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dna methylation

23794 relationships annotated with this phrase. Showing first 500 of 23794.
Source entity Relationship Target entity Species
chicory genome is comparable to maize genome methylation
OX-dml lines induce less DMRs Populus tremula × Populus alba
14 L. bicolor genes with DMRs are both DMGs and DMPs and common to fungi colonizing RNAi-ddm1 and OX-dml lines Laccaria bicolor; Populus tremula × Populus alba
RNAi-ddm1 lines display more abundant differentially methylated genes and DMPs Populus tremula × Populus alba
transposable elements and intergenic regions in L. bicolor genome are most represented in all methylation contexts Laccaria bicolor
RNAi-ddm1 lines display DMCs and DMRs mostly found in CHG context Populus tremula × Populus alba
120 genes and 1441 transposable elements (TEs) are differentially methylated in fungal genome Laccaria bicolor
(MAT3, AT2G36880) mutant reduced DNA methylation Arabidopsis thaliana
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant reduces to a lesser extent CG methylation Arabidopsis thaliana
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) (CMT2, AT4G19020) (CMT3, AT1G69770) and RdDM can methylate the same locus at the same time
hypomethylated poplar lines showed differential gene and TE methylation Populus tremula × Populus alba
L. bicolor genome from ectomycorrhizas formed on OX-dml poplar lines exhibits 28521 CpG, 47 CHG, and 93 CHH DMCs Laccaria bicolor; Populus tremula × Populus alba
(CMT2, AT4G19020) and (CMT3, AT1G69770) proteins are not solely responsible for increase in DNA methylation associated with high CO2 levels Arabidopsis thaliana
sulfamethazine treatment causes reduction of DNA methylation levels Arabidopsis thaliana
silencing of Tnt1 was associated with non-CG site methylation Arabidopsis thaliana
alteration of (de)methylation machinery in poplar induces methylome remodeling of fungal genome Laccaria bicolor; Populus tremula × Populus alba
(ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) (decreased in DNA Methylation 1) provides access to DNA for DNA methyltransferase
(AtSAM1, MAT1, METK1, SAM-1, SAM1, AT1G02500) mutant reduced DNA methylation Arabidopsis thaliana
DNA methylation marks on cytosine bases influence gene expression
RNAi lines for (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) knockdown (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) (decreased in DNA Methylation 1) Populus tremula × Populus alba
plants present symmetric CG and CHG methylation
180-bp CEN is independent of RNA-directed DNA methylation (RdDM) pathway Arabidopsis thaliana
idn2-3 fdm1-1 idp2-1 fdm3-2 fdm4-2 fdm5-2 sextuple mutations result in minor changes in DNA methylation Arabidopsis thaliana
CG methylation in genes that exclude (ATNACK2, NACK2, TES, AT3G43210) or repeats mainly occurred in gene bodies Arabidopsis thaliana
gene body methylation is found in about a third of expressed genes Arabidopsis thaliana
two copies of repeat sequences are sufficient for DNA methylation recruitment Arabidopsis thaliana
decreased S-adenosylmethionine (SAM) accessibility to methyltransferases mostly reduced CHH methylation Arabidopsis thaliana
(DMT7, DRM2, AT5G14620) was down-regulated in Chromatin Charting Lines (CCLs) Arabidopsis thaliana
gene adenines only 5.94% were methylated 6mA methylation level Ficus carica
11,838 3′-UTRs 1714 presented 4mC site Ficus carica
RNA POLYMERASE V ( (POL, AT2G46920) V) functions are independent of DRM2-dependent de-novo cytosine methylation Arabidopsis thaliana
cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1, AT3G12290) mutation leads to DNA hypomethylation Arabidopsis thaliana
TSIs (transcriptionally silent information sites) are independent of RNA-directed DNA methylation (RdDM) pathway Arabidopsis thaliana
180-bp CEN is regulated by DNA methylation Arabidopsis thaliana
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant displayed less CHH methylation in short (ATNACK2, NACK2, TES, AT3G43210) than (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) Arabidopsis thaliana
non-repeated SINE-related sequence is sufficient for epigenetic silencing of (FWA, HDG6, AT4G25530) by DNA methylation Arabidopsis thaliana
SAM-dependent methyltransferases transfer methyl group to DNA
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant mainly reduces CHG and CHH methylation Arabidopsis thaliana
imprinted genes remain methylated throughout the lifecycle of the plant Arabidopsis thaliana
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant decreases CHH DNA methylation Arabidopsis thaliana
decreased S-adenosylmethionine (SAM) accessibility to methyltransferases mostly reduced CHG methylation Arabidopsis thaliana
repeat region and close neighboring region of full-length (AGL37, PHE1, AT1G65330) transgene is de-novo methylated by (DRM1, AT5G15380) (DMT7, DRM2, AT5G14620) methyltransferases Arabidopsis thaliana
Frequency distribution histograms of significant methylation differences indicated that CHG and CHH methylation dramatically decreased in (AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) Arabidopsis thaliana
piRNAs contribute to de novo DNA methylation in the mouse germline Mus musculus
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant shows large decreases in CHG methylation Arabidopsis thaliana
non-repeated SINE-related sequence is likely to have reduced stability of DNA methylation Arabidopsis thaliana
CHH hypo-differentially methylated regions (DMRs) were enriched at miniature inverted-repeat (ATNACK2, NACK2, TES, AT3G43210) (MITEs) Oryza sativa
CHH hypo-DMRs were located in genic regions Oryza sativa
(DML3, AT4G34060) mutation leads to high DNA methylation
21,029 genes showed both 4mC and 6mA methylation sites Ficus carica
5-methylcytosine (5mC) occurs in CG sites
CHH methylation largely decreased in (AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) compared with L119 Arabidopsis thaliana
