Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China.
The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu, China.
BMC Genomics. 2024 Oct 29;25(1):1010. doi: 10.1186/s12864-024-10887-x.
The quality of Recombination signal sequences (RSSs), location, and genetics of mammalian V, D, and J genes synergistically affect the recombination frequency of genes; however, the specific regulatory mechanism and efficiency have not been elucidated. By taking advantage of single-cell RNA-sequencing (scRNA-seq) and high-throughput sequencing (HTS) to investigate V(D)J rearrangement characteristics in the CDR3 repertoire, we found that the distal and proximal V genes (or J genes) "to D" gene were involved in rearrangement significantly more frequently than the middle V genes (or J genes) in the TRB locus among various species, including Primates (human and rhesus monkey), Rodentia (BALB/c, C57BL/6, and Kunming mice), Artiodactyla (buffalo), and Chiroptera (Rhinolophus affinis). The RSS quality of the V and J genes affected their frequency in rearrangement to varying degrees, especially when the V-RSSs with recombination signal information content (RIC) score < -45 significantly reduced the recombination frequency of the V gene. The V and J genes that were "away from D" had the dual advantages of recombinant structural accessibility and relatively high-quality RSSs, which promoted their preferential utilization in rearrangement. The quality of J-RSSs formed during mammalian evolution was apparently greater than that of V-RSSs, and the D-J distance was obviously shorter than that of V-D, which may be one of the reasons for guaranteeing that the "D-to-J preceding V-to-DJ rule" occurred when rearranged. This study provides a novel perspective on the mechanism and efficiency of V-D-J rearrangement in the mammalian TRB locus, as well as the biased utilization characteristics and application of V and J genes in the initial CDR3 repertoire.
重排信号序列 (RSS) 的质量、位置和哺乳动物 V、D 和 J 基因的遗传学协同影响基因的重排频率；然而，具体的调控机制和效率尚未阐明。通过利用单细胞 RNA 测序 (scRNA-seq) 和高通量测序 (HTS) 研究 CDR3 库中 V(D)J 重排特征，我们发现各种物种（包括灵长类动物（人、恒河猴）、啮齿目动物（BALB/c、C57BL/6、昆明鼠）、偶蹄目动物（水牛）和翼手目动物（中华菊头蝠））的 TRB 基因座中，远端和近端 V 基因（或 J 基因）“到 D”基因的重排频率明显高于中间 V 基因（或 J 基因）。V 和 J 基因的 RSS 质量在不同程度上影响了它们的重排频率，尤其是当 V-RSS 具有重组信号信息含量（RIC）评分< -45 时，显著降低了 V 基因的重排频率。远离 D 的 V 和 J 基因具有重组结构可及性和相对高质量 RSS 的双重优势，这促进了它们在重排中的优先利用。哺乳动物进化过程中形成的 J-RSS 质量显然大于 V-RSS，D-J 距离明显短于 V-D，这可能是保证“D 到 J 先于 V 到 DJ 规则”发生的原因之一。本研究为哺乳动物 TRB 基因座中 V-D-J 重排的机制和效率提供了新的视角，以及 V 和 J 基因在初始 CDR3 库中的偏利用特征和应用。
