Table 1.
Pol II-dependent AID-catalyzed deamination on IGHV3-23*01 substrate
| Experiment | No. of sequenced Ca | No. of C to T mutations | Mutation rate (× 10−5)b | Average ± SD | t-testc | |
|---|---|---|---|---|---|---|
| Non-transcribed strand | ||||||
| NTS-control | 1 | 3469440 | 110 | 3.2 | - | |
| NTS +Pol II | 1 | 541824 | 15 | 2.8 | - | |
| NTS + AID | 1 | 1926144 | 76 | 3.9 | ||
| 2 | 5186928 | 191 | 3.7 | |||
| 3 | 6159120 | 227 | 3.7 | 3.8 ± 0.1 | ||
| NTS+ Pol II + AID | 1 | 648576 | 132 | 20.4 | ||
| 2 | 4347888 | 1405 | 32.3 | |||
| 3 | 4694496 | 1787 | 38.1 | 30.2 ± 7.4 | ||
| P = 0.046 | ||||||
| NTS + Pol II + AID + DSIF | 1 | 4221600 | 2400 | 56.9 | ||
| 2 | 4561776 | 2310 | 50.6 | 53.7 ± 3.1 | ||
| Transcribed strand | ||||||
| TS-control | 1 | 5574690 | 180 | 3.2 | - | |
| TS + Pol II | 1 | 1922052 | 49 | 2.5 | - | |
| TS + AID | 1 | 3291222 | 192 | 5.8 | ||
| 2 | 9993060 | 593 | 5.9 | |||
| 3 | 5402298 | 228 | 4.2 | 5.3 ± 0.8 | ||
| TS + Pol II + AID | 1 | 2713590 | 1573 | 58.0 | ||
| 2 | 6243336 | 2632 | 42.2 | |||
| 3 | 4165854 | 1672 | 40.1 | 46.8 ± 8.0 | ||
| P = 0.208 | ||||||
| TS + Pol II + AID + DSIF | 1 | 5415564 | 1719 | 31.7 | ||
| 2 | 4594854 | 1721 | 37.5 | 34.6 ± 2.9 |
aTotal number of all sequenced dC bases (48 sites on NTS strand and 66 sites on TS strand) from qualified UID family-reads (see Materials and Methods for details).
bMutation rates for each experiment were calculated as the total number of C to T mutations on the NTS or TS divided by the total numbers of all sequenced C templates on the NTS or TS, respectively. When shown, average mutation rates represent average ± standard deviation.
c P values from two-tailed Student's t-test are shown for comparison of NTS mutation rates in the absence and the presence of DSIF, and TS mutation rates in the absence and the presence of DSIF.