Touvrey C, Cowell L G, Lieberman A E, Marche P N, Jouvin-Marche E, Candéias S M
CEA, DSV, DRDC, Laboratoire d'Immunochimie; INSERM U548; UJF, 38054 Grenoble, France.
Immunogenetics. 2006 Nov;58(11):895-903. doi: 10.1007/s00251-006-0150-1. Epub 2006 Oct 5.
T cell receptor genes are assembled in developing T lymphocytes from discrete V, D, and J genes by a site-specific somatic rearrangement mechanism. A flanking recombination signal, composed of a conserved heptamer and a semiconserved nonamer separated by 12 or 23 variable nucleotides, targets the activity of the rearrangement machinery to the adjoining V, D, and J genes. Following the rearrangement of V, D, or J genes, their respective recombination signals are ligated together. Although these signal joints are allegedly invariant, created by the head-to-head abuttal of the heptamers, some do exhibit junctional diversity. Recombination signals were initially identified by comparison and alignment of germ-line sequences with the sequence of rearranged genes. However, their overall low level of sequence conservation makes their characterization solely from sequence data difficult. Recently, computational analysis unraveled correlations between nucleotides at several positions scattered within the spacer and recombination activity, so that it is now possible to identify putative recombination signals and determine and predict their recombination efficiency. In this paper, we analyzed the variability introduced in signal joints generated after rearrangement of the TRDD1 and TRDD2 genes in murine thymocytes. The recurrent presence of identical nucleotides inserted in these signal joints led us to reconsider the location and sequence of the TRDD1 recombination signal. By combining molecular characterization and computational analysis, we show that the functional TRDD1 recombination signal is shifted inside the putative coding sequence of the TRDD1 gene and, consequently, that this gene is shorter than indicated in the databases.
T细胞受体基因在发育中的T淋巴细胞中通过位点特异性体细胞重排机制由离散的V、D和J基因组装而成。一个侧翼重组信号由一个保守的七聚体和一个半保守的九聚体组成，中间间隔12或23个可变核苷酸，它将重排机制的活性靶向相邻的V、D和J基因。在V、D或J基因重排后，它们各自的重组信号被连接在一起。尽管这些信号接头据称是不变的，由七聚体的头对头对接产生，但有些确实表现出连接多样性。重组信号最初是通过将种系序列与重排基因的序列进行比较和比对来鉴定的。然而，它们总体较低的序列保守性使得仅从序列数据来表征它们很困难。最近，计算分析揭示了间隔区内几个分散位置的核苷酸与重组活性之间的相关性，因此现在有可能识别推定的重组信号并确定和预测它们的重组效率。在本文中，我们分析了小鼠胸腺细胞中TRDD1和TRDD2基因重排后产生的信号接头中引入的变异性。这些信号接头中反复出现相同核苷酸的插入，这使我们重新考虑TRDD1重组信号的位置和序列。通过结合分子表征和计算分析，我们表明功能性TRDD1重组信号在TRDD1基因的推定编码序列内发生了移位，因此，该基因比数据库中显示的要短。
