ArticleGenome biology2017
Intron retention enhances gene regulatory complexity in vertebrates.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 119 citations in OpenAlex.
- PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development.eLife · 2026Article
- The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis.Nature cell biology · 2026Article
- Intron retention in health and amyotrophic lateral sclerosis.Brain : a journal of neurology · 2026Review
- Intron Retention Controls Localization of lncRNAsbioRxiv : the preprint server for biology · 2026Article
- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- ScIsoX: a multidimensional framework for measuring isoform-level transcriptomic complexity in single cells.Genome biology · 2025Article
- Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation.Genes · 2025Review
- In Silico Analysis of s-DAPK-1: From Structure to Function and Regulation.Current issues in molecular biology · 2025Article
- Genome-wide identification and expression analysis of epigenetic regulator gene families in the medicinal mushroom Ganoderma lucidum.Archives of microbiology · 2025Article
- Advancing automated cell type annotation with large language models and single-cell isoform sequencing.Computational and structural biotechnology journal · 2025Review
- Alternative splicing drives a dynamic transcriptomic response duringMicrobial cell (Graz, Austria) · 2025Article
- Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises.Molecular ecology · 2025Article
- Phylogenetic Analysis of 590 Species Reveals Distinct Evolutionary Patterns of Intron-Exon Gene Structures Across Eukaryotic Lineages.Molecular biology and evolution · 2024Article
- The Intricate Functional Networks of Pre-mRNA Alternative Splicing in Mammalian Spermatogenesis.International journal of molecular sciences · 2024Review
- Systematic identification and characterization of exon-intron circRNAs.Genome research · 2024Article
- Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination.Microbial cell (Graz, Austria) · 2024Article
- DHX38 restricts chemoresistance by regulating the alternative pre-mRNA splicing of RELL2 in pancreatic ductal adenocarcinoma.PLoS genetics · 2023Article
- Cytoplasmic aggregation of mutant FUS causes multistep RNA splicing perturbations in the course of motor neuron pathology.Nucleic acids research · 2023Article
- Do not panic: An intron-centric guide to alternative splicing.The Plant cell · 2023Review
- MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundWhile intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution.
resultsOur RNA-sequencing-based analysis suggests that IR increases gene regulatory complexity, which is indicated by a strong anti-correlation between the number of genes affected by IR and the number of protein-coding genes in the genome of individual species. Our results confirm that IR affects many orthologous or functionally related genes in granulocytes. Further analysis uncovers new and unanticipated conserved characteristics of intron-retaining transcripts. We find that intron-retaining genes are transcriptionally co-regulated from bidirectional promoters. Intron-retaining genes have significantly longer 3' UTR sequences, with a corresponding increase in microRNA binding sites, some of which include highly conserved sequence motifs. This suggests that intron-retaining genes are highly regulated post-transcriptionally.
conclusionsOur study provides unique insights concerning the role of IR as a robust and evolutionarily conserved mechanism of gene expression regulation. Our findings enhance our understanding of gene regulatory complexity by adding another contributor to evolutionary adaptation.
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Registered trials
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.