ArticleGenome research2014
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
40 citing papers in PubMed, 70 citations in OpenAlex.
- DBR1 orchestrates the fate of lariat RNA: debranching-dependent turnover and function.Nucleic acids research · 2025Review
- A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants.Science China. Life sciences · 2024Article
- A tailed mirtron promotes longevity in Drosophila.Nucleic acids research · 2024Article
- Regulation of 3' splice site selection after step 1 of splicing by spliceosomal C* proteins.Science advances · 2023Article
- Intron turnover is essential to the development and pathogenicity of the plant pathogenic fungus Fusarium graminearum.Communications biology · 2022Article
- Evolution of the Early Spliceosomal Complex-From Constitutive to Regulated Splicing.International journal of molecular sciences · 2021Review
- The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome.Communications biology · 2021Article
- Saccharomyces cerevisiae RNA lariat debranching enzyme, Dbr1p, is required for completion of reverse transcription by the retrovirus-like element Ty1 and cleaves branched Ty1 RNAs.Molecular genetics and genomics : MGG · 2021Article
- Identification of Intronic Lariat-Derived Circular RNAs in Arabidopsis by RNA Deep Sequencing.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Identification of prognostic immune-related genes in the tumor microenvironment of endometrial cancer.Aging · 2020Article
- Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene.BMC evolutionary biology · 2019Article
- Fitness Landscape of the Fission Yeast Genome.Molecular biology and evolution · 2019Article
- A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants.The Plant cell · 2019Article
- Dual coding potential of a 2',5'-branched ribonucleotide in DNA.RNA (New York, N.Y.) · 2019Article
- Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast.RNA (New York, N.Y.) · 2018Article
- Pre-mRNA modifications and their role in nuclear processing.Quantitative biology (Beijing, China) · 2018Article
- Article
- Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.Bioinformatics (Oxford, England) · 2018Article
- Article
- A heuristic model for computational prediction of human branch point sequence.BMC bioinformatics · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Both canonical and alternative splicing of RNAs are governed by intronic sequence elements and produce transient lariat structures fastened by branch points within introns. To map precisely the location of branch points on a genomic scale, we developed LaSSO (Lariat Sequence Site Origin), a data-driven algorithm which utilizes RNA-seq data. Using fission yeast cells lacking the debranching enzyme Dbr1, LaSSO not only accurately identified canonical splicing events, but also pinpointed novel, but rare, exon-skipping events, which may reflect aberrantly spliced transcripts. Compromised intron turnover perturbed gene regulation at multiple levels, including splicing and protein translation. Notably, Dbr1 function was also critical for the expression of mitochondrial genes and for the processing of self-spliced mitochondrial introns. LaSSO showed better sensitivity and accuracy than algorithms used for computational branch-point prediction or for empirical branch-point determination. Even when applied to a human data set acquired in the presence of debranching activity, LaSSO identified both canonical and exon-skipping branch points. LaSSO thus provides an effective approach for defining high-resolution maps of branch-site sequences and intronic elements on a genomic scale. LaSSO should be useful to validate introns and uncover branch-point sequences in any eukaryote, and it could be integrated into RNA-seq pipelines.
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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.