A Unifying Model for Molecular Determinants of the Pre-selection Vb Repertoire [RNA-Seq]

The primary antigen receptor repertoire is sculpted by the process of V(D)J recombination, which must strike a balance between diversification and favoring gene segments with specialized functions. The precise determinants of how often gene segments are chosen to complete variable region coding exons remain elusive. We have quantified Vbeta usage in the pre-selection Tcrb repertoire and report relative contributions of 14 distinct features in shaping their recombination efficiencies, including transcription, chromatin environment, spatial proximity to their DbetaJbeta targets, and quality of recombinase recognition elements. Computational analyses provide a unifying model, revealing a minimal set of eight parameters that are predictive of Vbeta usage, dominated by chromatin modifications associated with transcription, but largely independent of the precise spatial proximity to DbetaJbeta clusters. Transcription profiles of mouse DN thymocytes from Rag1 KO mice were generated by deep sequencing, using Illumina Hi-Seq 2000.原发性抗原受体库（primary antigen receptor repertoire）的塑造依赖于V(D)J重排（V(D)J recombination）过程，该过程需在生成受体多样性与优先选择具备特定功能的基因片段之间维持平衡。目前，关于基因片段被选择以组装可变区编码外显子的频率的精确调控决定因素仍未明确。我们对预选择阶段的Tcrb库中的Vβ使用情况进行了定量分析，并报道了14种不同特征对其重排效率的相对贡献，这些特征包括转录活性、染色质微环境、与DβJβ靶位点的空间邻近性，以及重组酶识别元件的质量。计算分析构建了一个统一模型，揭示了可预测Vβ使用模式的最小8参数集，该模型以与转录相关的染色质修饰为核心决定因素，但在很大程度上不受与DβJβ基因簇精确空间邻近性的影响。本研究通过Illumina Hi-Seq 2000测序平台，完成了Rag1基因敲除小鼠（Rag1 KO mice）双阴性胸腺细胞（DN thymocytes）的转录组深度测序。