ArticleMolecular cell2021
Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing.
Article in Molecular cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 98 citations in OpenAlex.
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- YTHDC1 recognizes METTL16-dependent mProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Unraveling branch point-driven SR45a splicing dynamics in heat stress for plant adaptation.Science advances · 2026Article
- Isoforms in action: The impact of transcript diversity in phenotype.Genetics and molecular biology · 2026Article
- Article
- Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites.RNA biology · 2025Article
- Alternative splicing: from tumorigenesis to neoantigen-mediated cancer immunotherapy.Biomarker research · 2025Review
- Control of gene output by intron RNA structure.bioRxiv : the preprint server for biology · 2025Article
- 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
- Structural basis of RECQL5-induced RNA polymerase II transcription braking and subsequent reactivation.Nature structural & molecular biology · 2025Article
- Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo.Nature structural & molecular biology · 2025Article
- TAS-seq enables subcellular single-stranded adenosine profiling by signal peptide-assisted adenosine deamination.Cell reports methods · 2025Article
- FASTKD5 processes mitochondrial pre-mRNAs at noncanonical cleavage sites.Nucleic acids research · 2025Article
- Mapping HIV-1 RNA structure, homodimers, long-range interactions and persistent domains by HiCapR.eLife · 2025Article
- The regulation and function of post-transcriptional RNA splicing.Nature reviews. Genetics · 2025Review
- Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II.Molecular cell · 2025Article
- Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.Molecular cell · 2025Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Most RNA processing occurs co-transcriptionally. We interrogated nascent pol II transcripts by chemical and enzymatic probing and determined how the "nascent RNA structureome" relates to splicing, A-I editing and transcription speed. RNA folding within introns and steep structural transitions at splice sites are associated with efficient co-transcriptional splicing. A slow pol II mutant elicits extensive remodeling into more folded conformations with increased A-I editing. Introns that become more structured at their 3' splice sites get co-transcriptionally excised more efficiently. Slow pol II altered folding of intronic Alu elements where cryptic splicing and intron retention are stimulated, an outcome mimicked by UV, which decelerates transcription. Slow transcription also remodeled RNA folding around alternative exons in distinct ways that predict whether skipping or inclusion is favored, even though it occurs post-transcriptionally. Hence, co-transcriptional RNA folding modulates post-transcriptional alternative splicing. In summary, the plasticity of nascent transcripts has widespread effects on RNA processing.
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