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Series GSE17638 Query DataSets for GSE17638
Status Public on Oct 16, 2009
Title The Ess1 prolyl isomerase is required for the transcription termination of small non-coding RNAs via Nrd1 pathway
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary Genome-wide studies have identified abundant small, non-coding RNAs including snRNAs, snoRNAs, cryptic unstable transcripts (CUTs), and upstream regulatory RNAs (uRNAs) that are transcribed by RNA polymerase II (pol II) and terminated by a Nrd1-dependent pathway. Here, we show that the prolyl isomerase, Ess1, is required for Nrd1-dependent termination of ncRNAs. Ess1 binds the carboxy terminal domain (CTD) of pol II and is thought to regulate transcription by conformational isomerization of Ser-Pro bonds within the CTD. In ess1 mutants, expression of ~10% of the genome was altered, due primarily to defects in termination of snoRNAs, CUTs, SUTs and uRNAs. Ess1 promoted dephosphorylation of Ser5 (but not Ser2) within the CTD, most likely by the Ssu72 phosphatase, and we provide evidence for a competition between Nrd1 and Pcf11 for CTD-binding that is regulated by Ess1-dependent isomerization. This is the first example of a prolyl isomerase required for interpreting the “CTD code.”
Overall design Two separate experiments were done: a standard Expression Array, and a Tiling Array.

For the Expression Array, two independent methods were used. First, we compared wild-type and ess1(H164R) ts-mutants, where the mutant allele is integrated at the normal genomic locus. Cells were shifted to 34°C for 2 hr and RNA was prepared. In the second method, we used ESS1 deletion mutants that carried wild-type or H164R on a centromeric plasmid driven by the GAL1 promoter. These constructs were activated by a GAL4-ER-VP16 driver, which even in the absence of beta-estradiol (“0 hormone”), drives low level protein expression.

For the Tiling Array we compared wild-type and ess1(H164R) ts-mutants after a shift to 34°C for 2 hr.
Contributor(s) Singh N, Ma Z, Gemill T, Wu X, DeFiglio H, Rossettini A, Rabeler C, Beane O, Morse R, Palumbo M, Hanes SD
Citation(s) 19854134
Submission date Aug 13, 2009
Last update date Jul 01, 2016
Contact name Steven D Hanes
Phone 518-473-4213
Organization name Wadsworth Center
Department Developmental Genetics
Lab CMS5102
Street address 150 New Scotland Ave
City Albany
State/province NY
ZIP/Postal code 12208
Country USA
Platforms (2)
GPL90 [YG_S98] Affymetrix Yeast Genome S98 Array
GPL7250 [Sc03b_MR] Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array
Samples (16)
GSM440152 WT W3031A replicate 1 after 2hr at 34 C
GSM440153 WT W3031A replicate 2 after 2hr at 34 C
GSM440154 Ess1 H164R mutant replicate 1 after 2hr at 34 C
BioProject PRJNA118579

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
GSE17638_RAW.tar 241.4 Mb (http)(custom) TAR (of CEL, CHP) 16.0 Mb (ftp)(http) BAR 14.1 Mb (ftp)(http) BAR
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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