(ATNRPD1B, DMS5, DRD3, NRPD1B, NRPE1, AT2G40030) and (CHR35, DMS1, DRD1, AT2G16390) mutants do not cause losses of methylation at 180-bp centromere repeats Arabidopsis thaliana
(ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) mutant showed greater reductions in CG methylation compared with (AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) in gene body regions Arabidopsis thaliana
(CMT3, AT1G69770) (CHROMOMETHYLASE3) methylates CpNpG sites Arabidopsis thaliana
Dnmt3 class of DNA methyltransferases are responsible for de novo methylation Mus musculus
KRYPTONITE ( (KYP, SDG33, SUVH4, AT5G13960) also known as ), (SGD9, SUVH5, AT2G35160) and (SDG23, SUVH6, AT2G22740) function in a locus-specific manner to undergo cytosine methyltransferase3 (CMT3, AT1G69770) -mediated non-CG DNA methylation Arabidopsis thaliana
RNA-directed DNA methylation (RdDM) pathway catalyzes de novo cytosine methylation
SMRT sequencing analysis observed 1,515,639 4mC sites Ficus carica
methylated sites found 41% in CHG sequence logo Ficus carica
8,052 genes represented 21.27% of all genes Ficus carica
11,528 5′-UTRs 1365 represented 11.84% of 5′-UTRs Ficus carica
4mC modification levels were higher compared with 6mA modifications Ficus carica
4mC and 6mA profiles at gene and TE levels found 69.58% and 66.03% of 4mC and 6mA sites over TE bodies Ficus carica
SDG728 down-regulation led to decrease in DNA methylation of Tos17 locus
(ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) and (ATSWI3B, CHB2, SWI3B, AT2G33610) influence DNA methylation landscape Arabidopsis thaliana
genes with two exons compared with genes with higher exon number Ficus carica
transcription of TS–GUS locus and LINEs was drastically induced under conditions when systematic analysis did not reveal pronounced changes in symmetric (CG and CHG) and asymmetric (CHH) cytosine methylation Arabidopsis thaliana
MITEs in the promoter of IPA1 are not differentially methylated in WT and osnrpd1-1 Oryza sativa
genes with two exons seem more prone to 4mC modification Ficus carica
DNA methylation levels between generative cell (GC) and its daughter sperm cells (SCs) did not show significant difference Solanum lycopersicum
vegetative cell (VC) had 2,205 hypermethylated CHH differentially methylated regions (DMRs) Solanum lycopersicum
simultaneous inhibition of H1 histone variant gene expression by RNAi induces DNA hypo or hypermethylation Arabidopsis thaliana
hypo-DMRs in (ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) and (ATSWI3B, CHB2, SWI3B, AT2G33610) are significantly overlapped in CHG methylation context Arabidopsis thaliana
11,838 3′-UTRs 1594 presented 6mA site Ficus carica
methylated sites found 38% in CG sequence logo Ficus carica
6mA methylation sites found 9% for GAGG sequence logo Ficus carica
11,528 5′-UTRs 643 showed both 4mC and 6mA sites Ficus carica
RNA-directed DNA methylation (RdDM) mediates initiation and maintenance of DNA methylation Arabidopsis thaliana
salinity treatment produces no prominent effect on global DNA methylation or its distribution along chromosomes Arabidopsis thaliana
non-CG methylation in sperm cells (SCs) is lower in vegetative cell (VC) Oryza sativa
tomato had higher methylation level in all three contexts (CG, CHG and CHH) than Arabidopsis Solanum lycopersicum; Arabidopsis thaliana
DNA methylation-mediated expression variation in starch synthesis genes was uncovered dynamics Zea mays
MITE #1 nested in the downstream region of (D14, AT3G03990) was hypomethylated in osnrpd1-1 / 2 Oryza sativa
Arabidopsis jmjC gene is involved in genic DNA methylation Arabidopsis thaliana
(ATSWI3B, CHB2, SWI3B, AT2G33610) and (ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) influence DNA methylation landscape Arabidopsis thaliana
4mC and 6mA profiles at gene and TE levels found 15.22% and 17.13% of 4mC and 6mA sites in genic regions Ficus carica
CHG methylation showed similar methylation pattern to CG but had a higher proportion of hypomethylation Phyllostachys edulis
11,838 3′-UTRs 1368 represented 11.55% of 3′-UTRs Ficus carica
6mA profile showed most represented modifications could not be associated to specific motif Ficus carica
methylation in CHH context is catalyzed by specific family of DNA methyltransferases
11,838 3′-UTRs 1368 presented both methylation sites Ficus carica
DNA methylation is carried out by DNA methyltransferases
4mC and 6mA modifications shared very similar distribution profile Ficus carica
7,531 genes represented 19.9% of all genes Ficus carica
hypo-DMRs in (ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) and (ATSWI3B, CHB2, SWI3B, AT2G33610) are significantly overlapped in CG methylation context Arabidopsis thaliana
N6-methyladenine (N6mA) is present in fig (Ficus carica L.) genes Ficus carica L.
hypo-DMRs in (ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) and (ATSWI3B, CHB2, SWI3B, AT2G33610) are significantly overlapped in CHH methylation context Arabidopsis thaliana
(AGO4, OCP11, AT2G27040) mutants show genome-wide methylation changes Arabidopsis thaliana
ago4-2 mutant shows 191 CHH hypomethylated differentially methylated regions (DMRs) Arabidopsis thaliana
hypermethylated CHH differentially methylated regions (DMRs) in vegetative cell (VC) marked 293 genes and 2,336 transposable elements (TEs) Solanum lycopersicum
generative cell (GC) had 5,993 hypomethylated CHG differentially methylated regions (DMRs) Solanum lycopersicum
leaf had higher correlation with microspore at CG and CHG context than other pollen cell types Solanum lycopersicum
differentially methylated region (DMR)-marked genes were related to CG and CHG methylation rather than CHH methylation Solanum lycopersicum
de novo CHH methylation in (ATNACK2, NACK2, TES, AT3G43210) is maintained during post-embryogenesis independently of siRNAs
21/22-siRNAs in vegetative cells might counteract targeted DNA hypomethylation at transposable elements (TEs) Arabidopsis thaliana
N6-methyladenine (N6mA) is present in transposable elements Ficus carica L.
