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Series GSE115595 Query DataSets for GSE115595
Status Public on Aug 10, 2018
Title Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast
Organisms Schizosaccharomyces pombe; Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Unexpectedly, we show here that NNS-like transcription termination is not conserved in fission yeast. Instead, genome-wide location analyses show global recruitment of mRNA 3’ end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We further show that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.
 
Overall design Exp1: Rpb1 ChIP-seq in WT and 4 NNS mutants. Exp2: ChIP-seq of Rpb1, RNApolII CTD modifications and 3' end processing factors in WT cells. Exp3: ChIP-seq of Rpb1 and Rpb3 in WT and dhp1-depleted cells using S. cerevisiae as spike-in. Exp4: ChIP-seq of RNApolII CTD modification in WT and dhp1-depleted cells using S. cerevisiae spike-in. Exp5: ChIP-seq of Rpb1 in WT and ysh1-depleted cells using S. cerevisiae as spike-in
 
Contributor(s) Larochelle M, Robert M, Jacques P, Bachand F
Citation(s) 30341288
Submission date Jun 11, 2018
Last update date Mar 25, 2019
Contact name Pierre-Étienne Jacques
E-mail(s) Pierre-Etienne.Jacques@USherbrooke.ca
Phone 819 821-8000
Organization name Université de Sherbrooke
Department Biologie
Street address 2500 Boulevard de l'Université
City Sherbrooke
State/province Quebec
ZIP/Postal code J1K 2R1
Country Canada
 
Platforms (4)
GPL13988 Illumina HiSeq 2000 (Schizosaccharomyces pombe)
GPL17225 Illumina HiSeq 2500 (Schizosaccharomyces pombe)
GPL24177 Illumina HiSeq 2500 (Saccharomyces cerevisiae; Schizosaccharomyces pombe)
Samples (53)
GSM3184602 IP_Rpb1_WT_RM_exp1
GSM3184603 WCE_Rpb1_WT_RM_exp1
GSM3184604 IP_Rpb1_mut-nab3_RM_exp1
Relations
BioProject PRJNA475551
SRA SRP150226

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
GSE115595_RAW.tar 346.8 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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