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Series GSE69887 Query DataSets for GSE69887
Status Public on Jul 10, 2017
Title PAR-TERRA RNA directs homologous sex chromosome pairing
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including to the PAR and Xic. During X-chromosome pairing, PAR-TERRA anchors the Xic to the PAR, creating a ‘tetrad’ of pairwise homologous interactions (Xic–Xic, PAR–PAR, and Xic–PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We propose a ‘constrained diffusion model’ in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.
Overall design Identify genome-wide binding sites for TERRA RNA by CHIRT-seq in ES cells and MEFs. TERRA capture RNA-seq to discover TERRA sequence.
Investigation of PAR-interacting domains using 4C-Seq.

Please note that GSM2429690-93 are duplicated sample records of GSM1711915-18, respectively, for the convenient retrieval of the complete raw data from SRA.
Contributor(s) Chu HP, Froberg JE, Kesner B, Oh HJ, Pinter SF, Ji F, Sadreyev R, Lee JT
Citation(s) 28692038
Submission date Jun 15, 2015
Last update date May 15, 2019
Contact name Hsueh-Ping Chu
Organization name MGH, Harvard Medical School
Department molecular biology
Lab Jeannie T. Lee
Street address 185 Cambridge St
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (25)
GSM1711914 Cab10: ES d0 PAR CHIRT-seq
GSM1711919 Cab11: MEF PAR CHIRT-seq
GSM1711920 Cab11: MEF TERRA CHIRT-seq
BioProject PRJNA287027
SRA SRP059505

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Supplementary file Size Download File type/resource
GSE69887_RAW.tar 5.9 Gb (http)(custom) TAR (of BW, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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