Table 2.

Frequencies of RT template switching in different regions of the direct repeats adjacent to one another or separated by a spacer fragment of 818 bp

Region of direct repeata (length [bp])KD-HTT4*KKD-HTpT4*K
No. of clones% RT template switchingNo. of clones% RT template switching
Per regionbPer 100 bpcPer regionPer 100 bp
A (153)11302077046
B (110)7161553330
C (158)8159104025
D (180)474274
E (100)477277
Total3426
• a See Fig. 4 for definition of regions.

• b The percent RT template switching per region was adjusted to the length of each region to estimate the percent RT template switching per 100 bp by using the following formula: (% RT template switching per region/length of region [bp]) × 100 bp. For example, the % RT template switching per 100 bp for region A of KD-HTT4*K was (30%/153 bp) × 100 bp = 20%.

• c The percent RT template switching per 100 bp was calculated as follows. First, the fraction of RTs that underwent a template switch and reconstituted a functional HTK gene (57% for KD-HTTK and 91% for KD-HTpTK) was used to estimate the theoretical population of undeleted and deleted clones analyzed. Specifically, 34 clones of KD-HTT4*K underwent direct repeat deletion, which represents 57% of 60 clones. Similarly, 26 clones of KD-HTpT4*K underwent direct repeat deletion, which represents 91% of 29 clones. Next, the number of RTs that copied each region was estimated by subtraction of the fraction of RTs that switched templates 3′ to the region by using the following formula: (number of clones that switched templates in region)/(theoretical population − number of clones that switched templates in regions 3′ to the region) × 100. For example, the number of RTs that copied region A of KD-HTT4*K was 11/(60 − 23) × 100% = 30%. This calculation indicates that 30% of RTs that copied region A of KD-HTT4*K underwent a template switch.