CTCF-binding elements mediate control of V(D)J recombination

Abstract

Immunoglobulin heavy chain (IgH) variable region exons are assembled from VH, D and JH gene segments in developing B lymphocytes. Within the 2.7-megabase mouse Igh locus, V(D)J recombination is regulated to ensure specific and diverse antibody repertoires. Here we report in mice a key Igh V(D)J recombination regulatory region, termed intergenic control region 1 (IGCR1), which lies between the VH and D clusters. Functionally, IGCR1 uses CTCF looping/insulator factor-binding elements and, correspondingly, mediates Igh loops containing distant enhancers. IGCR1 promotes normal B-cell development and balances antibody repertoires by inhibiting transcription and rearrangement of DH-proximal VH gene segments and promoting rearrangement of distal VH segments. IGCR1 maintains ordered and lineage-specific VH(D)JH recombination by suppressing VH joining to D segments not joined to JH segments, and VH to DJH joins in thymocytes, respectively. IGCR1 is also required for feedback regulation and allelic exclusion of proximal VH-to-DJH recombination. Our studies elucidate a long-sought Igh V(D)J recombination control region and indicate a new role for the generally expressed CTCF protein.

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Figure 1: Mutation of IGCR1 CBEs impairs B-cell development.
Figure 2: IGCR1 mutations alter V H usage, germline transcription and rearrangement order.
Figure 3: IGCR1/CBE mutations lead to V H (D)J H and V H D rearrangements in thymocytes.
Figure 4: IGCR1 is required to allow feedback regulation of proximal V H -to-DJ H recombination.
Figure 5: IGCR1 mediates long-distance Igh chromosomal loops.

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Acknowledgements

We thank Y. Fujiwara and P.-Y. Huang for generating chimaeric mice. This work was supported by NIH grants RO1 AI20047 (to F.W.A.), RO1 HL48702 and AI40227 (to M.S.S.), CA054198-20 (to C.M.) and K08 AI070839 (to C.C.G.). M.B. was supported by the Austrian GEN-AU initiative and Boehringer Ingelheim. C.G. is supported by an Irvington Institute Postdoctoral Fellowship from the Cancer Research Institute. C.V. is supported by a Marie Curie Fellowship. C.B. is supported by an EMBO fellowship. F.W.A. is an Investigator of the Howard Hughes Medical Institute.

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C.G., H.S.Y., A.F., C.C.G. and F.W.A. conceived, designed and/or peformed most experiments, interpreted most results, and wrote the manuscript. With respect to other authors, S.J. performed experiments for Figs 2, 3, 4 and Supplementary Fig. 11 and contributed to interpretation of the data; A.E. and M.B. contributed the work in Fig. 2c and Supplementary 7a–c. C.V., J.G.B. and M.S.S. contributed the work in Supplementary Fig. 10; and C.B. and C.M. performed FISH experiments on IGCR1−/− cells that helped frame aspects of the discussion and models; all of these authors contributed to polishing the manuscript. All other authors provided technical assistance with various experiments or data analysis.

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Correspondence to Cosmas C. Giallourakis or Frederick W. Alt.

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Guo, C., Yoon, H., Franklin, A. et al. CTCF-binding elements mediate control of V(D)J recombination. Nature 477, 424–430 (2011). https://doi.org/10.1038/nature10495

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