Down-regulation of DNA ligase IIIα decreases the end-joining efficiency and repair using DNA sequence microhomologies, but increases the misrepair frequency and has no effect on the percentage of large deletions. An in vivo LacZα plasmid reactivation assay was used to measure end joining in siRNA DNA ligase IIIα down-regulated cells and compared with that using siRNA controls. (A) Relative percentage of colonies, indicating the efficiency of end joining. (B) The percentage of misrepair, that is, the number of white colonies as a percentage of total colonies (blue + white). (C) Graph of percentage of large deletions, defined as more than 20 bp. (D) Agarose gel showing PCR products of repaired colonies in siRNA nontarget controls and siRNA knockdown of DNA ligase IIIα. (E) The percentage of plasmids repaired using DNA sequence microhomologies of 1 to 6 bp. Fifteen plasmids were sequenced. Values significantly different are marked with an asterisk (Student t test; P < .01 for panels A and B and P < .001 for panel E). Error bars reflect the standard error of the mean.