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Series GSE76142 Query DataSets for GSE76142
Status Public on Apr 16, 2016
Title Divergence of Transcription Regulation and the Function of a Conserved Elongation Factor in Budding and Fission Yeast
Organisms Schizosaccharomyces pombe; Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet mechanistic details of this evolution remain elusive. By comparing the transcriptional landscape of distantly related budding and fission yeast, we catch a glimpse of divergence in gene regulation. Using an adapted Precision Run-On sequencing (PRO-seq) approach, we have mapped the positions of RNA polymerase (RNA Pol II) active sites genome-wide in S. pombe and S. cerevisiae at base-pair resolution. We further mapped preferred sites of transcription initiation in each organism, exposing the origins of nascent transcription. Performing PRO-seq in strains lacking Spt4, a highly conserved elongation factor subunit, results in globally elevated levels of transcribing Pol II within genes in both species. Messenger RNA abundance, however, does not reflect the increases in RNA Pol II density, indicating a possible global elongation rate defect. Unexpectedly, we identify a novel pause in early elongation, specific to S. pombe, which requires Spt4, suggesting regulatory potential similar to promoter-proximal pausing in mammals.
Overall design Examination transcriptional landscapes in S. cerevisiae and S. pombe and the changes that result from the deletion of Spt4.
Contributor(s) Booth GT, Lis JT
Citation(s) 27197211
Submission date Dec 18, 2015
Last update date May 15, 2019
Contact name Gregory Thomas Booth
Phone 607-351-5499
Organization name Cornell University
Department Molecular Biology and Genetics
Lab John Lis
Street address 526 Campus Road
City Ithaca
State/province New York
ZIP/Postal code 14853
Country USA
Platforms (3)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
GPL13988 Illumina HiSeq 2000 (Schizosaccharomyces pombe)
GPL20584 Illumina NextSeq 500 (Schizosaccharomyces pombe)
Samples (10)
GSM1974983 S_cerevisiae_WT_PROseq
GSM1974984 S_cerevisiae_spt4Δ_PROseq
GSM1974985 S_pombe_WT_PROseq
BioProject PRJNA306424
SRA SRP067557

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Supplementary file Size Download File type/resource
GSE76142_RAW.tar 199.7 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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