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Series GSE60047 Query DataSets for GSE60047
Status Public on Sep 11, 2014
Title Transcriptome-wide mapping reveals widespread dynamic regulated pseudouridylation of mRNA
Organisms Saccharomyces cerevisiae; Candida albicans; Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Pseudouridine is the most abundant modification occurring on RNA, yet with the exception of a few well-studied RNA molecules little is known about the modified positions and their function(s). Here, we develop Ψ-seq, a method for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with synthetic spike-ins and de novo identification of the vast majority of previously reported pseudouridylated positions. Ψ-seq permits discovery of hundreds of novel pseudouridine modifications in human and yeast mRNAs and snoRNAs. Knockdown and knockout of pseudouridine synthases uncovers the cognate PUSs mediating pseudouridine catalysis at these individual novel sites and their target sequence features. In both human and yeast pseudouridine formation on mRNA depends on both site-specific PUSs – often guided by a specific sequence motif - and snoRNA-guided PUSs. Importantly, upon heat shock in yeast, Pus7-mediated pseudouridylation is induced at >200 sites in diverse mRNAs. Pus7 deletion in yeast leads to decreased recovery from heat shock and decreased RNA levels at otherwise pseudouridylated messages, suggesting a role for pseudouridine in enhancing transcript stability. Pseudouridine stoichiometries in rRNA are highly conserved from yeast to mammals, but are reduced in cells derived from dyskeratosis congenita patients, where the pseudouridine synthase DKC1 is mutated, compared to age matched controls. Our results establish pseudouridine as a ubiquitous and dynamic modification in mRNA, and provide a sensitive, quantitative and transcriptome-wide methodology to address its underlying mechanisms and function.
Overall design Examination of m6A methylation in human Hek293 and A549 cell lines, in human embryonic stem cells (ESCs) undergoing differentiation to neural progenitor cells (NPCs), in OKMS inducible fibroblasts reprogrammed into iPSC, and upon knockdown of factors using siRNAs or shRNAs.
Contributor(s) Schwartz S, Bernstein D, Mumbach M, Lander ES, Fink G, Regev A
Citation(s) 25219674
Submission date Aug 04, 2014
Last update date May 15, 2019
Contact name Schraga Schwartz
Street address Herzl 234, Department of Molecular Genetics
City Rehovot
State/province Choose a State or Province
ZIP/Postal code 7610001
Country Israel
Platforms (4)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
Samples (86)
GSM1464152 Lib73PUcbf5rep1_CMC_treatment
GSM1464153 Lib73PUcbf5rep1_input
GSM1464154 Lib73PUcbf5rep2_CMC_treatment
BioProject PRJNA257386
SRA SRP045222

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60047_AllHumanSitesDetailed.txt.gz 71.5 Kb (ftp)(http) TXT
GSE60047_YeastHeatShockSitesDetailed.txt.gz 65.8 Kb (ftp)(http) TXT
GSE60047_YeastPanKOAllSitesDetailed.txt.gz 57.0 Kb (ftp)(http) TXT
GSE60047_YeastPanKOrRNADetailed.txt.gz 12.8 Kb (ftp)(http) TXT
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