GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE140672 Query DataSets for GSE140672
Status Public on Jan 01, 2020
Title Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [HTGTS]
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary During V(D)J recombination RAG proteins introduce DNA double strand breaks (DSBs) adjacent to conserved recombination signal sequences (RSS) that contain either 12- or 23-nucleotide spacer regions. Coordinated cleavage following the “12/23” rule predicts that DSBs at variable (V) gene segments should not exceed the level of breakage at joining (J) segments, thereby ensuring that V regions do not engage in undesirable recombination events with one another. Here we report abundant RAG dependent DSBs at a multitude of V gene segments within the Ig locus independent of V-J rearrangement. We discover that a large fraction of V gene segments are flanked not only by a bone-fide 12 spacer, but also an overlapping, 23 spacer flipped RSS. These compatible pairs of RSS mediate recombination and deletion inside the V cluster even in the complete absence of J gene segments, and support a novel recombination center (RC) independent of the conventional J-centered RC. We propose a model that explains V gene segment usage by taking into account not only the probability of V-to-J rearrangement but also the surprisingly frequent, evolutionarily conserved intra-V cluster recombination events. These findings shed light on the diverse molecular strategies that shape the primary antigen receptor repertoires.
Overall design HTGTS profile in abelson-transformed pre-B cells, primary splenic B cells, bone marrow B cells, and human PBMC B cells.
Contributor(s) Shindoa K, Maman Y, Canela A, Shchatz DG, Livak F, Nussenzweig A
Citation(s) 31875554
Submission date Nov 19, 2019
Last update date Jul 02, 2021
Contact name Yaakov Maman
Organization name Bar-Ilan University
Department Azrieli Faculty of Medicine
Lab Genome Instability & Cancer
Street address Henrietta Szold 8
City Safed
ZIP/Postal code 1311502
Country Israel
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (41)
This SubSeries is part of SuperSeries:
GSE140677 Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire
BioProject PRJNA590491
SRA SRP230629

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
GSE140672_HTGTS_BMPB_VK1_117.tlx.txt.gz 546.8 Kb (ftp)(http) TXT
GSE140672_HTGTS_PBMC_B_JK1.tlx.txt.gz 1022.8 Kb (ftp)(http) TXT
GSE140672_HTGTS_PBMC_B_VK2_28.tlx.txt.gz 479.4 Kb (ftp)(http) TXT
GSE140672_HTGTS_PBMC_B_VK3_20.tlx.txt.gz 401.7 Kb (ftp)(http) TXT
GSE140672_HTGTS_PB_JK1_WT.tlx.txt.gz 1.5 Mb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_ART_clone1.tlx.txt.gz 7.7 Kb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_ART_clone2.tlx.txt.gz 7.2 Kb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_CRISPR.tlx.txt.gz 1.7 Mb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_CRISPR_NO_STI.tlx.txt.gz 396.6 Kb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_DELJK.tlx.txt.gz 3.0 Mb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_LIG4.tlx.txt.gz 10.4 Kb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_RAG1.tlx.txt.gz 291.9 Kb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK1_117_WT.tlx.txt.gz 3.1 Mb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK8_34_DELJK.tlx.txt.gz 352.5 Kb (ftp)(http) TXT
GSE140672_HTGTS_PB_VK8_34_WT.tlx.txt.gz 1.1 Mb (ftp)(http) TXT
GSE140672_HTGTS_Spl_B_JK1.tlx.txt.gz 1.1 Mb (ftp)(http) TXT
GSE140672_HTGTS_Spl_B_VK1_117.tlx.txt.gz 275.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap