Interacts with EME1 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks, nicked Holliday junctions and also intact Holliday junctions with a reduced efficiency. May be required in mitosis for the processing of stalled or collapsed replication fork intermediates. Plays a role in DNA repair and in genotoxic stress-induced homologous recombination (HR) in somatic cells. Mediates a subset of meiotic recombination events that are insensitive to crossover interference. Together with SEND1, essential for the resolution of toxic replication structures to ensure genome stability, and to maintain telomere integrity and replication (PubMed:26704385). Forms a heterodimer with EME1A or EME1B. Ubiquitous but preferentially expressed in young flowers buds, notably in anthers. By DNA-damaging treatments such as MMS, cisplatin and gamma-radiation. Sensitive to the mutagens MMS and MMC. Increased sensitivity to gamma radiation. Deficiency in homologous recombination in somatic cells but only after induction by genotoxic stress. Decreased pollen viability with morphologically aberrant (small and misshaped) grain. Moderate reduction in meiotic crossovers. The double mutant mus81 send1 exhibits severe developmental defects (e.g. strong growth retardation and impaired leaf and shoot development), increased endoreduplication, slower cell cycle progression, spontaneous cell death and genome instability associated with a dramatic loss of telomeric repeats (PubMed:26704385). Two distinct classes of crossovers have been demonstrated in Arabidopsis. Class I is MSH4 dependent and exhibits crossover interference. Class II is MUS81 dependent and exhibits no interference. Belongs to the XPF family.