Studies have identified a sub-group of SGS3-LIKE proteins including FDM1-5 and IDN2 as key components of RNA-directed DNA methylation pathway (RdDM). Although FDM1 and IDN2 bind RNAs with 5' overhangs, their functions in the RdDM pathway remain to be examined. Here we show that FDM1 interacts with itself and with IDN2. Gel filtration suggests that FDM1 may exist as a homodimer in a heterotetramer complex in vivo. The XH domain of FDM1 mediates the FDM1-FDM1 and FDM1-IDN2 interactions. Deletion of the XH domain disrupts FDM1 complex formation and results in loss-of-function of FDM1. These results demonstrate that XH domain-mediated complex formation of FDM1 is required for its function in RdDM. In addition, FDM1 binds unmethylated but not methylated DNAs through its coiled-coil domain. RNAs with 5' overhangs does not compete with DNA for binding by FDM1, indicating that FDM1 may bind DNA and RNA simultaneously. These results provide insight into how FDM1 functions in RdDM.
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