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Series GSE47128 Query DataSets for GSE47128
Status Public on Jun 01, 2013
Title Allele specific analysis of the immunoglobulin heavy chain locus by simultaneous analysis of the productive and the non-productive allele through paired-end 4C sequencing analysis in mature B cells
Organism Mus musculus
Experiment type Other
Summary In developing B cells the immunoglobulin heavy chain (IgH) locus is thought to move from repressive to permissive chromatin compartments to facilitate its scheduled rearrangement. In mature B cells, maintenance of allelic exclusion has been proposed to involve recruitment of the non-productive IgH allele to pericentromeric heterochromatin. Here we used an allele-specific chromosome conformation capture combined with sequencing (4C-seq) approach to unambigously follow the individual IgH alleles in mature B lymphocytes. Despite their physical and functional difference, productive and non-productive IgH alleles in B cells and unrearranged IgH alleles in T cells share many chromosomal contacts and largely reside in active chromatin. In brain, however, the locus resides in a different, repressive environment. We conclude that IgH adopts a lymphoid-specific nuclear location that is however unrelated to maintenance of allelic exclusion. We additionally find that in mature B cells - but not in T cells – the distal VH regions of both IgH alleles position themselves away from active chromatin. This, we speculate, may help to restrict enhancer activity to the productively rearranged VH promoter element.
Overall design Allele specific analysis of the nuclear organization of the IgH locus in resting and activated B cells and T cells and fetal brain cells
Contributor(s) Holwerda SJ, van de Werken HJ, Ribeiro de Almeida C, Bergen IM, de Bruijn MJ, Verstegen MJ, Simonis M, Splinter E, Wijchers PJ, Hendriks RW, de Laat W
Citation(s) 23748562
Submission date May 21, 2013
Last update date May 15, 2019
Contact name sjoerd holwerda
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platforms (2)
GPL9185 Illumina Genome Analyzer (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (45)
GSM1145529 IgH_IgMa_D0_C_reg_46015_BL6_3RR
GSM1145530 IgH_IgMa_D0_C_reg_145501_BL6_Cy3
GSM1145531 IgH_IgMa_D0_V_reg_22552_BL6_distalV
This SubSeries is part of SuperSeries:
GSE47129 Allele specific analysis of the immunoglobulin heavy chain locus
BioProject PRJNA203805
SRA SRP022938

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Supplementary file Size Download File type/resource
GSE47128_RAW.tar 10.1 Mb (http)(custom) TAR (of WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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