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Series GSE43008 Query DataSets for GSE43008
Status Public on Sep 30, 2013
Title Flexible chromatin loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire
Organism Mus musculus
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH- rearranged gene segment in the proximal Igh domain. By high-resolution mapping of long-range interactions, we now demonstrate that an array of local interaction domains establishes the three- dimensional structure of the extended Igh locus in lymphoid progenitors and thymocytes. In pro- B cells, these local domains engage in long-range interactions across the entire Igh locus, which depend on the transcription factors Pax5, YY1 and CTCF. The large VH gene cluster thereby undergoes flexible long-range interactions with the more rigidly structured 3’ proximal domain, which ensures that all VH genes can participate with similar probability in VH-DJH recombination to generate a diverse antibody repertoire. Notably, these long-range interactions appear to be an intrinsic feature of the VH gene cluster, as they are still generated upon mutation of the Eμ enhancer, IGCR1 insulator or 3’ regulatory region present in the 3’ proximal Igh domain.
Overall design 4C sequencing from mutliple celltypes with multiple viewpoints; uneven number of replicates
Contributor(s) Medvedovic J, Ebert A, Jaritz M, Tagoh H, Busslinger M
Citation(s) 23973221
Submission date Dec 18, 2012
Last update date May 15, 2019
Contact name Meinrad Busslinger
Phone 00431-79730
Organization name Instutute of Molecular Pathology
Street address Dr. Bohrgasse 7
City Vienna
ZIP/Postal code 1030
Country Austria
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (112)
GSM1054817 HS3B-HD 9062 628NCAAXX 6
GSM1054818 7183.16-HD 9062 628NCAAXX 6
GSM1054819 PAIR4-HD 9062 628NCAAXX 6
SRA SRP017609
BioProject PRJNA184341

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43008_RAW.tar 1.2 Gb (http)(custom) TAR (of BED)
GSE43008_geo_rename_4c-2.txt.gz 1.1 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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