Table 1.

Gene	Genome Identifier	Gene product	Function	Suggested Reference
DRM2	AT5G14620	DNA methyltransferase	De novo methylation and maintainance of CHH methylation through RdDM	[40]
DRM1	AT5G15380	DNA methyltransferase	A homolog of DRM2	[40]
MET1	AT5G49160	DNA methyltransferase	Maintains CG methylation	[43, 44]
CMT3	AT1G69770	DNA methyltransferase	Maintains CHG methylation	[50, 51]
CMT2	AT4G19020	DNA methyltransferase	Maintains DNA methylation at heterochromatin	[44, 58]
NRPD1	AT1G63020	Largest subunit of Pol IV	Generates 24-nt siRNA precursors in RdDM	[15, 16]
NRPE1	AT2G40030	Largest subunit of Pol V	Generates scaffold transcripts in RdDM	[11, 85, 86]
NRPB2	AT4G21710	Second largest subunit of Pol II	Generaes scaffold transcripts at some RdDM target loci	[27]
CLSY1	AT3G42670	SNF2-like chromatin remodelling protein	Interacts with Pol IV, functions in 24-nt siRNA precursor biogenesis	[18]
DRD1	AT2G16390	SNF2-like chromatin remodelling protein	Part of the DDR complex, functions in the recruitment of Pol V to RdDM target loci	[28, 29]
DDM1	AT5G66750	SNF2-like chromatin remodelling protein	Functions in the maintenance of DNA methylation at heterochromatin	[58, 87]
SUVH2	AT2G33290	SRA domain methylcytosine-binding protein	Functions in the recruitment of Pol V to RdDM loci	[33, 88]
SUVH9	AT4G13460	SRA domain methylcytosine-binding protein	A homolog of SUVH2	[33, 88]
VIM1	AT1G57820	SRA domain methylcytosine-binding protein	Functions in the maintenance of CG methylation	[45, 46]
VIM2	AT1G66050	SRA domain methylcytosine-binding protein	A homolog of VIM1	[46]
VIM3	AT5G39550	SRA domain methylcytosine-binding protein	A homolog of VIM1	[46]
RDM4	AT2G30280	IWR (Interacts with Pol II)-type transcription factor	Interacts with Pol IV, functions in 24-nt siRNA precursor biogenesis	[19, 20]
RDR2	AT4G11130	RNA dependent RNA polymerase	Interacts with Pol IV, functions in 24-nt siRNA precursor biogenesis	[89, 90]
SHH1	AT1G15215	SAWADEE domain and homeodomain containing protein	Interacts with Pol IV, functions in 24-nt siRNA precursor biogenesis	[17, 21]
DCL3	AT3G43920	Dicer-like protein	Generates 24-nt siRNA duplexes in RdDM	[89]
AGO4	AT2G27040	Argonaute protein	Binds to 24-nt siRNAs, functions in RdDM	[25, 42, 91]
HEN1	AT4G20910	Small RNA methyltransferase	Methylates siRNA duplexes	[24]
DMS3	AT3G49250	Structural maintenance of chromosomes (SMC) hinge domain-containing protein	Part of the DDR complex, functions in the recruitment of Pol V to RdDM target loci	[29, 31]
RDM1	AT3G22680	Contains a domain of unknown function	Part of the DDR complex, functions in the recruitment of Pol V to RdDM target loci	[28–30]
STA1	AT4G03430	PRP6-like splicing factor	Functions in scaffold transcript biogenesis	[35]
KTF1	AT5G04290	Transcription elongation factor SPT5-like protein	Functions downstream of scaffold transcripts in RdDM	[36, 37]
IDN2	AT3G48670	dsRNA-binding protein	Functions downstream of scaffold transcripts in RdDM	[38, 92]
KYP	AT5G13960	Histone H3K9 methytransferase	Functions in the maintenance of CHG methylation through CMT3	[93]
SUVH5	AT2G35160	Histone H3K9 methytransferase	A homolog of KYP	[94, 95]
SUVH6	AT2G22740	Histone H3K9 methytransferase	A homolog of KYP	[54]
IBM1	AT3G07610	Histone demethylase	Functions in preventing ectopic DNA methylation at gene bodies	[55, 56]
ROS1	AT2G36490	DNA glycosylase	Demethylates DNA	[60, 62]
DML2	AT3G10010	DNA glycosylase	A homolog of ROS1	[59, 96]
DML3	AT4G34060	DNA glycosylase	A homolog of ROS1	[59, 96]
DME	AT5G04560	DNA glycosylase	A homolog of ROS1 that is active in central cells	[69–71]
ROS4	AT3G14980	MBD domain-containing Histone H3 acetyltransferase	Functions in DNA demethylation at some ROS1 target loci	[61]
ROS3	AT5G58130	RNA-binding protein	Functions in DNA demethylation	[66]
ZDP	AT3G14890	Phosphoesterase	Functions downstream of ROS1 in DNA demethylation	[63]
ATXRCC1	AT1G80420	DNA repair protein	Functions in DNA demethylation	[65]