ArticleGenome research2021
Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 58 citations in OpenAlex.
- 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
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1.PLoS genetics · 2026Article
- Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes.bioRxiv : the preprint server for biology · 2026Article
- Efficient co-transcriptional splicing enforces rapid microexon definition and inclusion by SRRM4.bioRxiv : the preprint server for biology · 2026Article
- Decoding exonic intron retention from sequence: an exploratory study in the human genome.Frontiers in bioinformatics · 2026Article
- Origins and implications of intron retention quantitative trait loci in human tissues.American journal of human genetics · 2025Article
- EIciRNAs in focus: current understanding and future perspectives.RNA biology · 2025Review
- Productive mRNA chromatin escape is promoted by PRMT5 activity.Molecular cell · 2025Article
- Intron Retention: A Reemerging Paradigm in RNA Biology and Post-Transcriptional Gene Regulation.Genes · 2025Review
- The regulation and function of post-transcriptional RNA splicing.Nature reviews. Genetics · 2025Review
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms.Nucleic acids research · 2025Article
- Shiba: A versatile computational method for systematic identification of differential RNA splicing across platforms.bioRxiv : the preprint server for biology · 2025Article
- Article
- RBM4-mediated intron excision of Hsf1 induces BDNF for cerebellar foliation.Communications biology · 2024Article
- An RNA-centric view of transcription and genome organization.Molecular cell · 2024Review
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- The lncRNAGenes & development · 2024Article
- Alternative splicing of a chromatin modifier alters the transcriptional regulatory programs of stem cell maintenance and neuronal differentiation.Cell stem cell · 2024Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Steps of mRNA maturation are important gene regulatory events that occur in distinct cellular locations. However, transcriptomic analyses often lose information on the subcellular distribution of processed and unprocessed transcripts. We generated extensive RNA-seq data sets to track mRNA maturation across subcellular locations in mouse embryonic stem cells, neuronal progenitor cells, and postmitotic neurons. We find disparate patterns of RNA enrichment between the cytoplasmic, nucleoplasmic, and chromatin fractions, with some genes maintaining more polyadenylated RNA in chromatin than in the cytoplasm. We bioinformatically defined four regulatory groups for intron retention, including complete cotranscriptional splicing, complete intron retention in the cytoplasmic RNA, and two intron groups present in nuclear and chromatin transcripts but fully excised in cytoplasm. We found that introns switch their regulatory group between cell types, including neuronally excised introns repressed by polypyrimidine track binding protein 1 (PTBP1). Transcripts for the neuronal gamma-aminobutyric acid (GABA) B receptor, 1 (
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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.