| Proteins | AGI number of gene | Seewt Olive number of gene | Description |
| NUCLEAR RNA POLYMERASE D1 (NRPD1) | AT1G63020 | - | The unique, largest subunit of Pol IV |
| NRPE1 | AT2G40030 | Contig244.60 Contig203.117 |
The unique, largest subunit of Pol V |
| NRPD2/NRPE2* | AT3G23780 | Contig164.137 | The shared second largest subunit of Pol IV and Pol V |
| NRPD4/NRPE4* | AT4G15950 | - | The shared fourth largest subunit of Pol IV and Pol V |
| NRPE5 | AT3G57080 | - | A special fifth largest subunit of Pol V |
| NRPE9B | AT4G16265 | - | A special ninth largest subunit required for Pol V activity |
| NRPB1 | AT4G35800 | Contig16.21 Contig72.102 |
The largest subunit of Pol II |
| RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) | AT4G11130 | Contig19.58 | An RNA-dependent RNA polymerase |
| DICER-LIKE 3 (DCL3) | AT3G43920 | - | A Dicer endonuclease that produces 24-nucleotide siRNAs |
| HUA ENHANCER 1 (HEN1) | AT4G20910 | - | A small RNA methyltransferase |
| ARGONAUTE 4 (AGO4) | AT2G27040 | Contig266.111 Contig302.26 Contig185.127 Contig49.12 |
An Argonaute protein |
| AGO6 | AT2G32940 | Contig168.49 | An Argonaute protein |
| AGO9 | AT5G21150 | Contig185.127 Contig49.12 Contig266.111 Contig302.26 |
An Argonaute protein |
| CLASSY 1 (CLSY1) | AT3G42670 | Contig35.108 | A putative SWI/SNF chromatin remodeller; involved in the Pol IV pathway |
| DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1) | AT2G16390 | Contig327.72 | A putative SWI/SNF chromatin remodeller; part of the DDR complex; involved in the Pol V pathway |
| DEFECTIVE IN MERISTEM SILENCING 3 (DMS3) | AT3G49250 | - | A SMC solo hinge protein; part of the DDR complex; involved in the Pol V pathway |
| RNA-DIRECTED DNA METHYLATION 1 (RDM1) KOW DOMAIN-CONTAINING | AT3G22680 | - | An AGO4- and Pol II-interacting protein; part of the DDR complex; involved in the Pol V pathway |
| TRANSCRIPTION FACTOR 1 (KTF1) | AT5G04290 | Contig12.174 | Contains the AGO hook motif; involved in Pol V transcription |
| INVOLVED IN DE NOVO 2 (IDN2) | AT3G48670 | - | A dsRNA-binding protein in the Pol V pathway |
| IDN2 PARALOGUE 1 (IDP1) | AT1G15910 | - | Forms a complex with IDN2 |
| IDP2 | AT4G00380 | - | Forms a complex with IDN2 |
| DMS4 | AT2G30280 | - | Associated with Pol V and Pol II |
| DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) | AT5G14620 | Contig349.32 | A de uovo DNA methyltransferase |
| SUVH2 | AT2G33290 | - | An SRA domain protein that binds to methylated DNA and recruits Pol V |
| SUVH9 | AT4G13460 | Contig155.59 | An SRA domain protein that binds to methylated DNA and recruits Pol V |
| SUVR2 | AT5G43990 | - | A putative histone methyltransferase |
| MICRORCHIDIA 1 (MORC1) | AT4G36290 | Contig156.11 | A MORC-type ATPase |
| MORC6 | AT1G19100 | Contig19.14 | A MORC-type ATPase |
| SAWADEE HOMEODOMAIN HOMOLOGUE 1 (SHH1) | AT1G15215 | - | Binds to methylated H3K9 and recruits Pol IV |
| HISTONE DEACETYLASE 6 (HDA6) | AT5G63110 | Contig106.94 | A histone deacetylase |
| JUMONJI 14 (JMJ14) | AT4G20400 | Contig14.443 Contig247.4 |
A histone demethylase |
| LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 (LDL1) | AT1G62830 | Contig136.132 | A histone demethylase |
| LDL2 | AT3G13682 | Contig464.22 Contig398.19 Contig164.109 |
A histone demethylase |
| UBIQUITIN-SPECIFIC PROTEASE 26 (UBP26) | AT3G49600 | Contig176.13 | A histone H2B deubiquitinase |
| Additional factors | |||
| NEEDED FOR RDR2-INDEPENDENT DNA METHYLATION (NERD) | AT2G16485 | Contig22.119 Contig58.173 Contig128.43 |
Involved in non-canonical RdDM |
| CHROMOMETHYLASE 2 (CMT2) | AT4G19020 | Contig64.48 Contig64.62 |
A DNA methyltransferase specific to CHH‡ |
| CMT3 | AT1G69770 | - | A DNA methyltransferase specific to CHG‡ |
| METHYLTRANSFERASE 1 (MET1) | AT5G49160 | Contig41.102 Contig88.99 |
A DNA methyltransferase specific to CG |
| SUVH4 | AT5G13960 | Contig403.46 Contig142.45 |
A H3K9 methyltransferase |
| DECREASED DNA METHYLATION 1 (DDM1) | AT5G66750 | Contig500.21 Contig245.96 |
A chromatin remodeller |