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Series GSE17064 Query DataSets for GSE17064
Status Public on Dec 22, 2010
Title Genome-wide identification of Polycomb-associated RNAs by RIP-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Large-scale analyses have revealed that 60-90% of the mammalian genome is transcriptionally active. Because <2% of sequences have protein-coding potential, why so much cellular energy is expended on RNA synthesis is a major question in the post-genomic era. The hypothesis that RNA may serve as recruiting platforms for chromatin modifiers has gained ground with discoveries linking long ncRNAs, such as RepA, Xist, and Tsix, to locus-specific targeting of Polycomb proteins to the X-chromosome. Long ncRNAs have also been associated with Polycomb proteins at human HOX loci. Here, we ask if RNA targeting may be a general feature of regulation for mouse Polycomb repressive complex 2 (PRC2). We develop a method to capture the 'PRC2 transcriptome' by combining RNA immunoprecipitation (RIP) with deep sequencing (seq). RIP-seq of mouse embryonic stem cells identifies >3000 RNAs in the PRC2 transcriptome. Approximately 14% of RNAs originate from previously described PRC2-binding sites and many are promoter-associated. The transcriptome includes a large number of unannotated noncoding and antisense RNAs, with the X-chromosome exhibiting a high density of PRC2 RNAs. Imprinted genes and other disease genes, including those involved in cancer, are also well-represented. Functional validation of select candidates confirms RNA-PRC2 interactions in vivo and recruitment of Polycomb proteins in cis. Thus, RNA cofactors may be one general mechanism, among others, for targeting mammalian PRC2. Given PRC2's essential roles during stem cell renewal, development, and cancer, the PRC2 transcriptome described herein will provide a valuable resource for regenerative medicine and cancer biology.
Overall design Identification and characterization of RNAs associated with PRC2 complex in mouse embryoinc stem cells
Contributor(s) Zhao J, Kung JT, Ohsumi T, Borowsky M, Lee JT
Citation(s) 21172659
Submission date Jul 13, 2009
Last update date May 15, 2019
Contact name Mark L Borowsky
Organization name MGH
Department Molecular Biology
Street address 185 Cambridge Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (7)
GSM426848 Ezh2 RIP-seq
GSM489990 Ezh2 RIP-seq technical replicate
GSM489991 Ezh2 RIP-seq biological replicate
SRA SRP002224
BioProject PRJNA119843

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Supplementary file Size Download File type/resource
GSE17064_s.WT.BR.uniq.noribo.nohomop.tsv.gz 50.2 Mb (ftp)(http) TSV
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Raw data are available in SRA

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