5-methylcytosine (5mC) occurs in CHG sites
DNA methylation status is maintained by DNA demethylases
CYTOSINE METHYLTRANSFERASE 3 (CMT3, AT1G69770) was down-regulated in Chromatin Charting Lines (CCLs) Arabidopsis thaliana
CG context methylation is higher in sperm cell (SC) lineage Solanum lycopersicum
SlDML4 (Solyc03g123440.3) high expression in generative cell (GC) is consistent with decreased CHG methylation level in generative cell (GC) Solanum lycopersicum
few genes were simultaneously marked by hyper- and hypomethylation differentially methylated regions (DMRs) Solanum lycopersicum
tDNA Pro clusters present elevated 5 mC levels compared to the dispersed tDNA Pro population Arabidopsis thaliana
animals largely display CG methylation
methylation levels of CG, CHG, and CHH in (AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) were lower than levels of CG (25.2%), CHG (8.2%), and CHH (2.4%) in L119 Arabidopsis thaliana
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant reduced CG methylation in gene body regions by ∼2.5% Arabidopsis thaliana
FIS PcG complex targets and methylates (AGL38, PHE2, AT1G65300)
plant genome methylation is controlled by new/novel DNA methylation
ago4-3 specific DMRs show similar methylation level in ago4-2 as in wild type Arabidopsis thaliana
hypomethylated CHH differentially methylated regions (DMRs) in generative cell (GC) compared with VC marked 1,421 LTR/Gypsy and 962 LTR/Copia elements Solanum lycopersicum
null mutation in (MOS1, AT4G24680) results in altered DNA methylation in genomic region upstream of (BAL, SNC1, AT4G16890) Arabidopsis thaliana
Hypermethylation in embryos observed in chickpea Cicer arietinum
soybean embryos derived from somatic cells show hypermethylation Glycine max
DNA methylation may be passively erased during replication
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) is Arabidopsis homolog of the vertebrate Dnmt1 methyltransferase Arabidopsis thaliana
6mA motif analysis found CAAG motif Ficus carica
6mA motif analysis found ACCT motif Ficus carica
genes with both modified bases in all GO categories appeared no correlation between gene function and methylation Ficus carica
local differential methylation induced by Fe-deficiency is not mediated by known methyltransferases and canonical RdDM components Oryza sativa
DMRs exhibiting strongest reduction in DNA methylation (>10%) correspond to TE genes and TE fragments Arabidopsis thaliana
(ATNACK2, NACK2, TES, AT3G43210) in heterochromatic regions are heavily methylated DNA methylation
DNA methylation occurs in symmetric CG context
DNA methyltransferases catalyze addition of a methyl group on cytosines
PMC methylome data shows lower CHH methylation compared to sporophytic tissues Arabidopsis thaliana
(DML3, AT4G34060) (DEMETER-LIKE 3) is DNA demethylase
CG methylation in sperm cells (SCs) is higher than CG methylation in vegetative cell (VC) Oryza sativa
Fe-deficiency results in widespread hypermethylation, especially for the CHH context Oryza sativa
DNA methylation status is maintained by DNA methyltransferases
DNA methylation shows major changes in CHH methylation Arabidopsis thaliana
differentially methylated regions (DMRs) less than 20% are located in protein-coding genes, non-coding genes or pseudogenes Arabidopsis thaliana
CHG context methylation is higher in microspore Solanum lycopersicum
vegetative cell has lower levels of CG Arabidopsis thaliana
DNA methylation patterns are mitotically inherited during vegetative growth
easiRNAs accumulate in mutants with reduced DNA methylation Arabidopsis thaliana
EgDRM1 is most similar to NtDRM1 of tobacco Elaeis guineensis; Nicotiana tabacum
more highly expressed METI-like gene in carrot plays dominant role in maintaining DNA methylation Daucus carota
fast-growing calli show average decrease in methylation level of 19.3% Elaeis guineensis
CG methylation levels in microspore and sperm cells (SCs) are retained in microspore and sperm cells (SCs) Arabidopsis thaliana
Hypermethylation in embryos observed in Arabidopsis Arabidopsis thaliana
DNA methylation occurs in CG, CHG, and CHH contexts
catalytic loop of (DMT7, DRM2, AT5G14620) intercalates into DNA
rice with GC-rich clusters in their genomes show higher non-CG methylation in these regions Oryza sativa
SMRT sequencing analysis focused on 4mC and 6mA modifications Ficus carica
4mC and 6mA modification levels in (ATNACK2, NACK2, TES, AT3G43210) were three-fold those of genes Ficus carica
ago4-2 allele encodes AGO4 protein with lower influence on methylation levels than wild type Arabidopsis thaliana
hypomethylated CHG differentially methylated regions (DMRs) in generative cell (GC) compared with VC marked 676 genes and 5,949 transposable elements (TEs) Solanum lycopersicum
cytosine methylation in CHG, CG, and CHH was high during early and late phases of endosperm development Zea mays
CG and CHG methylation contexts remain unaffected in RdDM mutants compared with wild type Arabidopsis thaliana
infection of diploid wheat Aegilops tauschii with the biotrophic pathogen Blumeria graminis f. sp. tritici (Bgt) reduces CHH methylation in stress response genes Aegilops tauschii
increased CHH methylation levels at specific loci such as (ATNACK2, NACK2, TES, AT3G43210) in sperm cells is associated with reduced CG methylation levels in the corresponding loci in vegetative cells Arabidopsis thaliana; Oryza sativa
environmental stress causes hyper- and hypo-DNA methylation genome-wide
WUSCHEL (PGA6, WUS, WUS1, AT2G17950) and ARGONAUTE 4 (AGO4, OCP11, AT2G27040) interaction promotes DNA methylation
(AtDRM1, DRM1, DYL1, AT1G28330) mutants do not show loss of asymmetric methylation Arabidopsis thaliana
ago4-2 mutant produces (AGO4, OCP11, AT2G27040) weak allele Arabidopsis thaliana
methylation gain between non-stress and stress conditions shows no differences for (ATNRPD1B, DMS5, DRD3, NRPD1B, NRPE1, AT2G40030) ago4-2 and ago4-3 mutants Arabidopsis thaliana
CG methylation levels decreased from microspore to vegetative cell (VC) Arabidopsis thaliana
hypomethylated CHG differentially methylated regions (DMRs) in generative cell (GC) compared with VC marked 2,619 LTR/Gypsy and 1,792 LTR/Copia elements Solanum lycopersicum
hypermethylated CHH differentially methylated regions (DMRs) in tomato generative cell (GC) overlapped with hypomethylated CG differentially methylated regions (DMRs) in VC Solanum lycopersicum
DNA methylation pattern is non-random Arabidopsis thaliana
met1-3 mutant has severely reduced global CG methylation Arabidopsis thaliana
targeted DNA hypomethylation at transposable elements (TEs) is conserved mechanism in different plant species
(AGO4, OCP11, AT2G27040) and (AGO6, AT2G32940) proteins show very low redundancy function Arabidopsis thaliana
phosphate starvation leads to methylation changes preferentially in TE located close to genes strongly up-regulated Oryza sativa
highly methylated CG and CHG in sperm is common feature of the MiMC and microspore Arabidopsis thaliana
CHROMOMETHYLASE 2 (CMT2, AT4G19020) catalyze methylation at CHH contexts Arabidopsis thaliana
generative cell (GC) had 6,377 hypomethylated CHG differentially methylated regions (DMRs) compared with VC Solanum lycopersicum
transposable elements (TEs) marked by CHG differentially methylated regions (DMRs) hypomethylated in generative cell (GC) tend to mark different (ATNACK2, NACK2, TES, AT3G43210) Solanum lycopersicum
leaf had relatively few differentially methylated sites (DMSs) compared with SC lineage Solanum lycopersicum
mutation in (MSA1, SHM7, AT1G36370) resulted in a global reduction of DNA methylation levels Arabidopsis thaliana
expressed and repressed transposable elements (TEs) gain CHH methylation in a similar manner CHH methylation Oryza sativa
histone H2A variants are important to DNA methylation dynamics
24-nucleotide siRNAs from repetitive sequences and (ATNACK2, NACK2, TES, AT3G43210) trigger DNA methylation at CG, CHG, and CHH sites
HinP1I may not cleave all recognition sites in ptDNA due to sensitivity to cytosine methylation
N6-methyladenine (N6mA) sites led to identification of ANHGA motif Ficus carica L.
