The V(DD)J recombination is currently viewed as an aberrant and inconsequential variant of the canonical V(D)J recombination. Moreover, since the classical 12/23 rule for the V(D)J recombination fails to explain the V(DD)J recombination, the molecular mechanism of tandem D-D fusions has remained unknown since they were discovered three decades ago. Revealing this mechanism is a biomedically important goal since tandem fusions contribute to broadly neutralizing antibodies with ultralong CDR3s. We reveal previously overlooked cryptic nonamers in the recombination signal sequences of human IGHD genes and demonstrate that these nonamers explain the vast majority of tandem fusions in human repertoires. We further reveal large clonal lineages formed by tandem fusions in antigen-stimulated immunosequencing data sets, suggesting that such data sets contain many more tandem fusions than previously thought and that about a quarter of large clonal lineages with unusually long CDR3s are generated through tandem fusions. Finally, we developed the SEARCH-D algorithm for identifying D genes in mammalian genomes and applied it to the recently completed Vertebrate Genomes Project assemblies, nearly doubling the number of mammalian species with known D genes. Our analysis revealed cryptic nonamers in RSSs of many mammalian genomes, thus demonstrating that the V(DD)J recombination is not a “bug” but an important feature preserved throughout mammalian evolution.

中文翻译：

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V(DD)J 重组是产生具有异常长 CDR3 的抗体的重要且进化保守的机制。


V(DD)J 重组目前被视为典型 V(D)J 重组的异常且无关紧要的变体。此外，由于V(D)J重组的经典12/23规则无法解释V(DD)J重组，串联DD融合的分子机制自三十年前被发现以来仍然未知。揭示这一机制是生物医学上的一个重要目标，因为串联融合有助于广泛中和具有超长 CDR3 的抗体。我们揭示了人类 IGHD 基因重组信号序列中先前被忽视的神秘九聚体，并证明这些九聚体解释了人类库中的绝大多数串联融合。我们进一步揭示了抗原刺激的免疫测序数据集中由串联融合形成的大型克隆谱系，这表明此类数据集包含比之前想象的更多的串联融合，并且大约四分之一的具有异常长CDR3的大型克隆谱系是通过串联融合产生的。最后，我们开发了用于识别哺乳动物基因组中 D 基因的 SEARCH-D 算法，并将其应用于最近完成的脊椎动物基因组计划组件，使具有已知 D 基因的哺乳动物物种数量几乎增加了一倍。我们的分析揭示了许多哺乳动物基因组的 RSS 中隐藏的九聚体，从而证明 V(DD)J 重组不是一个“错误”，而是整个哺乳动物进化过程中保留的一个重要特征。