Article Figures & Data
Figures
- FIGURE 1.
HCDR3 diversity during human ontogeny. Top row, First trimester fetal liver VDJCμ+ transcripts. Middle row, Second trimester fetal liver and bone marrow VDJCμ+ transcripts. Bottom row, Adult blood VDJCμ+ transcripts from the published work of Yamada et al. (17). Left column, Percentage of transcripts that utilize members of the designated DH families. A “?” designates transcripts where the DH family cannot be determined. The D7 (DQ52) gene segment contributed to 19 of 37 first trimester, 40 of 117 second trimester, and 2 of 99 adult VDJCμ transcripts; whereas D3 (DXP) gene segments contributed to 2 of 37, 13 of 117, and 29 of 99 transcripts, respectively (p < 0.0001 χ2). Middle column, Distribution of the lengths of the CDR 3 intervals of the transcripts (residues 93–102 (8;9;12)) divided into 3 residue intervals (e.g., <9, 10–12, 13–15, 16–18, 19–21, 22–24, and >24 codons). Right column, Percentage of transcripts that utilize the designated JH gene segment. For each developmental stage, the number of transcripts analyzed is indicated by the value of n. The arrows are intended to emphasize the major differences between fetal and adult transcripts.
- FIGURE 2.
HCDR3 length distribution during human ontogeny. Shown are average HCDR3 lengths in VDJCμ transcripts from: A, 34 fetal liver samples ranging in age from 8 to 28 wk gestation, B, 35 fetal spleen samples of which 17 derive from the first trimester of gestation and 16 from the second trimester, and C, 72 samples of cord blood and peripheral blood from infants ranging in age from birth to 18 mo of age. The dotted lines denote 5% and 95% confidence limits for the distribution of lengths over time.
- FIGURE 3.
A dissection of the components contributing to HCDR3 length in D3- and D7-containing H chain variable domains. The potential contribution of the germline sequence of VH gene segments, P junctions, N region addition, DH gene segments, and JH gene segments to HCDR3 length is illustrated. The actual contribution of these components to 28 adult D3-containing HCDR3 intervals, 12 fetal D3-containing intervals, and 59 fetal D7-containing intervals is shown below. Also shown beside the DH gene segment is the average 5′ and 3′ loss of sequence for D3 and D7 gene segments. All components are shown to scale.
- FIGURE 4.
JH utilization among DJ transcripts during human ontogeny. Depicted are the percentage of transcripts that use the designated JH gene segment. Left column, D3-J transcripts. Right column, D7-J transcripts. Shown by row from top to bottom are transcripts from 8-wk fetal liver, 12-wk fetal liver, 19-wk FBM, ABM, and the blood and bone marrow of patients with XLA, respectively. For each category, the number of transcripts analyzed is indicated by the value of n. The arrows are intended to emphasize the major differences between fetal and adult transcripts.
- FIGURE 5.
Patterns of N addition during human ontogeny. Distribution of the extent of N addition in D7- and D3-containing DJ transcripts from normal fetal and adult B lineage cells, and from the blood and bone marrow of patients with XLA. Statistically, there was no difference in N addition between D7-J and D3-J transcripts in the adult (8.5 ± 1.2 vs 7.8 ± 1.0 nucleotides, respectively; p = 0.67, Student’s t test).
- FIGURE 6.
Distribution of average HCDR3 lengths of VH3DJCμ transcripts from FBM and ABM as a function of B cell differentiation.
- FIGURE 7.
The distribution of HCDR3 lengths is controlled in mouse. The distribution of HCDR3 lengths in VDJCμ+ transcripts from neonatal liver, spleen, and adult spleen (7). Shown is the average length of sequences using the DFL16.1 and DQ52 gene segments, and members of the DSP family, as well as the average length of HCDR3 intervals for the population as a whole.
- FIGURE 8.
Three dimensional molecular models of human Fv domains with emphasis on the consequences of lengthening HCDR3. A, Fv structures from the side. The Ag-binding site is at the top with Vκ on the left and VH on the right. B, Fv structures from the top, looking down into the Ag-binding site. The color scheme for both is as follows: (numbers are according to Kabat (9)). Blue = VH, violet = Vκ (Humkv325 with a 9-amino acid CDR3 and Jκ1), white = HCDR1 (31 to 35); HCDR2 (50 to 65), Vκ LCDR1 (24 to 34); LCDR2 (50 to 56); LCDR3 (89 to 97). Gray = HCDR3 (93–102). Top, V3-23 with D7-27 and JH3 and a 12-amino acid HCDR3. Bottom left, V3-23 with JH5 and an HCDR3 of 18 amino acids (clone 18/2 (59)). Bottom right, V3-23 with JH6 and a 24-amino acid HCDR3. The 3-dimensional raster representation includes side chains on all residues.
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