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Series GSE49966 Query DataSets for GSE49966
Status Public on Oct 11, 2013
Title Spliceosome-Mediated-Decay (SMD) regulates expression of non-intronic genes in budding yeast
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study were to determine whether the spliceosome interacts with non-intronic mRNAs

Methods: RNAseq was performed on RNA that immunoprecipitated with the yeast SMD1 protein. Tandem-affinity-purified RNAs were extracted and RNAseq libraries were generated using the EpiCentre ScriptSeq kit (v1). We also performed RNAseq experiments on rRNA depleted total RNA extracted from an exosome mutant (rrp6Δ), a temperature-sensitive splicing mutant (prp40-1) and a parental strain (BY4741). The rRNA was depleted using the Invitrogen RiboMinus kit, according to manufactureres procedures. The depleted RNA was subsequently treated with Turbo DNAse I (Ambion) and RNAseq libraries were generated using the EpiCentre ScriptSeq kit (v1).

Results: The SM RNAseq data identified a number of non-intronic mRNAs that appeard to be bound by the spliceosome. Among these was the BDF2 mRNA, which enocdes for a bromo-domain protein. BDF2 was highly enriched in both SM-IP datasets and was therefore analyzed in more detail. To determine if other non-intronic mRNAs could be regulated by the spliceosome, we analysed the transcriptome in the rrp6Δ, the prp40-1 and a parental strain. Bioinformatic analysis of these data sets revealed that roughly 1% of the non-intronic mRNAs in yeast could be targeted by the spliceosome. TopHat revealed cannonical splice junctions in roughly 30 non-intronic mRNAs, indicating that these messages are spliced.

Conclusions: We demonstrate, for the first time, that the spliceosome can regulate expression of non-intronic mRNAs via one and/or two RNA cleavage events. We refer to this process as Spliceosome Mediated Decay (SMD).
 
Overall design We report RNAseq data for two SM immunoprecipitation experiments and RNAseq datasets for the parental strain (BY4741), the prp40-1 mutant, and the rrp6Δ strain.
 
Contributor(s) Granneman S, Vasilieva L
Citation(s) 24065768
Submission date Aug 19, 2013
Last update date May 15, 2019
Contact name Sander Granneman
E-mail(s) Sander.Granneman@ed.ac.uk
Organization name University of Edinburgh
Department Centre for Synthetic and Systems Biology
Lab Granneman lab
Street address Mayfield Road, Kings Buildings, Waddington building, room 3.06
City Edinburgh
ZIP/Postal code EH9 3JD
Country United Kingdom
 
Platforms (2)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (7)
GSM1210901 BY4741
GSM1210902 Rrp6
GSM1210903 Prp40
Relations
BioProject PRJNA215712
SRA SRP028893

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Supplementary file Size Download File type/resource
GSE49966_RAW.tar 63.2 Mb (http)(custom) TAR (of BEDGRAPH, GTF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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