Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data
Joint Authors
Převorovský, Martin
Hálová, Martina
Abrhámová, Kateřina
Libus, Jiří
Folk, Petr
Source
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-12-06
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Převorovský, Martin& Hálová, Martina& Abrhámová, Kateřina& Libus, Jiří& Folk, Petr. 2016. Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data. BioMed Research International،Vol. 2016, no. 2016, pp.1-9.
https://search.emarefa.net/detail/BIM-1097891
Modern Language Association (MLA)
Převorovský, Martin…[et al.]. Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data. BioMed Research International No. 2016 (2016), pp.1-9.
https://search.emarefa.net/detail/BIM-1097891
American Medical Association (AMA)
Převorovský, Martin& Hálová, Martina& Abrhámová, Kateřina& Libus, Jiří& Folk, Petr. Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data. BioMed Research International. 2016. Vol. 2016, no. 2016, pp.1-9.
https://search.emarefa.net/detail/BIM-1097891
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1097891