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LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

Bitton, Danny A and Rallis, Charalampos and Jeffares, Daniel C and Smith, Graeme C and Chen, Yuan YC and Codlin, Sandra and Marguerat, Samuel and Bähler, Jürg (2014) 'LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.' Genome Research, 24 (7). pp. 1169-1179. ISSN 1054-9803

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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.

Item Type: Article
Uncontrolled Keywords: Humans; Schizosaccharomyces; RNA Precursors; RNA, Fungal; Chromosome Mapping; Gene Expression Profiling; Computational Biology; Genomics; Transcription, Genetic; RNA Splicing; Gene Deletion; Base Sequence; Regulatory Sequences, Nucleic Acid; Introns; Exons; Algorithms; Databases, Nucleic Acid; Position-Specific Scoring Matrices; High-Throughput Nucleotide Sequencing; Transcriptome; Nucleotide Motifs
Divisions: Faculty of Science and Health
Faculty of Science and Health > Life Sciences, School of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 18 Jun 2021 13:59
Last Modified: 18 Aug 2022 10:32

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