ArticleNucleic acids research2020
Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 30 citations in OpenAlex.
- Review
- CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo.Nature structural & molecular biology · 2025Article
- Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.Nucleic acids research · 2025Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- How does precursor RNA structure influence RNA processing and gene expression?Bioscience reports · 2023Review
- Chemical Probing of RNA Structure In Vivo Using SHAPE-MaP and DMS-MaP.Methods in molecular biology (Clifton, N.J.) · 2023Article
- SHAPE to Probe RNA Structure and RNA-Protein Interactions In Vitro.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly.Nucleic acids research · 2022Article
- Donor Splice Site Variant inMedicina (Kaunas, Lithuania) · 2022Article
- Secondary structures in RNA synthesis, splicing and translation.Computational and structural biotechnology journal · 2022Review
- Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.RNA biology · 2021Article
- Long-read technologies identify a hidden inverted duplication in a family with choroideremia.HGG advances · 2021Article
- Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets.NAR genomics and bioinformatics · 2021Article
- Induction of cryptic pre-mRNA splice-switching by antisense oligonucleotides.Scientific reports · 2021Article
- Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code.Nucleic acids research · 2021Article
- Transcription Regulation Through Nascent RNA Folding.Journal of molecular biology · 2021Review
- Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing.Molecular cell · 2021Article
- Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing.Nature communications · 2021Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem-loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.
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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.