A single fork-arrest induces GCRs that are stimulated by inverted repeats near the site of fork arrest.

<p>A. Diagrams of chromosome II containing or not the <i>RTS1</i> sequence (blue arrow or <i>RTS1-d</i>) and of chromosome III containing <i>ura4⁺</i> alone or associated with <i>RTS1-</i>RFB constructs. The <i>RTS1</i> sequence maps near the <i>mat1</i> locus where it helps to ensure unidirectional replication <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002976#pgen.1002976-Dalgaard1" target="_blank">[62]</a>. Primers used for amplifying the 1 Kb <i>ura4</i> fragment or the 650 bp <i>rng3</i> fragment are depicted in red and grey, respectively. Primers used to amplify the translocation junction (1.2 kb) are represented in orange on chromosome II (TLII) and in black on chromosome III (TLIII). B. Representative PCR-amplifications from 5-FOA^R colonies of the indicated strains; ON and OFF refers to the <i>RTS1</i>-RFB being active or not, respectively. PCR products and their sizes are indicated on the figure. C. Effect of intra- and inter-chromosomal recombination between <i>RTS1</i> repeats on fork-arrest-induced genomic deletion. <i>RTS1</i>-RFB activity and <i>ura4</i> location with respect to the RFB are given for each construct. The % of deletion events, as determined by the PCR assay, was used to balance the rate of <i>ura4</i> loss. Then, the RFB-induced deletion rate was calculated by subtracting the rate obtained in the presence of thiamine (Rtf1 being repressed) from the rate obtained in the absence of thiamine (Rtf1 being expressed). The values reported are means of at least 3 independent median rates. Error bars correspond to the standard error (SE). D. Effect of Rqh1 on RFB-induced deletions (left) and translocations (right), as described for panel C. Error bars indicate SE. Statistically significant fold differences between the <i>rqh1-d</i> and the wild-type strains are indicated with an *. E. Representative PCR amplifications from 5-FOA^R colonies of the <i>rqh1-d t-ura4 strain, as described for panel B. (Refer to <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002976#pgen.1002976.s001" target="_blank">Figure S1</a> for corresponding rates of deletion and translocation when Rtf1 is expressed or not).</i>