title: Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data.
abstract: Pre-mRNA splicing represents an important regulatory layer of eukaryotic gene expression. In the simple budding yeastSaccharomyces cerevisiae, about one-third of all mRNA molecules undergo splicing, and splicing efficiency is tightly regulated, for example, during meiotic differentiation.S. cerevisiaefeatures a streamlined, evolutionarily highly conserved splicing machinery and serves as a favourite model for studies of various aspects of splicing. RNA-seq represents a robust, versatile, and affordable technique for transcriptome interrogation, which can also be used to study splicing efficiency. However, convenient bioinformatics tools for the analysis of splicing efficiency from yeast RNA-seq data are lacking. We present a complete workflow for the calculation of genome-wide splicing efficiency inS. cerevisiaeusing strand-specific RNA-seq data. Our pipeline takes sequencing reads in the FASTQ format and provides splicing efficiency values for the 5' and 3' splice junctions of each intron. The pipeline is based on up-to-date open-source software tools and requires very limited input from the user. We provide all relevant scripts in a ready-to-use form. We demonstrate the functionality of the workflow using RNA-seq datasets from three spliceosome mutants. The workflow should prove useful for studies of yeast splicing mutants or of regulated splicing, for example, under specific growth conditions.
authors.affiliation: Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 43 Prague 2, Czech Republic.
authors.forename: Martin
authors.identifier: 0000-0003-0277-8361
authors.initials: M
authors.lastname: Převorovský
authors.affiliation: Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 43 Prague 2, Czech Republic.
authors.forename: Martina
authors.identifier: 0000-0003-0040-9773
authors.initials: M
authors.lastname: Hálová
authors.affiliation: Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 43 Prague 2, Czech Republic.
authors.forename: Kateřina
authors.identifier: 0000-0002-6299-8641
authors.initials: K
authors.lastname: Abrhámová
authors.affiliation: Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 43 Prague 2, Czech Republic.
authors.forename: Jiří
authors.identifier: 0000-0002-8604-9547
authors.initials: J
authors.lastname: Libus
authors.affiliation: Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 128 43 Prague 2, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Folk
mesh_terms: D030561:Databases, Nucleic Acid; D009154:Mutation / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D017381:Spliceosomes / Q000235:genetics; D057188:Workflow
chemical_list: D012322:RNA Precursors