adenine modification in gene bodies similar levels for ANHGA and GAGG motifs Ficus carica
5-methylcytosine (5mC) occurs in CHH sites
decrease in CG methylation levels in pericentromeric regions is attributed to transcriptional repression of (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160)
bisulphite sequencing was carried out to clarify de novo DNA methylation status in target and flanking regions Nicotiana benthamiana
(ATNRPD1B, DMS5, DRD3, NRPD1B, NRPE1, AT2G40030) mutant shows 1481 CHH hypomethylated differentially methylated regions (DMRs) Arabidopsis thaliana
differentially methylated regions (DMRs) are located within transposable elements (TE genes and fragments) Arabidopsis thaliana
CHH context methylation is highest in vegetative cell (VC) Solanum lycopersicum
vegetative cell (VC) had four hypomethylated CG differentially methylated regions (DMRs) Solanum lycopersicum
hypermethylated CHH differentially methylated regions (DMRs) in generative cell (GC) marked 796 LTR/Gypsy and 577 LTR/Copia elements Solanum lycopersicum
(ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) is involved in DNA methylation at loci that are not targeted by RdDM Arabidopsis thaliana
genes are often methylated genic methylation
DECREASED DNA METHYLATION 1 (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) is required for CG methylation Arabidopsis thaliana
ago4-2 specific DMRs present lower methylation than wild-type DMRs in ago4-3 and (ATNRPD1B, DMS5, DRD3, NRPD1B, NRPE1, AT2G40030) genotypes Arabidopsis thaliana
DNA methylation surrounding primary miRNAs was examined for lowly expressed and silent miRNAs Zea mays
genetic analyses are revealing patterns and dynamic changes of DNA methylation in plants Arabidopsis thaliana
Hypermethylation in embryos observed in soybean Glycine max
abiotic and biotic stress can alter DNA methylation patterns
CG sites in 5′-flanking region of empty control plants showed methylation of approximately 80% Nicotiana benthamiana
DNA deformation mechanism of (DMT7, DRM2, AT5G14620) promotes (DMT7, DRM2, AT5G14620) methylation on CHH substrates
sequences flanking retroelements (class I) were methylated methylation Oryza sativa
(AGO4, OCP11, AT2G27040) (AGO6, AT2G32940) mutants show genome-wide methylation changes Arabidopsis thaliana
246 genes were jointly marked by CG and CHG hypomethylation differentially methylated regions (DMRs) Solanum lycopersicum
chromatin-remodeling factor (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) allows access by methyltransferases
long, heterochromatic transposable elements (TEs) accumulate CHH-methylation predominately at the edges of the TE Arabidopsis thaliana
global CHH methylation levels increase in heterochromatin
ANHGA motif is prevalent in fig (Ficus carica L.) genes Ficus carica L.
1,228 genes showed 6mA site only Ficus carica
condensed methylation regions were not observed within Pro35s promoter in roots of line 1b Arabidopsis thaliana
EgCMT1 transcript levels increase in variant fast-growing calli Elaeis guineensis Jacq.
