Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination

Summary

Variable (V), diversity (D), and joining (J) (V(D)J) recombination is the first determinant of antigen receptor diversity. Understanding how recombination is regulated requires a comprehensive, unbiased readout of V gene usage. We have developed VDJ sequencing (VDJ-seq), a DNA-based next-generation-sequencing technique that quantitatively profiles recombination products. We reveal a 200-fold range of recombination efficiency among recombining V genes in the primary mouse Igh repertoire. We used machine learning to integrate these data with local chromatin profiles to identify combinatorial patterns of epigenetic features that associate with active V _H gene recombination. These features localize downstream of V _H genes and are excised by recombination, revealing a class of cis-regulatory element that governs recombination, distinct from expression. We detect two mutually exclusive chromatin signatures at these elements, characterized by CTCF/RAD21 and PAX5/IRF4, which segregate with the evolutionary history of associated V _H genes. Thus, local chromatin signatures downstream of V _H genes provide an essential layer of regulation that determines recombination efficiency.

Graphical Abstract

Highlights

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  VDJ-seq enables precise quantification of antibody V(D)J recombination products

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  Two distinct cis-regulatory designs characterize actively recombining V genes

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  Putative recombination regulatory elements map downstream of mouse Igh V genes

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  Recombination regulatory architecture reflects the V genes’ evolutionary history

Abstract

Bolland et al. develop a technique to quantitatively profile antigen receptor diversity. Using VDJ-seq in the mouse Igh locus, they uncover the regulatory logic underlying the highly varying recombination rates of V gene segments, with implications for immune disorders and aberrant recombination in cancer.