The HIS4 and URA3 loci are denoted throughout this paper in red and blue, respectively, and are in Red1/Hop1 enriched and depleted regions, respectively (see Figure 4A and Figure 4—figure supplement 1, below). (A) Left—map of VDE-reporter inserts at HIS4, showing digests used to detect recombination intermediates and products. One parent (P1) contains ARG4 sequences with a VDE-recognition site (arg4-VRS), flanked by an nourseothricin-resistance module [natMX, (Goldstein and McCusker, 1999)] and the Kluyveromyces lactis TRP1 gene [KlTRP1, (Stark and Milner, 1989)]; the other parent (P2) contains ARG4 sequences with a mutant, uncuttable VRS site [arg4-VRS103, (Nogami et al., 2002) flanked by URA3 and pBR322 sequences. Digestion with HindIII (H) and VDE (V) allows detection of crossovers (CO1 and CO2) and noncrossovers (NCO); digestion with HindIII alone allows detection of crossovers and DSBs. P2, CO1 and CO2 fragments are drawn only once, as they are the same size in HindIII digests as in HindIII + VDE digests. Right—representative Southern blots. HindIII-alone digests are probed with a fragment (probe 2) that hybridizes to the insert loci and to the native ARG4 locus on chromosome VIII; this latter signal serves as a loading control (LC). Times after induction of meiosis that each sample was taken are indicated below each lane. (B) map of VDE-reporter inserts at URA3 and representative Southern blots; details as in (A). Strain, insert and probe details are given in Materials and methods and Supplementary file 1.