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

Highlights

• Igh locus contraction occurs in pro-B cells prior to VDJ joining

• Pro-B cell-specific chromatin looping at the multi-megabase scale defines locus contraction

• A subset of these exceptionally long chromatin loops are Pax5 dependent

• VH gene rearrangement is dependent upon independently regulated chromatin topologies

Summary

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 V_H gene family that become juxtaposed in pro-B cells via megabase-scale chromatin looping. The transcription factor Pax5 organizes the subdomain that spans the V_HJ558 gene family. In its absence, the J558 V_H genes fail to associate with the proximal V_H genes, thereby providing a plausible explanation for reduced V_HJ558 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.