genome-wide hypomethylation link with elevated expression of EgMET1 and EgCMT1 in fast-growing callus Elaeis guineensis
(CMT2, AT4G19020) retains CHH methylation Arabidopsis thaliana
methylation is not static static state Arabidopsis thaliana
some transposable element (TE) families are associated with DNA methylation that spreads beyond their boundaries following transposition Zea mays
methylation spreading associated with transposable elements (TEs) has been shown in other species
cytosine methylation (5mC) occurs in CG, CHG, and CHH contexts Arabidopsis thaliana
DNA methylation in three DNA contexts (CG, CHG and CHH) exhibit different dynamic patterns during development Arabidopsis thaliana; Oryza sativa; Solanum lycopersicum
large, TE-rich genomes are more extensively methylated than smaller, more compact plant genomes
H3K9me2 recruits CHROMOMETHYLASE 2 (CMT2, AT4G19020) and (CMT3, AT1G69770) Arabidopsis thaliana
rice sperm cells show lower non-CG methylation Oryza sativa
chromomethylases control non-CG methylation
rice egg cells exhibit enriched CHH and CHG methylation on (ATNACK2, NACK2, TES, AT3G43210) Oryza sativa
(AtROS1, DML1, ROS1, AT2G36490) (REPRESSOR OF SILENCING 1) is DNA demethylase
RdDM-defective mutants (ago4-3, ago4-2, nrpe1-11) show no strong differences in global proportion of methylated cytosines compared with wild type Arabidopsis thaliana
(ACG1, ATMSI4, FVE, MSI4, NFC04, NFC4, AT2G19520) and (ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) may affect DNA methylation via different mechanisms Arabidopsis thaliana
hypomethylated status is partially restored by RdDM-independent pathway
Arabidopsis thaliana PMC has higher CG methylation Arabidopsis thaliana
methyltransferase 1 (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) mutant exhibits decrease of CpG methylation Arabidopsis thaliana
DNA methylation level in 35S promoter region in silenced root was similar to DNA methylation level in silenced leaf tissue Nicotiana benthamiana
methylated cytosines in CHH context account for 5.8% in male flowers and 3.6% in female flowers Populus trichocarpa
miRNA genes are extensively methylated in plants
histone H1 is major regulator of Arabidopsis DNA methylation Arabidopsis thaliana
release of TGS in ros1rpa2 cannot be correlated with loss of cytosine methylation Arabidopsis thaliana
DNA methylation occurs at CNG residues Arabidopsis thaliana
methylated cytosines in symmetrical contexts (CG and CHG) are maintained by methyltransferases (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) and (CMT3, AT1G69770) Arabidopsis thaliana
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) and (CMT3, AT1G69770) unable to methylate completely demethylated paternal alleles of FWA-GFP Arabidopsis thaliana
complete silencing of FWA-GFP observed in more than 25% embryos implies RdDM would methylate CG, CHG, and CHH de novo in the embryo Arabidopsis thaliana
mutation of methyltransferases in some crop species can be lethal
(chr31, CLSY3, AT1G05490) and (CHR40, CLSY4, AT3G24340) tend to mediate RdDM at (CMT2, AT4G19020) loci Arabidopsis thaliana
knockout of all four demethylases exhibits extensive DNA hypermethylation on genes and (ATNACK2, NACK2, TES, AT3G43210) Arabidopsis thaliana
embryo hypermethylation is directed in a cell-autonomous manner Brassica rapa
establishment of CHGm on PEGs depends on FIS-PRC2 activity
allosteric activation of ZMET2 stimulates binding of ZMET2 to mCHG substrates
CHG sites in target promoter region showed methylation of approximately 80% Nicotiana benthamiana
Suppressor–mutator (Spm)-encoded protein TnpA is associated with DNA hypomethylation
(DMT7, DRM2, AT5G14620) establishes CHH methylation Arabidopsis thaliana
DRM class is DNA methyltransferase family Elaeis guineensis Jacq.
EgMET1 transcript levels increase in variant fast-growing calli Elaeis guineensis Jacq.
DNA methyltransferases (DNMTs) mediate cytosine methylation
oil palm (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) is more closely related to methyltransferases from monocotyledonous plants Elaeis guineensis
DRM and CMT methyltransferases in Arabidopsis are partially redundant Arabidopsis thaliana
EgCMT1 shows high similarity to DNMTs identified in other plant species Elaeis guineensis
DNA METHYL TRANSFERASE 1 (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) is DNA methylation writer Arabidopsis thaliana
hypomethylated CHH differentially methylated regions (DMRs) in generative cell (GC) compared with VC marked 584 genes and 3,469 transposable elements (TEs) Solanum lycopersicum
hypomethylated CHH differentially methylated regions (DMRs) marked 584 genes Solanum lycopersicum
some regions of the genome are rarely methylated methylation Arabidopsis thaliana
Certain loci in PMC are hypermethylated Arabidopsis thaliana
DNA methylation may be actively removed by DNA glycosylases
recognition of substrates underpinned by DNA deformation has strong implications in establishment and maintenance of sequence-specific DNA methylation in plants
embryogenic cells or germline cells contain hypomethylated DNA
negligible methylation level in 3′-flanking region was almost equivalent to methylation level obtained with empty control Nicotiana benthamiana
DNA methylation at the 5-position of cytosine yields 5-methylcytosine
higher expression levels of methyltransferases and RdDM genes in roots indicates that methyltransferases and RdDM play important role in difference of methylation level between tissues Oryza sativa
ago4-2 mutant shows small methylation decrease compared with ago4-3 mutant Arabidopsis thaliana
DNA methylation occurs in cytosine bases of all three sequence contexts: CG, CHG and CHH
DNA methylation occurs in symmetric CHG context
endosperm demethylation does not show clear correlation with CHH hypermethylation in embryos Brassica rapa
non-CG contexts tend to have cytosines and adenine Populus tomentosa
loss of H1 causes genome-wide hypermethylation ascomycete fungi
somatic organs like leaves show a decrease in CG methylation levels in pericentromeric regions
(CMT2, AT4G19020) specifically functions in CHH context
rosette and cauline leaves exhibit lower non-CG methylation levels
bacterial N4-cytosine methyltransferase (DN4MT1a) uniquely methylates majority of Marchantia genome Marchantia polymorpha
carrot genome encodes two METI-like proteins Daucus carota
