Compositional characteristics of human peripheral TRBV pseudogene rearrangements

Figures

• 

  Figure 1. Gene frequency of the TRBV functional (F) genes, TRBV open reading frames (ORFs) and TRBV pseudogenes (P) in the healthy and disease groups. (A) The frequency of functional TRBV genes is significantly higher than that of the TRBV pseudogenes and ORFs. (B) TRBV pseudogenes and ORFs show unproductive rearrangements that are significantly used, while most functional genes are productive. These results are plotted with a box line diagram, which shows all the points to indicate each sample. The line indicates the median, and two error bars are used to represent the min and max.

• 

  Figure 2. Usage of TRBJ and TRBD genes in 4 healthy individuals and 4 patients. (A,B) Usage of the TRBJ genes show significant differences among three classes of rearrangements in the healthy and disease groups. The results are shown with the median value in each group. The p values were determined with a χ2 test using the median of four samples in each group. All statistically significant differences are indicated. *p < 0.05, **p < 0.01, ***p < 0.001. (C) Comparison of the TRBJ usage in the pseudogene between the healthy and disease group is shown. (D,E) Usage of TRBD genes in the three classes of rearrangements in the healthy and disease groups is shown. The results (C–E) are plotted with a box line diagram, which shows all the points to indicate each sample in each group. The line indicates the median, and the two error bars represent the min and max. The p values were determined with a χ2 test using the median of four samples in each group. All statistically significant differences are indicated. *p < 0.05, **p < 0.01, ***p < 0.001.

• 

  Figure 3. CDR3 lengths and overall amino acid usage of the CDR3 regions in in-frame functional TRBV gene rearrangements and in-frame TRBV pseudogene rearrangements. (A) Average CDR3 length distribution of in-frame TRBV functional gene rearrangements and in-frame TRBV pseudogene rearrangements in the healthy group are shown. (B) The amino acids are arranged by relative hydrophobicity values according to the Kyte-Doolittle scale13. The overall CDR3 amino acid composition differed significantly between the pseudogene rearrangements and functional gene rearrangements in the healthy group (χ2 test, p < 0.001). (C,D) Comparison of the average CDR3 length distribution and the overall CDR3 amino acid composition of the in-frame TRBV pseudogene rearrangements between the healthy and disease group shows no differences. The results are shown as the mean value in each group. The p values were determined using a χ2 test (B and D). All statistically significant differences are indicated. *p < 0.05, **p < 0.01, ***p < 0.001.

• 

  Figure 4. Amino acid frequencies at the ten specific positions selected for assessment of in-frame functional TRBV gene rearrangements in comparison with the putative amino acid utilization in in-frame TRBV pseudogene rearrangements grouped according to physical properties. CDR3 positions (105–117) are shown according to the IMGT unique numbering. The results are plotted with a heat map, which shows the mean in 4 healthy individuals of all the unique productive CDR3 sequences with different lengths.

• 

  Figure 5. Insertions and deletions of the nucleotides in V-D-J junctions of P, ORF, and F rearrangements in the healthy (P-H, ORF-H and F-H) and disease group (P-D, ORF-D and F-D). (A) The frequency profiles of the VD insertions of different nucleotide lengths in three classes of rearrangements. (B) The frequency profile of the DJ insertions of different nucleotide lengths in three classes of rearrangements. (C) The frequency profile of the V deletions of different nucleotide lengths in three classes of rearrangements. (D) The frequency profile of the J deletions of different nucleotide lengths in three classes of rearrangements. The results are shown as the mean of all unique unproductive sequences in each group.