ArticleNucleic acids research2022
Increased chromatin accessibility facilitates intron retention in specific cell differentiation states.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Intron retention in health and amyotrophic lateral sclerosis.Brain : a journal of neurology · 2026Review
- Sex-biased intron retention in Alzheimer's disease.Neural regeneration research · 2026Article
- Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.Genome biology · 2026Article
- Integrated chromatin and transcriptomic profiling reveals sex-specific mechanisms of gene regulation in hepatic nutrient responses.PLoS biology · 2026Article
- Decoding exonic intron retention from sequence: an exploratory study in the human genome.Frontiers in bioinformatics · 2026Article
- Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal-like and malignant urothelial cells.Molecular oncology · 2025Article
- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation.Genes · 2025Review
- ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA.Nucleic acids research · 2025Article
- Genomic diversity in functionally relevant genes modifies neurodevelopmental versus neoplastic risks in individuals with germline PTEN variants.NPJ genomic medicine · 2025Article
- guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel.BMC genomics · 2024Article
- Article
- Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads.Nucleic acids research · 2023Article
- Towards resolution of the intron retention paradox in breast cancer.Breast cancer research : BCR · 2022Article
- Phosphorylation-dependent association of human chromatin protein PC4 to linker histone H1 regulates genome organization and transcription.Nucleic acids research · 2022Article
- CTCF as a regulator of alternative splicing: new tricks for an old player.Nucleic acids research · 2021Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, 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. We integrated matched mRNA sequencing (mRNA-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. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
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