Comment[ArrayExpressAccession] E-GEOD-44219 MAGE-TAB Version 1.1 Public Release Date 2013-10-22 Investigation Title Competition between pre-mRNAs for a limiting splicing machinery drives global changes in splicing Comment[Submitted Name] Competition between pre-mRNAs for a limiting splicing machinery drives global changes in splicing Experiment Description During meiosis in yeast, global splicing efficiency increases. The mechanism for this is relief of competition for the splicing machinery by repression of intron-containing ribosomal protein genes (RPGs). Repression of RPGs with rapamycin also increases splicing efficiency in vegetative cells. Reducing levels of an RPG-dedicated transcription factor globally improves splicing and suppresses the temperature-sensitive growth defect of a spliceosome mutation. These results indicate that the spliceosome is limiting and pre-mRNAs compete with each other. Under these conditions, splicing efficiency of a given pre-mRNA therefore depends on both its concentration and affinity for the limiting splicing factor(s) as well as those of the competing pre-mRNAs. We propose that trans-competition control of splicing helps repress meiotic gene expression in vegetative cells, and promotes efficient meiosis. Competition between RNAs for a limiting factor may be a general condition important for function of a variety of post-transcriptional control mechanisms. Splicing and gene expression profiles of 1) wild type yeast cells treated with rapamycin (2 biological replicates) relative to untreated cells and 2) prp4-1 pGAL-IFH1 (down-regulated expression of IFH1 transcription factor(specific for ribosomal protein genes)) relative to prp4-1 yeast. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Shiue Munding Shiue Ares Person First Name Lily Elizabeth Lily Manuel Person Mid Initials M Person Email lshiue@soe.ucsc.edu Person Affiliation UCSC Person Phone 831-459-2612 Person Address MCD Biology, UCSC, 1156 High Street, Santa Cruz, CA, USA Person Roles submitter Protocol Name P-GSE44219-2 P-GSE44219-1 Protocol Description Illumina Casava1.8.2 software used for basecalling. Sequenced reads (100bp read1, 58bp read2) were mapped to sacCer3 using tophat, allowing for a maximum intron size of 1200bp, with an estimated mean distance between the read pairs of 85bp (std dev 100bp). A gtf file of previously known splice sites was supplied to tophat. Tophat's coverage search and segment search intron-finding algorithms were also enabled. In the case of multiply-mapped reads, the single best hit as scored by bowtie was kept. Expression values (i.e., reads per exon or per gene) are calculated by summing the coverage at each position and dividing by read length. Genome_build: sacCer3 Supplementary_files_format_and_content: spreadsheet containing summarized gene expression, intron and exon2 read counts, as well as calculated Intron Accumulation Indexes total RNA was extracted according to Rio et al., Cold Spring Harb Protoc, 2010 "Method 1" strand-specific libraries (dUTP/USER) were made from polyA selected mRNA; adaptors, end repair through enrichment steps using Illumina DNA Sample Prep kit V2 Protocol Type normalization data transformation protocol nucleic acid library construction protocol Experimental Factor Name TREATMENT GROWTH CONDITIONS GENOTYPE Experimental Factor Type treatment growth conditions genotype Publication Title Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Publication Author List Munding EM, Shiue L, Katzman S, Donohue JP, Ares M Jr PubMed ID 23891561 Publication DOI 10.1016/j.molcel.2013.06.012 Comment[SecondaryAccession] GSE44219 Comment[GEOReleaseDate] 2013-10-22 Comment[ArrayExpressSubmissionDate] 2013-02-11 Comment[GEOLastUpdateDate] 2013-10-22 Comment[AEExperimentType] RNA-seq of coding RNA Comment[AdditionalFile:Data1] GSE44219_Munding_processed_data.txt Comment[AdditionalFile:Data2] GSE44219_sacCer3_ares_tophat_mapping.gtf Comment[SecondaryAccession] SRP018547 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR701791-SRR701844 SDRF File E-GEOD-44219.sdrf.txt