Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells

Antibody repertoires are known to be shaped by selection for antigen binding. Unexpectedly, we now show that selection also acts on a non-antigen-binding antibody region: the heavy-chain variable (V-H)-encoded elbow between variable and constant domains. By sequencing 2.8 million recombined heavy-chain genes from immature and mature B-cell subsets in mice, we demonstrate a striking gradient in V-H gene use as pre-B cells mature into follicular and then into marginal zone B cells. Cells whose antibodies use V-H genes that encode a more flexible elbow are more likely to mature. This effect is distinct from, and exceeds in magnitude, previously described maturation-associated changes in heavy-chain complementarity determining region 3, a key antigen-binding region, which arise from junctional diversity rather than differential V-H gene use. Thus, deep sequencing reveals a previously unidentified mode of B-cell selection.