workflow for genome-wide determination of pre-mrna splicing efficiency from yeast rna-seq data

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ID: 200414
2016
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Abstract
Pre-mRNA splicing represents an important regulatory layer of eukaryotic gene expression. In the simple budding yeast Saccharomyces cerevisiae, about one-third of all mRNA molecules undergo splicing, and splicing efficiency is tightly regulated, for example, during meiotic differentiation. S. cerevisiae features 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 in S. cerevisiae using 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.
Reference Key
pevorovsk2016biomedworkflow Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Martin Převorovský;Martina Hálová;Kateřina Abrhámová;Jiří Libus;Petr Folk
Journal spectrochimica acta - part a: molecular and biomolecular spectroscopy
Year 2016
DOI
10.1155/2016/4783841
URL
http://dx.doi.org/10.1155/2016/4783841
Keywords
Medicine

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