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Series GSE81351 Query DataSets for GSE81351
Status Public on Sep 02, 2016
Title An ectopic CTCF binding element disturbs Vδ usage at the mouse Tcra-Tcrd locus by regulating contact between Vδ and Dδ gene segments
Organism Mus musculus
Experiment type Other
Summary Chromatin looping mediated by the CCCTC binding factor CTCF regulates V(D)J recombination at antigen receptor loci. CTCF-mediated looping can influence recombination signal sequence accessibility by regulating enhancer activation of germline promoters. CTCF-mediated looping has also been shown to limit directional tracking of the RAG recombinase along chromatin, and to regulate through-space interactions between recombination signal sequences, independent of the RAG recombinase. However, in all prior instances in which CTCF-mediated looping was shown to influence V(D)J recombination, it was not possible to fully resolve the relative contributions to the V(D)J recombination phenotype of changes in accessibility, RAG-tracking, and RAG-independent long-distance interactions. Here, to assess mechanisms by which CTCF-mediated looping can impact V(D)J recombination, we introduced an ectopic CTCF binding element (CBE) immediately downstream of Eδ in the murine Tcra-Tcrd locus. The ectopic CBE impaired inversional rearrangement of Trdv5 in the absence of measurable effects on Trdv5 transcription and chromatin accessibility. Moreover, although the ectopic CBE limited directional RAG tracking from the Tcrd recombination center, such tracking cannot account for Trdv5-to-Trdd2 inversional rearrangement. Rather, the defect in Trdv5 rearrangement could only be attributed to a reconfigured chromatin loop organization that limited RAG-independent through-space interactions between the Trdv5 and Trdd2 RSSs. We conclude that CTCF can regulate V(D)J recombination by segregating RSSs into distinct loop domains and inhibiting RSS synapsis, independent of any effects on transcription, RSS accessibility and RAG tracking.
 
Overall design RAG-initiatd Tcrd D segment rearrangements in developing thymocytes were generated by deep sequencing using illumine Miseq
 
Contributor(s) Zhao L, Alt FW
Citation(s) 27613698
Submission date May 11, 2016
Last update date May 15, 2019
Contact name Lijuan Zhao
E-mail(s) lexieljzhao@gmail.com
Phone 617-606-0189
Organization name Boston Children's Hospital
Lab Frederick W. Alt
Street address 1 Blackfan Circle
City Boston
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (12)
GSM2150956 Trdd2_5P_WT rep1
GSM2150957 Trdd2_5P_WT rep2
GSM2150958 Trdd2_5P_WT rep3
Relations
BioProject PRJNA321339
SRA SRP074861

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
GSE81351_RAW.tar 23.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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