EME2 (essential meiotic structure-specific endonuclease subunit 2) is the non-catalytic regulatory subunit of the heterodimeric MUS81-EME2 structure-specific endonuclease complex, essential for genome stability maintenance 1. EME2 is required for DNA cleavage, participating in DNA recognition and bending within the complex 2. MUS81-EME2 exhibits broader substrate specificity than its paralog MUS81-EME1, cleaving 3'-flaps, nicked Holliday junctions, D-loop recombination intermediates, and 5'-flap structures 1. The complex demonstrates higher endonuclease activity on intact Holliday junctions compared to MUS81-EME1 3. EME2 plays distinct temporal roles in DNA repair: MUS81-EME2 functions primarily during S phase, processing stalled replication forks by generating double-strand breaks that facilitate fork restart through homologous recombination 4. The complex also maintains telomeres in telomerase-negative ALT cells 4. MUS81-EME2 collaborates with FEN1 to remove flap structures during DNA transactions 5. Unlike MUS81-EME1, which operates in G2/M phase for recombination intermediate cleavage, EME2-containing complexes are restricted to S phase replication fork processing 4. Crystal structure analysis reveals MUS81-EME2 adopts a similar fold to MUS81-EME1 despite functional specialization 2. Small-molecule inhibitors targeting MUS81-EME2 represent potential therapeutic strategies 6.