de novo insertions near maternally expressed genes led to persistent DNA hypomethylation Arabidopsis thaliana
methylated promoters of miRNA genes in andromonoecious poplar most frequently methylated at ~90–96% Populus trichocarpa
met1-3 mutation shows complete elimination of CG methylation from AtSN1 Arabidopsis thaliana
dynamic changes in DNA methylation require the actions of both DNA methyltransferases and demethylases
pMET1-MET1:RFP fusion protein complemented loss of function of (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) Arabidopsis thaliana
reduced expression of DNA methyltransferases accounts for low levels of DNA methylation in endosperm Arabidopsis thaliana
RNA-directed DNA methylation (RdDM) pathway requires short interfering RNAs Arabidopsis thaliana
(DRM1, AT5G15380) and (DMT7, DRM2, AT5G14620) silences loci sensitive to DNA methylation Arabidopsis thaliana
absence of H3K4me alone is insufficient to trigger DNA methylation Arabidopsis thaliana
AtMET1 is expressed at much higher level than other members of this gene family Arabidopsis thaliana
Mutation of the (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) chromatin remodeler simultaneously disrupts maintenance of DNA methylation Arabidopsis thaliana
small interfering RNA (siRNA)-directed pathway is responsible for de novo DNA methylation in plants plants
histone h1 triple mutant endosperm has 64% methylated cytosine in maternal (EMB173, FIS1, MEA, SDG5, AT1G02580) promoter Arabidopsis thaliana
re-methylation is region-specific but random with respect to individual CG targets Arabidopsis thaliana
nodular-compact calli serve as control for fast-growing calli methylation comparison Elaeis guineensis
plant genomes encode three well-characterized classes of DNMTs
oil palm (BICAT2, CMT1, AT4G13590) is more closely related to methyltransferases from monocotyledonous plants Elaeis guineensis
single mutants of DRM and CMT methyltransferases have no phenotype Arabidopsis thaliana
immature 'mantled' inflorescences show significant hypomethylation of genomic DNA Elaeis guineensis
more highly expressed METI-like gene in rice plays dominant role in maintaining DNA methylation Oryza sativa
(IDN2, RDM12, AT3G48670) demonstrates mild defects in DNA methylation control Arabidopsis thaliana
methylated gene bodies in female flowers significantly higher than in male flowers Populus trichocarpa
35S–GFP DNAs were at least partially methylated in GFP-silenced or partitioned-silenced regions
wild-type shows heavy methylation at CpG sites Arabidopsis thaliana
113 methylated miRNA genes were identified in andromonoecious poplar Populus trichocarpa
miRNA genes 113 (~28.2% of all known miRNA genes of plants) are methylated in poplar Populus tomentosa
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) mutation eliminates CG methylation Arabidopsis thaliana
AtMETI is main maintenance methyltransferase targeting symmetric CpG dinucleotides Arabidopsis thaliana
methylated gene bodies in andromonoecious poplar most frequently methylated at ~31.5–48.5% Populus trichocarpa
(AtELP2, ELP2, AT1G49540) mutant shows reduced methylation frequency in (CYC1, CYCB1, CYCB1;1, AT4G37490) promoter cytosines Arabidopsis thaliana
up-regulation of CYCLIN B1 (CYC1, CYCB1, CYCB1;1, AT4G37490) in the (AtELP2, ELP2, AT1G49540) mutant may reflect reduced level of DNA methylation in the promoter and/or coding region of (CYC1, CYCB1, CYCB1;1, AT4G37490) Arabidopsis thaliana
loss of H1 reduces methylation at specific loci mouse
conserved motifs that comprise the catalytic domain of DRM have undergone circular permutation with respect to other DNMTs
one METI-like gene in carrot is more highly expressed than the other METI-like gene Daucus carota
(AtDRM2, DAP2, DRM2, AT2G33830) mutants show loss of asymmetric methylation Arabidopsis thaliana
loci demethylated by (AtROS1, DML1, ROS1, AT2G36490) accumulate DNA methylation Arabidopsis thaliana
extensive two-wave methylation reprogramming occurs in Marchantia polymorpha sperm cells Marchantia polymorpha
DNA methyltransferases are primary genetic factors contributing to methylation variation in plants
DNA methylation in 3′-flanking region did not increase Nicotiana benthamiana
(AtROS1, DML1, ROS1, AT2G36490) acting differently in different cells may contribute to a variety of methylation patterns Arabidopsis thaliana
developing embryos experience active de novo DNA methylation by the RdDM pathway Arabidopsis thaliana
amiTEK show reduced DNA methylation at CG, CNG, and CHH in (FWA, HDG6, AT4G25530) tandem repeats Arabidopsis thaliana
nearly all CNG targets of (KYP, SDG33, SUVH4, AT5G13960) are also (CMT3, AT1G69770) targets Arabidopsis thaliana
rdd mutant displays much stronger DNA hypermethylation than any of the three single demethylase mutants Arabidopsis thaliana
DNA methylation occurs by covalent addition of methyl group to cytosine
fast-growing oil palm calli show significant hypomethylation of genomic DNA Elaeis guineensis
EgMET1 shows high similarity to DNMTs identified in other plant species Elaeis guineensis
Overexpression of a novel splice variant of Dnmt3b has been associated with hypomethylation in tumour cells
'mantled' inflorescences show DNA methylation 7.4% lower than in normal inflorescences Elaeis guineensis
86 genes and 288 transposable elements (TEs) are differentially methylated between WT and hypomethylated lines Populus tremula × Populus alba
DNA methylation occurs in CHG sequence context
(AtELP2, ELP2, AT1G49540) contributes to DNA methylation
nucleosomes are substantial obstacles to DNA methylation
gradual silencing of FWA-GFP indicates DNA methylation takes place in the embryo Arabidopsis thaliana
targets of (CMT3, AT1G69770) (KYP, SDG33, SUVH4, AT5G13960) and (DRM1, AT5G15380) /2 are repeats of all types Arabidopsis thaliana
loss of (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) eliminates CG methylation and substantial fractions of CHG and CHH methylation Arabidopsis thaliana
CG and CHG methylation are depleted near gene ends Zea mays
methylation at CpG sites at (GASA8, AT2G39540) locus was induced in self-pollinated (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) (KYP, SDG33, SUVH4, AT5G13960) plants Arabidopsis thaliana
body methylation regions in (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) mutant frequently gained CNG methylation Arabidopsis thaliana
