Forms a complex with IDN2 and FDM1/IDNL1 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway. Forms a complex with IDN2 and FMD1/INDL1. Highly expressed in flowers and at lower levels in roots, leaves and stems. No visible phenotype under normal growth conditions. The double mutants idnl1-1 and idnl2-1 show a late-flowering phenotype and reduced level of DNA methylation (PubMed:22592791). The double mutants fdm1-1 and fdm2-1 show reduced level of DNA methylation and repeat-associated small interfering RNAs (ra-siRNAs) (PubMed:22302148).