Regulation of HR. Recruitment of the HR machinery to a DSB is regulated by both the major cell cycle kinase CDK1 and the checkpoint kinase Mec1. CDK1 phosphorylation is marked as a yellow circle and Mec1 phosphorylation is marked as a yellow star. A) Once a DSB is detected, the DNA ends are resected forming 3' ssDNA tails by multiple nucleases that are positively regulated by CDK1/B type cyclin kinase activity. RPA binds the ssDNA and recruits the ATR-ATRIP homolog Mec1-Ddc2 and the 9-1-1 complex comprised of Ddc1, Mec3 and Rad17 (indicated by Ddc1). Finally, Rad52 catalyzes the formation of a Rad51 nucleoprotein filament along the ssDNA before HR can proceed. B) The intra-S phase checkpoint proteins Mrc1, Tof1 and Csm3 travel with the fork during normal replication. In response to DNA damage, the replication fork stalls, activating Mec1 which in turn phosphorylates Mrc1. Phosphorylated Mrc1 promotes stable fork pausing and contributes to Mec1 retention at the fork. In the absence of Mec1, the replisome is not stable when the fork pauses or stalls, leading to the uncoupling of the MCM helicase and the polymerase (grey) and fork collapse (bottom right). The DNA replication clamp PCNA is the circle adjacent to MCM2-7. Rad52 is recruited to the collapsed fork and HR restarts replication by one-end invasion of the intact DNA molecule (here shown as lagging strand invasion of the leading strand template). C) In repetitive sequences (indicated by green arrows) the Smc5/6 complex is recruited to DSBs along with the DSBR machinery, shown in A, to mediate repair. Smc5/6 and the sumoylation state of Rad52 affect whether repair deletes or retains DNA sequences between repeats (purple triangles) during direct repeat recombination.