AtMETI has de novo methylation activity on silenced transgenes Arabidopsis thaliana
histone H3 lysine 9 di-methylation mark directly influences CHG and CHH methylation Arabidopsis thaliana
H1 mutations could have effect on methylation of 5′ direct repeats of (FWA, HDG6, AT4G25530) Arabidopsis thaliana
DNA METHYLTRANSFERASE1 (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) maintains methylation of symmetric CpG residues Arabidopsis thaliana
line 30.4 R4 plants and R2 plants differed when the restriction patterns of the methylation-sensitive enzyme Pst I were compared methylation status Solanum lycopersicum
methylation of AtSN1 was slightly increased in (ATCPSF100, CPSF100, EMB1265, ESP5, AT5G23880) mutant Arabidopsis thaliana
idn2-3 fdm1-1 idp2-1 fdm3-2 fdm4-2 fdm5-2 DNA shows weakly reduced CHG and CG methylation Arabidopsis thaliana
CHH methylation showed higher levels in male flowers compared to female flowers Populus trichocarpa
essentially all methylation in invertebrates is in CG context invertebrates
depletion of Histone H1 increases methylation of some (ATNACK2, NACK2, TES, AT3G43210) Arabidopsis thaliana
knockout mutation of (MEM1, ZC2HC1, AT1G48950) leads to 4519 CG hyper-DMRs Arabidopsis thaliana
PCR following methylation-dependent digestion with McrBC confirmed methylation level of AtCO promoter Arabidopsis thaliana
loss of H1 reduces methylation of euchromatic transposable elements Arabidopsis thaliana
(ATRPA2, ATRPA32A, ROR1, RPA2, RPA32A, AT2G24490) is not required for DNA methylation of the tested loci
(AtROS1, DML1, ROS1, AT2G36490) mutant shows increased methylation at CpXpG and CpXpX sites Arabidopsis thaliana
(AtROS1, DML1, ROS1, AT2G36490) shows more than tripled CpXpX methylation level at (ATGP1, ATYKT61, YKT61, AT5G58060) Arabidopsis thaliana
hypermethylation of endogenous and transgene (COR78, LTI140, LTI78, RD29A, AT5G52310) promoters in (AtROS1, DML1, ROS1, AT2G36490) is not changed by (ATRPA2, ATRPA32A, ROR1, RPA2, RPA32A, AT2G24490) mutation Arabidopsis thaliana
AtDRM1-HsDNMT3A orthology pair is enriched in female gametes of both species Arabidopsis thaliana; Homo sapiens
much stronger bands were observed in fully silenced plants (S-1 and S-2)
(ATGP1, ATYKT61, YKT61, AT5G58060) AtMU1, and AtLINE1-4 have higher levels of methylation in (AtROS1, DML1, ROS1, AT2G36490) mutant than in wild-type Arabidopsis thaliana
methylation patterns of the miRNA172b gene were validated in gynomonoecious poplar Populus trichocarpa
transposable elements (TEs) and gene bodies are preferentially methylated flowering plants flowering plants
35S–GFP DNAs were not methylated in GFP-expressing leaves
methylated regions in protein-coding gene body regions enriched in exons and introns Populus trichocarpa
CG methylation did not differ between female and male flowers Populus trichocarpa
CG methylation mainly located in gene bodies Populus trichocarpa
(AtELP2, ELP2, AT1G49540) is involved in somatic DNA demethylation/methylation Arabidopsis thaliana
methylation in three sequence contexts (CG, CHG, and CHH, where H ≠ G) affects transposable elements (TEs) flowering plants
(AtELP2, ELP2, AT1G49540) mutant shows low methylation level throughout promoter and coding regions of (ABR, PID, AT2G34650) Arabidopsis thaliana
(AtROS1, DML1, ROS1, AT2G36490) mutant plants show large increase in CpG methylation at the (ATM17, M17, AT2G41260) promoter region Arabidopsis thaliana
CHH methylation increased during embryo development Arabidopsis thaliana
(DRM1, AT5G15380) mutant no longer observed impact of CHH methylation Arabidopsis thaliana
Dnmt3 subfamily of DNA methyltransferases can methylate de novo methylation
(AT5G38550) Region 1 showed strong reduction in CHH methylation Arabidopsis thaliana
genes in Arabidopsis are methylated at CpG sites Arabidopsis thaliana
all three groups maintain robust non-CG methylation in (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) and h1met1 Arabidopsis thaliana
idr loci are not essential for DNA methylation of analysed targets Arabidopsis thaliana
(KYP, SDG33, SUVH4, AT5G13960) /suv4h mutant is defective in DNA methylation Arabidopsis thaliana
(AtROS1, DML1, ROS1, AT2G36490) shows increased CpXpX methylation levels at all loci except MEA-ISR Arabidopsis thaliana
AtSN1 and MEA-ISR showed relatively little or no increase in (AtROS1, DML1, ROS1, AT2G36490) mutant plants Arabidopsis thaliana
mechanism of de novo methylation compatible with stable maintenance of epialleles and silenced transgenes across generations Arabidopsis thaliana
CHROMOMETHYLASE3 maintains DNA methylation in the CHG sequence context plants
DNA methyltransferases (DNA methylase) and demethylases target TE sequences Arabidopsis thaliana
active de novo DNA methylation in the developing embryo provides mechanism that accounts for gradual remethylation in successive generations Arabidopsis thaliana
DOMAIN REARRANGED METHYLASE (DRM) is required for de novo DNA methylation in all sequence contexts and maintenance of DNA methylation in CHH context Arabidopsis thaliana
lack of CG methylation in H3K4me2- and H3K4me3-containing regions could be due to active mutual exclusion mechanism or differential localization of DNA methylation and H3K4me2/H3K4me3 Arabidopsis thaliana
three rdd-downregulated genes ( (AtCAPE3, AT4G33720) (CRK40, AT4G04570) (LBD26, AT3G27940) ) showed both increased CG methylation and reduced CHH methylation in rdd in comparison to Col-0 Arabidopsis thaliana
CG sites in Region 1 of (AT5G38550) were almost fully methylated in both rdd and Col-0 Arabidopsis thaliana
bm allele methylation is slightly lower than BM allele methylation of 9.6–25.4% Arabidopsis thaliana
central region of the 2 kb fragment is common target in all lines Arabidopsis thaliana
re-methylation frequencies in transformants are lower in transformants than in lines obtained by genetic crossing Arabidopsis thaliana
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) may be able to enhance (DMT7, DRM2, AT5G14620) activity
DNA methylation occurs at asymmetric cytosines (CNN) Arabidopsis thaliana
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) and (CMT3, AT1G69770) require methylated template Arabidopsis thaliana
DNA methylation of inverted repeat PAI1-PAI4 locus does not require (KYP, SDG33, SUVH4, AT5G13960) Arabidopsis thaliana
targets of methyltransferases include LTR retrotransposons Arabidopsis thaliana
