TY - JOUR
T1 - Reassignment of the murine 3′TRDD1 recombination signal sequence
AU - Touvrey, C.
AU - Cowell, L. G.
AU - Lieberman, A. E.
AU - Marche, P. N.
AU - Jouvin-Marche, E.
AU - Candéias, S. M.
N1 - Funding Information:
Acknowledgements C. Touvrey was supported in part by a grant from “l’Association pour la Recherche contre le Cancer.” L.G. Cowell is supported by a Career Award from the Burroughs Wellcome Fund. We are thankful to Dr. C. Aude-Garcia for her comments on the manuscript. We are grateful to Irène Maréchal and Soumalamya Bama for excellent animal care.
PY - 2006/11
Y1 - 2006/11
N2 - 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.
AB - 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.
KW - Junctional diversity
KW - Recombination signal
KW - Signal joint
KW - T cell receptor gene
KW - V(D)J recombination
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U2 - 10.1007/s00251-006-0150-1
DO - 10.1007/s00251-006-0150-1
M3 - Article
C2 - 17021860
AN - SCOPUS:33751374982
SN - 0093-7711
VL - 58
SP - 895
EP - 903
JO - Immunogenetics
JF - Immunogenetics
IS - 11
ER -