ArticleGenome biology2023
Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention.
Article in Genome biology, 2023. 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, 21 citations in OpenAlex.
- iMPI: An Integrative Database for MicroProteins Encoded by Intron Retention in Tumors.Proteomics · 2026Article
- Promoter identity shapes splicing outcomes and fidelity.Nature communications · 2026Article
- Causes and consequences of cytonuclear incompatibility in hybrids of flowering plants.Journal of experimental botany · 2026Review
- Integrated profiling of iPSC-derived motor neurons carrying C9orf72, FUS, TARDBP, or SOD1 mutations.Stem cell reports · 2025Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation.Genes · 2025Review
- Brain-Specific Gata4 Downregulation in Greywick Female Mice Models the Metabolic Subtype of Polycystic Ovary Syndrome.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Universal features of alternative splicing and the regulatory roles of transcription factors in this process under diverse environmental stimuli in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Alternative Splicing in Tumorigenesis and Cancer Therapy.Biomolecules · 2025Review
- Higher Intron Retention Levels in Female Alzheimer's Brains May Be Linked to Disease Prevalence.Aging cell · 2025Article
- The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.PLoS computational biology · 2025Article
- The Negative Regulators of the Basal Defence WRKY7, WRKY11 and WRKY17 Modulate the Jasmonic Acid Pathway and an Alternative Splicing Regulatory Network in Response to Pseudomonas syringae in Arabidopsis thaliana.Molecular plant pathology · 2024Article
- mRNA initiation and termination are spatially coordinated.bioRxiv : the preprint server for biology · 2024Article
- Neuronal RNA processing: cross-talk between transcriptional regulation and RNA-binding proteins.Frontiers in molecular neuroscience · 2024Review
- Homeobox regulator Wilms Tumour 1 is displaced by androgen receptor at cis-regulatory elements in the endometrium of PCOS patients.Frontiers in endocrinology · 2024Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- Evidence-Based Guide to Using Artificial Introns for Tissue-Specific Knockout in Mice.International journal of molecular sciences · 2023Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative splicing is a widespread regulatory phenomenon that enables a single gene to produce multiple transcripts. Among the different types of alternative splicing, intron retention is one of the least explored despite its high prevalence in both plants and animals. The recent discovery that the majority of splicing is co-transcriptional has led to the finding that chromatin state affects alternative splicing. Therefore, it is plausible that transcription factors can regulate splicing outcomes.
resultsWe provide evidence for the hypothesis that transcription factors are involved in the regulation of intron retention by studying regions of open chromatin in retained and excised introns. Using deep learning models designed to distinguish between regions of open chromatin in retained introns and non-retained introns, we identified motifs enriched in IR events with significant hits to known human transcription factors. Our model predicts that the majority of transcription factors that affect intron retention come from the zinc finger family. We demonstrate the validity of these predictions using ChIP-seq data for multiple zinc finger transcription factors and find strong over-representation for their peaks in intron retention events.
conclusionsThis work opens up opportunities for further studies that elucidate the mechanisms by which transcription factors affect intron retention and other forms of splicing. AVAILABILITY: Source code available at https://github.com/fahadahaf/chromir.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.