To study the role of structural maintenance of chromosome (SMC)4-1 and SMC4-2 during programmed genome rearrangement in Paramecium tetraurelia. Paramecium SMC4-1 and SMC4-2 was tagged with 3 FLAG and HA at its C-terminal separately. The recombinant plasmid was microinjected into macronuclear and used for co-immunoprecipitation and Mass spectrometry studies to identify interacting proteins of SMC4-1 and SMC4-2 that indicates the different functions between Paramecium SMC4s.