Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire

Cell Rep. 2016 Feb 2;14(4):896-906. doi: 10.1016/j.celrep.2015.12.083. Epub 2016 Jan 21.


Early B cell development is characterized by large-scale Igh locus contraction prior to V(D)J recombination to facilitate a highly diverse Ig repertoire. However, an understanding of the molecular architecture that mediates locus contraction remains unclear. We have combined high-resolution chromosome conformation capture (3C) techniques with 3D DNA FISH to identify three conserved topological subdomains. Each of these topological folds encompasses a major VH gene family that become juxtaposed in pro-B cells via megabase-scale chromatin looping. The transcription factor Pax5 organizes the subdomain that spans the VHJ558 gene family. In its absence, the J558 VH genes fail to associate with the proximal VH genes, thereby providing a plausible explanation for reduced VHJ558 gene rearrangements in Pax5-deficient pro-B cells. We propose that Igh locus contraction is the cumulative effect of several independently controlled chromatin subdomains that provide the structural infrastructure to coordinate optimal antigen receptor assembly.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Antibodies / genetics*
  • B-Lymphocytes / metabolism*
  • Cell Line
  • Cells, Cultured
  • Chromatin / chemistry
  • Chromatin / genetics*
  • Chromatin Assembly and Disassembly
  • Genetic Loci
  • Mice
  • Mice, Inbred C57BL
  • PAX5 Transcription Factor / metabolism


  • Antibodies
  • Chromatin
  • PAX5 Transcription Factor
  • Pax5 protein, mouse