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Series GSE122704 Query DataSets for GSE122704
Status Public on Jun 11, 2019
Title The Paf1 complex broadly impacts the transcriptome of Saccharomyces cerevisiae
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by genome tiling array
Summary The polymerase associated factor 1 complex (Paf1C) is a multifunctional epigenetic regulator of RNA polymerase II (Pol II) transcription. Paf1C controls gene expression by stimulating the placement of co-transcriptional histone modifications, influencing nucleosome occupancy in coding regions, facilitating transcription termination, and regulating nuclear export of RNAs. In this study, we investigate the extent to which these functions of Paf1C combine to influence the Saccharomyces cerevisiae transcriptome. Using conditions that enrich for unstable transcripts, we show that deletion of PAF1 affects all classes of Pol II-transcribed RNAs including multiple classes of noncoding transcripts. Gene ontology analysis revealed that mRNAs encoding genes involved in iron and phosphate homeostasis were differentially affected by deletion of PAF1. We further investigated these two groups of mRNAs with the goal of identifying overarching mechanisms of up and down-regulation in cells lacking Paf1. Our results indicate that only a subset of the observed changes result from loss of Paf1C-promoted histone modifications. We also found that transcription of the FET4 gene is differentially regulated by Paf1 and an upstream CUT. Together these data highlight the complexity of the epigenetic regulation of Pol II transcription imposed by Paf1C and identify a role for Paf1C in promoting CUT transcription.
Overall design Four yeast strains were tested and arrays were performed in triplicate
Contributor(s) Ellison MA, Lederer AR, Warner MH, Mavrich T, Heisler LE, Gebbia M, Nislow C, Lee MT, Arndt KM
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Submission date Nov 19, 2018
Last update date Jun 13, 2019
Contact name Karen M. Arndt
Organization name University of Pittsburgh
Department Biological Sciences
Lab A311 Langley Hall
Street address 4249 Fifth Avenue
City Pittsburgh
State/province Pennsylvania
ZIP/Postal code 15260
Country USA
Platforms (1)
GPL19774 [Scerevisiae_tlg] Affymetrix Saccharomyces cerevisiae tiling array
Samples (12)
GSM3525960 WT_1 Tiling Array
GSM3525961 WT_2 Tiling Array
GSM3525962 WT_3 Tiling Array
BioProject PRJNA506041

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE122704_RAW.tar 373.8 Mb (http)(custom) TAR (of CEL)
GSE122704_all_rna_before_limma.csv.gz 1.3 Mb (ftp)(http) CSV
GSE122704_bedgraph.tar.gz 399.4 Mb (ftp)(http) TAR
GSE122704_downregulated_in_paf1_vs_wt_window_20_1.5-fold_annotations.bed.gz 15.7 Kb (ftp)(http) BED
GSE122704_downregulated_regions_paf1trf4_vs_trf4_window_20_1.5-fold_annotations.bed.gz 24.9 Kb (ftp)(http) BED
GSE122704_pafVSwt.all.fix.csv.gz 455.3 Kb (ftp)(http) CSV
GSE122704_paftrfVStrf.all.fix.csv.gz 457.1 Kb (ftp)(http) CSV
GSE122704_upregulated_in_paf1_vs_wt_window_20_1.5-fold_annotations.bed.gz 5.8 Kb (ftp)(http) BED
GSE122704_upregulated_in_paf1trf4_vs_trf4_window_20_1.5-fold_annotations.bed.gz 18.7 Kb (ftp)(http) BED
Processed data are available on Series record

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