Together with RDM3, required for transcriptional gene silencing (TGS) by DNA methylation and repressive histone modifications (H3K9me2) of several chromatin loci (PubMed:21738482). Component of the RISC complex that associate with the small interfering RNA (siRNA) pathway involved in direct cytosine methylation at endogenous DNA repeats. Forms a AGO4/NRPE1/siRNA complex in cajal body, facilitating its function in RNA-directed gene silencing of target loci. Required for CpNpG and asymmetric DNA methylation as well as histone H3 'Lys-9' methylation (H3K9me) at SUP and SN1 loci. May be not required for CpG methylation. Required for the production and maintenance of retrotransposon SN1 and Copia and ribosomal 5S 25 nucleotide siRNAs specialized in gene silencing at chromatin level. Involved in de novo methylation of FWA gene and required for the maintenance of RNA-directed DNA methylation (RdDM) triggered by inverted repeat transgenes. Interacts with miRNA miR390 and miR172, targeting respectively TAS3 and AP2 mRNAs, and mediates cleavage of miRNA targets. Associates mainly with small RNAs of 24 nucleotide in length and preferentially recruits small RNAs with a 5' terminal adenosine. Targeted by the turnip yellows virus (TuYV) protein P0 (via F-box-like domain) for probable proteasome degradation and thereby inactivating AGO4 function in RNA silencing. Required for resistance to the bacterial pathogen P.syringae. Works independently of the RdDM pathway in mediating resistance to P.syringae. RdDM is involved in viral genome methylation as an epigenetic defense against geminiviruses (PubMed:12522258, PubMed:14988555, PubMed:15242620, PubMed:16839878, PubMed:16839879, PubMed:16998468, PubMed:17869110, PubMed:17938239, PubMed:17993621, PubMed:18342361, PubMed:18596098, PubMed:19377477, PubMed:20173091). Interacts with NRPE1 (via C-terminus). Binding to NRPE1 is required for its function in RdDM. Interacts with turnip crinkle virus (TCV) capsid protein P38; this interaction inhibits probably RNA silencing ability of AGO4. Interacts with SDE3 (PubMed:16839879, PubMed:17938239, PubMed:19377477, PubMed:20439431, PubMed:22940249). Binds to RDM3 (PubMed:19410546, PubMed:19343051). Binds chromatin at loci subject to transcriptional silencing (PubMed:21738482). Interacts with MBD6 (PubMed:28229965). Also located in AB-bodies that are distincts from the Cajal bodies and immediately adjacent to the condensed 45S ribosomal DNA (rDNA) loci (PubMed:18266474). Colocalizes with AGO4 and polymerase V in the nucleoplasm (PubMed:19410546). Expressed in embryos, mature leaves, vascular tissue of the sepals, stamens and stigma, at the tip of the style and siliques. Decreased DNA cytosine methylation at CpNpG and asymmetric positions at different DNA loci corresponding to retroelements, transposons and repetitive DNA sequences (PubMed:12522258, PubMed:17993621, PubMed:21738482). Reduced H3K9me2 at IGN5 and IGN26 loci (PubMed:21738482). Belongs to the argonaute family. Ago subfamily.