ArticleNature communications2021
Conserved long-range base pairings are associated with pre-mRNA processing of human genes.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 40 citations in OpenAlex.
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- Advances and challenges of splicing prediction with AI.Nature genetics · 2026Review
- MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) regulates long-range alternative splicing in Drosophila.Nucleic acids research · 2026Article
- Regulatory paradigm of Dscam1 stochastic alternative splicing through conserved long-range RNA structures.Nucleic acids research · 2026Article
- Unveiling Functional Long-Range RNA Structures via RIC-seq Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Ancestral intronic splicing regulatory elements in the SCNbioRxiv : the preprint server for biology · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data.Nucleic acids research · 2025Article
- Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions.bioRxiv : the preprint server for biology · 2025Article
- Human introns contain conserved tissue-specific cryptic poison exons.NAR genomics and bioinformatics · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- RNA structure in alternative splicing regulation: from mechanism to therapy.Acta biochimica et biophysica Sinica · 2024Review
- Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes.Scientific reports · 2024Article
- Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction.Briefings in bioinformatics · 2024Article
- Article
- Transcriptome- and proteome-wide effects of a circular RNA encompassing four early exons of the spinal muscular atrophy genes.Research square · 2024Article
- Causes, functions, and therapeutic possibilities of RNA secondary structure ensembles and alternative states.Cell chemical biology · 2024Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3'-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.
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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.