TABLE 2.
Coding joints and rejoined I-SceI breaks mediated by the PQR>ala mutant have excessive nucleotide loss, whereas those mediated by the PQR>asp mutant have minimal nucleotide lossa
| Transfectant | V(D)J coding joint result
|
I-SceI joint result
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| No. of sequences | bp loss/joint | % Complete ends | % Sequences with SSH | % P segments/complete end | % N+ joints | N segmented length | No. of sequences | bp loss/joint | % Complete ends | |
| Wild type | 74 | 4.8 | 31 (46/148) | 50 (37/74) | 24 (11/46) | 63 (24/38) | 2.3 | 30 | 11.7 | 10 (6/60) |
| Wild type + Tdt | 38 | 5.6 | 28 (21/76) | 36 (5/14) | 38 (8/21) | |||||
| PQR>ala | 67 | 14.1 | 9 (12/134) | 66 (44/67) | 8 (1/12) | 48 (13/27) | 1.8 | 33 | 31.4 | 1.5 (1/66) |
| PQR>ala + Tdt | 27 | 10.5 | 6 (3/54) | 71 (10/14) | 0 (0/3) | |||||
| PQR>asp | 40 | 2.2 | 56 (45/80) | 20 (6/30) | 16 (7/45) | |||||
| ABCDE>ala | 29 | 1.4 | 71 (41/58) | 0 (0/29) | 32 (13/41) | 38 (6/16) | 1.2 | 33 | 6 | 19.7 (13/66) |
| ABCDE>ala +Tdt | 16 | 2.6 | 66 (21/32) | 20 (2/10) | 62 (13/21) | |||||
| ABCDE>asp | 25 | 3.1 | 38 (19/50) | 52 (13/25) | 26 (5/19) | |||||
| ABCDE+PQR>ala | 39 | 6.7 | 46 (36/78) | 28 (11/39) | 36 (13/36) | 33 | 25.4 | 6.1 (4/66) | ||
| RAGS/I-SceI only | 16 | 14.7 | 41 (13/32) | 31 (5/16) | 85 (11/13) | 33 | 19.8 | 6.1 (4/66) | ||
Some of the coding joint sequences presented (61/74 of the wild type without Tdt, 28/29 of the ABCDE>ala without Tdt, and 16/16 of the vector) are from reference 9. Average nucleotide loss/joint, % intact coding ends, % sequences with SSH (calculated only from joints lacking N segments), % P segments/complete end, % N segment containing (% N+) joints, and N segmented length were calculated from sequences presented in Fig. S1 in the supplemental material. Although only mean nucleotide loss is presented, both the median and the average were calculated and did not differ substantially from one another. The one ABCDE+PQR>ala sequence with a 200-bp deletion was not included in calculating the mean nucleotide loss.