the important role of chromatin architecture in IR regulation. Our results have profound implications for the analysis of other forms of alternative splicing as well. Since an increasing number of studies describe pathogenic alterations in splicing regulation and novel therapeutic approaches that target aberrant splicing, our findings will inform the development of novel epigenetic therapies. Keywords: nucleosome occupancy, intron retention, epigenetics, alternative splicing, histone marks, CpG methylation, chromatin accessibility

Sex-specific transcript diversity is regulated by a maternal transcription factor in earlyDrosophilaembryos

“…In females but not in males, CLAMP binds near the early promoter of the sxl gene (SxlPe) and governs the chromatin environment at exon three of sxl , normally spliced out in females ( Fig 6B ). Consistent with recent literature 56, 57 , we hypothesize that closed chromatin at exon3 induces exclusion of this exon from female sxl transcripts whereas more open chromatin in males result in its inclusion in the male sxl transcript. In the absence of CLAMP in females, the chromatin becomes more open, and therefore exon 3 is included in sxl transcripts which prevents translation due to the incorporation of a stop codon.…”

“…To determine a possible mechanism by which CLAMP regulates splicing of sxl, we mined our previously generated Micrococcal Nuclease sequencing data 26 Our results suggest that increased chromatin accessibility in males compared to females results in retention of exon3 in the male sxl transcript. Consistent with our results, recent reports provide strong evidence that increased chromatin accessibility contributes substantially to the retention of introns during AS 56 . In addition, splicing-associated chromatin signatures have recently been identified 57 .…”

“…Furthermore, CLAMP regulates chromatin as a pioneer TF 26, 48 and recent literature links chromatin and splicing 56, 57 . For example, closed chromatin marks have recently been linked to exon exclusion and open chromatin has been linked to exon inclusion 56, 57 . Thus, we hypothesize that CLAMP may recruit spliceosome complex components to regulate their splicing by altering the chromatin environment similar to the regulation that occurs at the sxl locus ( Fig 6A ).…”

CTCF as a regulator of alternative splicing: new tricks for an old player

“…Nucleosomes are preferentially positioned in exons rather than introns or alternatively spliced exons, highlighting a role for nucleosome positioning in exon definition ( 77–80 ). Furthermore, nucleosome occupancy has been correlated with regulating AS, specifically exon inclusion ( 78–80 ) and intron retention ( 81 ). Exon-associated nucleosomes are enriched in active H3K36me3 and repressive H3K27me2 histone modifications, which help demarcate exon-intron boundaries ( 77 , 82 ).…”

Towards resolution of the intron retention paradox in breast cancer

“…IR is regulated by cis - and trans -acting modulators 2,17,18 facilitating cellular responses to a range of environmental stimuli 19 . Intron-retaining mRNA transcripts are often degraded via nonsense-mediated decay (NMD), thereby causing down-regulation of the host gene.…”