The characterization of the human T-cell receptor (TCR) repertoire has made remarkable progress, with most of the work focusing on the TCR chains. tandem TRBD (TRB D gene) usage in ~2% of the productive human TCR CDR3 sequences. Electronic supplementary material The online version of this article (doi:10.1007/s13238-014-0060-1) contains supplementary material, which is available to authorized users. < 0.001)). In aggregate, these results are consistent with T previous reports (Freeman et al., 2009; Robins et al., 2009; Warren et al., 2011), which validates our approaches. TRAV/TRAJ usage and TRAV-TRAJ pairing pattern in healthy donors When examining the frequency of the TRAV segments listed according to their chromosomal locations, we found that the TRAV usage was notably biased in a given individual (Fig.?2A). Some TRAV segments such as TRAV8-1, 13-1, 20, 27, and 38-2 are preferentially used in comparison with those like 8-3, 8-6, and 8-7, which are almost undetectable. Furthermore, the frequencies of the TRAV segments that are most proximal to the TRAJ cluster were not the highest, while those most distal to the TRAJ cluster were not the rarest. These data indicate that TRAV segments were selected irrespective of distance from TRAJ gene segments. Most intriguingly, pairwise comparisons of TRAV usage between donors produced a Pearson correlation coefficient of 0.90 0.04 (mean SD), indicating marked similarity in the TRAV frequency among individuals. Figure?2 TRAV, TRAJ gene usage and TRAV-TRAJ pairing are highly correlated among donors. Relative frequency of TRAV and TRAJ segments are listed in (A) and (B), respectively, according to their chromosome locations. (C) The heat map of the TRAV and TRAJ pairings … Likewise, TRAJ usage was also non-uniform in a given donor (Fig.?2B). Furthermore, the TRAJ usage patterns observed in the three healthy donors were quantitatively similar to each other, with an average Pearson correlation coefficient of 0.66 0.04 (mean SD). As illustrated in the heat map (Fig.?2C), the abundance of TRAV-TRAJ pairings was strongly correlated among individuals. The average Pearson coefficient of TRAV-TRAJ pairing was 0.334 (< 0.001). Though the TRAV and TRAJ gene segments usage was strikingly quantitatively similar among donors, the extent of TRAV-TRAJ pairing similarity was somewhat reduced. Especially when focusing on the most abundant TRAV-TRAJ parings, we found that they were unique for each individual. Moreover, as the TRAV and TRAJ gene segments are shown according to their chromosomal positions (5 to 3 direction), we determined that the TRAV-TRAJ pairing in humans is not compatible INCB28060 with the sequential coordinate gene recombination hypothesis, which means 5 to 3 polarized utilization of the TRAJ library may be coordinated with a 3 to 5 5 polarized utilization of the library of the TRAV gene segments (Fuschiotti et al., 2007; Huang and Kanagawa, 2001; Krangel, 2009; Pasqual et al., 2002; Roth et al., 1991). This situation is analogous to a recent report focusing on TRA in mice (Genolet et al., 2012). TRDV1 is used as a common TRAV gene segment: TRAV42/DV1 The TRD locus spans 60 kb on chromosome 14 at 14q11.2 and is nested within the TRA locus (Fig.?3A). The TRD locus is composed of a cluster of one TRDV gene (TRDV2), three TRDD genes, and four TRDJ genes, upstream of the unique TRDC gene (Lefranc, 2001). Another TRDV gene (TRDV3) is located downstream of the TRDC gene, in inverted transcription orientation (Lefranc and Rabbitts, 1990). Resembling the five TRAV/DV gene segments, TRDV1 is dispersed in the TRAV cluster rather than TRDV2 and TRDV3 (Lefranc, 2001). Hence, TRDV1 has a INCB28060 high potential to be a shared TRAV/DV segment. Figure?3 TRDV1 is also a shared TRAV/DV gene segments. (A) TRDV gene segments dispersed INCB28060 in the TRA locus in chromosome 14 (14q11.2). TRDV1, TRDV2, and TRDV3 (yellow squares) were not shared with TRA in previous report, while the other five TRDV segments (green ... As illustrated in Fig.?3B, TRDV1 had at least 927 copies, while both TRDV2 and TRDV3, which are believed to exclusively join to TRDD segments (Lefranc, 2001), had zero copies in all donors after noisy sequence elimination. Furthermore, TRDV1 had the same usage level as the other five shared TRAV/DV segments, for which the number of copies ranged from several hundred to several thousands (Fig.?3B). The TRA gene locus contains 61 TRAJ gene segments, of which 50 are INCB28060 functional, INCB28060 while the others are pseudogenes or open reading frames (ORFs). We found that there was absolutely no signal from the.