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Series GSE58242 Query DataSets for GSE58242
Status Public on Jan 09, 2015
Title X-chromosome dynamics revealed by the RNA interactome and chromosomal binding of CTCF
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary CTCF is a master regulator that plays a role in genome architecture and gene expression. A key aspect of CTCF’s mechanism involves bringing together distant genetic elements for intra- and inter-chromosomal interactions. Evidence from epigenetic processes, such as X-chromosome inactivation (XCI), suggests that CTCF may carry out its functions through interacting RNAs. Using genome-wide approaches to investigate the relationship between CTCF’s RNA interactome and its epigenomic landscape, here we report that CTCF interacts with thousands of transcripts in mouse embryonic stem cells (mESC), many in close proximity to CTCF’s genomic binding sites. Biochemical analysis demonstrates that CTCF is a high-affinity RNA binding protein that contacts RNA directly and specifically. In the XCI model, CTCF binds the active and inactive X-chromosomes allele-specifically. At the X-inactivation center, Tsix RNA binds CTCF and targets CTCF to a region associated with X-chromosome pairing. Our work implicates CTCF-RNA interactions in long-range chromosomal interactions in trans and adds a new layer of complexity to CTCF regulation. The genome-wide datasets reported here will provide a useful resource for further study of CTCF-mediated epigenomic regulation.
 
Overall design CTCF RNA interactome was identified by UV-crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq), and was compared to CTCF's epigenomic landscape as obtained by chromatin immunoprecipitation (ChIP-seq).
 
Contributor(s) Kung JT, Kesner B, Lee JT
Citation(s) 25578877
Submission date Jun 05, 2014
Last update date May 15, 2019
Contact name Johnny T Kung
Organization name HHMI, Massachusetts General Hospital, Harvard Medical School
Department Molecular Biology
Lab Jeannie Lee lab
Street address 185 Cambridge St
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (16)
GSM1404609 d0 RNAseq
GSM1404610 d3 RNAseq
GSM1540984 d0 CLIP rep1 [pUV]
Relations
BioProject PRJNA251684
SRA SRP042961

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Supplementary file Size Download File type/resource
GSE58242_RAW.tar 14.0 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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