The complex of MUS81 and EME1 or EME2 acts as an endonuclease and processes D-loops by cleaving the sister chromatid strand complementary to the invading strand at the junction point. MUS81:EME2 complex has a higher catalytic activity than MUS81:EME1 complex and, in vitro, cleaves D-loops at several other sites in addition to the junction point (Osman et al. 2003, Pepe and West 2014). The yeast Mus81:Eme1 (Mus81:Mms4) complex also acts on D-loops (Schwartz et al. 2012).