ArticleGenome research2017
Large-scale analysis of branchpoint usage across species and cell lines.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
What it found
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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
85 citing papers in PubMed.
- Decoding splicing variants in high-throughput sequencing: a functional validation approach integrating deep learning tools.European journal of human genetics : EJHG · 2026Article
- Evolutionarily conserved spliceosome-exosome pathway in nuclear mRNA surveillance.Genes & development · 2026Article
- Intron location and sequence modulate gene expression in Yarrowia lipolytica.Nucleic acids research · 2026Article
- Sm-site containing mRNAs can accept Sm-rings and are downregulated in Spinal Muscular Atrophy.Nucleic acids research · 2025Article
- DBR1 orchestrates the fate of lariat RNA: debranching-dependent turnover and function.Nucleic acids research · 2025Review
- Mutations in the small nuclear RNA gene RNU2-2 cause a severe neurodevelopmental disorder with prominent epilepsy.Nature genetics · 2025Article
- Cancer-associated SF3B1 mutation K700E causes widespread changes in U2/branchpoint recognition without altering splicing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SF3B1: from core splicing factor to oncogenic driver.RNA (New York, N.Y.) · 2025Review
- Splicing accuracy varies across human introns, tissues, age and disease.Nature communications · 2025Article
- Circular RNA Formation and Degradation Are Not Directed by Universal Pathways.International journal of molecular sciences · 2025Review
- Formation of Circular RNAs.Advances in experimental medicine and biology · 2025Review
- Cancer-associated SF3B1 mutation K700E causes widespread changes in U2/branchpoint recognition without altering splicing.bioRxiv : the preprint server for biology · 2024Article
- Branch site recognition by the spliceosome.RNA (New York, N.Y.) · 2024Review
- Etiology of craniofacial and cardiac malformations in a mouse model ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers.PLoS genetics · 2024Article
- Latent Dirichlet allocation mixture models for nucleotide sequence analysis.NAR genomics and bioinformatics · 2024Article
- LINE-1 transcription activates long-range gene expression.Nature genetics · 2024Article
- SpliceAPP: an interactive web server to predict splicing errors arising from human mutations.BMC genomics · 2024Article
- A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants.Science China. Life sciences · 2024Article
- The debranching enzyme Dbr1 regulates lariat turnover and intron splicing.Nature communications · 2024Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2-5 linkage. Here, we report large-scale mapping of the branchpoints from deep sequencing data in three different species and in the SF3B1 K700E oncogenic mutant background. We have developed a novel method whereby raw lariat reads are refined by U2snRNP/pre-mRNA base-pairing models to return the largest current data set of branchpoint sequences with quality metrics. This analysis discovers novel modes of U2snRNA:pre-mRNA base-pairing conserved in yeast and provides insight into the biogenesis of intron circles. Finally, matching branch site usage with isoform selection across the extensive panel of ENCODE RNA-seq data sets offers insight into the mechanisms by which branchpoint usage drives alternative splicing.
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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.