IntroductionThe immunoglobulin heavy chain locus (IgH) undergoes multiple changes along B-cell differentiation, affecting transcription and accessibility to V(D)J or class switch recombination (CSR). The iE enhancer upstream of C mostly promotes V(D)J recombination, 1 whereas IgH 3ЈRR enhancers (hs3a, hs1,2, hs3b, and hs4) have controversial roles. A role in CSR was suggested by replacing mouse hs1,2 with a neomycin resistance gene, thus affecting germline transcription and CSR to ␥2a, ␥2b, ␥3, and ⑀. 2 However, deletion of this neo cassette restored CSR. 3 hs3a, hs3b, and hs4 also proved individually dispensable for CSR. 3-5 Enhancer redundancies might explain that their individual deletion only results in minor effect. Indeed, joint hs3b/hs4 deletion impaired germline transcription and CSR to most isotypes except and ␥1. 6 Reporter genes also demonstrated synergies between 3ЈRR enhancers, 7 which altogether promote CSR into large transgenes. 8 The 3ЈRR is followed with DNase hypersensitive sites (hs5-7) lacking enhancer activity but binding CCCTC-binding factor and constituting the 3Ј locus boundary. 9 To reconcile the controversial phenotypes of focal mutations, potentially attenuated by functional redundancies, we evaluated IgH expression and CSR after deleting the whole 30-kb extent of the 3ЈRR.

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 3′ proximal Igh domain. By using high-resolution mapping of long-range interactions, we demonstrate that local interaction domains established the three-dimensional structure of the extended Igh locus in lymphoid progenitors. In pro- B cells, these local domains engaged in long-range interactions across the Igh locus, which depend on the regulators Pax5, YY1, and CTCF. The large VH gene cluster underwent flexible long-range interactions with the more rigidly structured proximal domain, which probably ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. These long-range interactions appear to be an intrinsic feature of the VH gene cluster, because they are still generated upon mutation of the Eµ enhancer, IGCR1 insulator, or 3′ regulatory region in the proximal Igh domain.

Somatic hypermutation in variable heavy chain rearranged regions is abrogated in the absence of the 3′ regulatory region enhancer, whereas transcription rate in the Ig heavy chain is only partially reduced.