Harris Justin C, Byrum Jennifer N, McKinney Cooper B, Fairchild Victoria, Wu Dee H, Fagg Andrew H, Rodgers Karla K
Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences, Oklahoma City, OK 73104, United States.
Department of Microbiology and Immunology, University of Oklahoma Health Sciences, Oklahoma City, OK 73104, United States.
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf551.
In developing lymphocytes, V(D)J recombination assembles functional antigen receptor (AgR) genes through rearrangement of the AgR loci to adjoin component gene segments. Each candidate gene segment for recombination is flanked by a recombination signal sequence (RSS), composed of heptamer and nonamer motifs separated by 12 or 23 base pairs. To initiate V(D)J recombination, the recombination activating proteins RAG1 and RAG2 create DNA double-stranded breaks between a 12/23-RSS pair and their adjoining gene segments. The basis for selection of individual RSSs during each V(D)J recombination event is not well understood due, in part, to the wide-spread distribution of the semi-conserved RSSs across the AgR loci. Using publicly-available data for V(D)J recombination efficiencies on randomized 12-RSSs, we first built a neural network model that delineates how changes in sequence at certain positions in the RSS affects recombination efficiency. Second, to interpret the model's decision-making process, we repurposed the game theoretic SHapley Additive exPlanations (SHAP) approach, with the results illustrating how nucleotides at pairwise positions in the heptamer provide synergistic contributions to recombination efficiency. Third, we trained a nonamer-informed neural network model with varied nonamer RSS substrates, and subsequently identified interdependent effects between the heptamer and nonamer regions on recombination efficiency.
在发育中的淋巴细胞中，V(D)J重组通过重排抗原受体（AgR）基因座以连接组成基因片段来组装功能性抗原受体（AgR）基因。每个用于重组的候选基因片段两侧都有一个重组信号序列（RSS），该序列由七聚体和九聚体基序组成，中间间隔12或23个碱基对。为了启动V(D)J重组，重组激活蛋白RAG1和RAG2在12/23-RSS对与其相邻的基因片段之间产生DNA双链断裂。由于半保守的RSS在AgR基因座上广泛分布，每个V(D)J重组事件中单个RSS选择的基础尚未完全了解。利用公开的随机12-RSS上V(D)J重组效率的数据，我们首先构建了一个神经网络模型，该模型描绘了RSS中某些位置的序列变化如何影响重组效率。其次，为了解释模型的决策过程，我们重新利用了博弈论的SHapley加法解释（SHAP）方法，结果说明了七聚体中成对位置的核苷酸如何对重组效率提供协同贡献。第三，我们用不同的九聚体RSS底物训练了一个九聚体信息神经网络模型，随后确定了七聚体和九聚体区域对重组效率的相互依赖效应。
