Table 2.
Distribution of end joining types in yeast strains
| Strains | No. sequenced | End joining
|
P value* | ||
|---|---|---|---|---|---|
| Flap (%) | Blunt (%) | Miscellaneous (%) | |||
| YW112 | 40 | 24 (60) | 5 (12.5) | 11 (27.5) | NA |
| rad27 | 40 | 9 (22.5) | 13 (32.5) | 18 (45) | 0.0024 |
| rad 27 complemented | 34 | 18 (52.9) | 5 (14.7) | 11 (32.4) | 0.830 |
| exo1 | 31 | 20 (64.5) | 3 (9.7) | 8 (25.8) | 0.905 |
The strains from YW112, rad27, rad27 complemented with RAD27 plasmid, and exol strains were transformed with BamHI–XhoI double-digested pBX2 substrate. For YW112, exol, and rad27, plated to minimal medium lacking uracil and containing 10 μg/ml adenine. The overexpression strain pretransformed with the expression plasmid was plated on minimal medium lacking both uracil and leucine and containing 10 μg/ml adenine after being retransformed with substrate. To efficiently recover the low-copy ura3 plasmid from the overexpression strain, the high-copy LEU2 plasmid was first segregated out by consecutively streaking yeast on minimal medium lacking uracil. All ura3-plasmids were recovered from white colonies for each strain and sequenced. The percentage of events proceeding by the flap configuration defined in Fig. 1 is shown in bold.
The appropriate comparison between the wild-type and mutant strains is for the formation rate of a particular type of joint in the different strains. This formation rate can be calculated by multiplying the normalized rate of formation of the appropriate colony color by the percentage of those colonies that contain the joint of interest. Thus, the flap joint rate for YW112 is 0.028 × 0.234 × 0.60 = 0.0039, which is the product of the BamHI–XhoI transformation efficiency from Table 1 times the percentage of white to total colonies in the last column of Table 1 times the percentage of flap joints (bold). The flap joint rate for rad27 is 0.027 × 0.148 × 0.225 = 0.00090. The ratio of these two rates is 4.4; hence, the rad27 strain has a >4-fold reduction in the rate of flap joining.
P values are the χ2 probability obtained from the 2 × 3 table of strain vs. joint type, each in comparison to YW112. The P value of the 4 × 3 table of strain vs. joint type is 0.007, increasing to 0.913 for the 3 × 3 table that excludes the rad27 strain.