CG methylation is also significantly depleted in H3K4me2- and H3K4me3-containing regions Arabidopsis thaliana
genomic regions free of H3K4me frequently lack DNA methylation Arabidopsis thaliana
methylation at CG site in (AT3G46370) (LRR kinase) was increased upon Fo infection in rdd Arabidopsis thaliana
RNAi is dispensable for DNA methylation by DIM2 Neurospora crassa
gene body methylation (gbM) is concentrated in exons of evolutionarily conserved, stably and constitutively expressed genes plants; invertebrates
met1-3 mutation shows only minor effect on non-CG methylation Arabidopsis thaliana
transposable elements in (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) mutants lose non-CG methylation Arabidopsis thaliana
many other loci are affected primarily in non-CpG contexts Arabidopsis thaliana
control cross endosperm (Col-0 female × RLD male) has 12% methylated cytosine in maternal (EMB173, FIS1, MEA, SDG5, AT1G02580) promoter Arabidopsis thaliana
histone h1 triple mutant endosperm (Col-0 female × L er male) has 55% methylated CpG, 22% CpHpG and 11% CpHpH in maternal 5′ repeat region of (FWA, HDG6, AT4G25530) Arabidopsis thaliana
mutations in histone H1 result in increase in DNA methylation in the (EMB173, FIS1, MEA, SDG5, AT1G02580) promoter Arabidopsis thaliana
methylation level of (CAT2, AT4G35090) C3′ sequence was 4.8, 4.3 and 4.8%, respectively in non-silenced and silenced plants
little or no methylation was found in promoters or coding sequences of (AtWAK1, PRO25, WAK1, AT1G21250) and (PR-5, PR5, AT1G75040) Arabidopsis thaliana
24 nucleotide small RNAs (sRNAs) mediate DNA methylation
mutations in maternal H1 affect methylation status of maternal (EMB173, FIS1, MEA, SDG5, AT1G02580) promoter Arabidopsis thaliana
cell culture may influence global methylation patterns, including transgenes
AtMET1 is the only family member that has been shown to have methyltransferase activity Arabidopsis thaliana
FISH analysis coupled with immunodetection of 5mC revealed heavy DNA methylation at ACR of P. notatum Paspalum notatum
CG methylation includes gene-body methylation Arabidopsis thaliana
R-loops correlate with low DNA methylated regions Homo sapiens; Arabidopsis thaliana
DNA methylation is deposited by DNA methyltransferases such as (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160)
tandem repeats in (FWA, HDG6, AT4G25530) promoter are necessary and sufficient for de-novo DNA methylation Arabidopsis thaliana
other mutant lines showed less pronounced or no differences in DNA methylation at AtMU1 locus Arabidopsis thaliana
Os07g0182900 gene encodes cytosine-5 DNA methyltransferase1 Oryza sativa
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant dramatically decreases CHG methylation Arabidopsis thaliana
CG methylation in (AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) decreased approximately by 9.2% compared to L119 Arabidopsis thaliana
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant showed similar CHG methylation in short (ATNACK2, NACK2, TES, AT3G43210) and CHH methylation in long as (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) Arabidopsis thaliana
DOMAIN REARRANGED METHYLTRANSFERASE 2 (DMT7, DRM2, AT5G14620) catalyzes de-novo cytosine methylation at CHG sites Arabidopsis thaliana
SAMS RNAi transgenic rice lines show reduced DNA methylation Oryza sativa
X 21 X 21 / Y ccat500 Y ccat500 / Z C Z C plants (silenced) show CGN and CHG methylation of Z C at 66 to 85% and 58 to 80%, respectively
physical interaction of (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) with FIS-PRC2 core component (EMB173, FIS1, MEA, SDG5, AT1G02580) suggests mechanistic link between histone methylation pathway and DNA methylation pathway Arabidopsis thaliana
sirton-derived siRNAs may methylate DNA of the host gene Oryza sativa
(AtROS1, DML1, ROS1, AT2G36490) mutation affects some but not other loci Arabidopsis thaliana
active silencing of DNA methylation-sensitive targets reflected by gradual silencing of FWA-GFP Arabidopsis thaliana
reinforcement of DNA methylation pattern on target loci maintains genome stability Arabidopsis thaliana
mutations in histone H1 from maternal parent cause increase in DNA methylation of maternal (EMB173, FIS1, MEA, SDG5, AT1G02580) promoter Arabidopsis thaliana
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) mutant shows CG methylation levels of 0.3%/0.8% Arabidopsis thaliana
Tr2 transformant did not display significant re-methylation Arabidopsis thaliana
P. trichocarpa shoot apical meristematic cells has DNA methylation coverage of approximately 10% coverage Populus trichocarpa
weak (ATSAHH1, EMB1395, HOG1, MEE58, SAH1, SAHH1, AT4G13940) mutation causes reduced whole-genome DNA methylation Arabidopsis thaliana
TSIs (transcriptionally silent information sites) are regulated by DNA methylation Arabidopsis thaliana
SAM (S-adenosylmethionine) is a donor for DNA methylation Arabidopsis thaliana
CHG and CHH methylation decreased to a lesser extent at 35S promoter in (AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) compared with L119 Arabidopsis thaliana
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant shows decreased CG methylation Arabidopsis thaliana
r-CCC4 shows higher CHH methylation levels in transposable elements (TEs)
4mC sites have about 21% within gene regions Casuarina equisetifolia
ZMET2 methyltransferase domain causes deformation of DNA around target cytosine Zea mays
SLM CG methylation in RdDM ( (CHR35, DMS1, DRD1, AT2G16390) (DMT7, DRM2, AT5G14620) and (AtRDR2, RDR2, SMD1, AT4G11130) ) mutant somatic tissues correlates with wild-type somatic tissues
Mutation of (ATDCL3, DCL3, AT3G43920) has a lesser effect on CNN methylation Arabidopsis thaliana
IGN5 shows significantly reduced DNA methylation in null mutant for RNA-dependent RNA polymerase 2 (AtRDR2, RDR2, SMD1, AT4G11130)
solo LTR shows significantly reduced DNA methylation in null mutant for RNA-dependent RNA polymerase 2 (AtRDR2, RDR2, SMD1, AT4G11130)
rdm3-3 mutant reduces methylation levels at AtSN1 to 50.0% at CG sites, 14.3% at CHG, and 1.2% at CHH Arabidopsis thaliana
KRYPTONITE ( (KYP, SDG33, SUVH4, AT5G13960) ), (SGD9, SUVH5, AT2G35160) and (SDG23, SUVH6, AT2G22740) are primary H3K9 methyltransferases Arabidopsis thaliana
(ORTH1, VIM3, AT5G39550) mutant does not affect CG methylation
HISTONE DEACETYLASE 6 (ATHDA6, AXE1, HDA6, HDAC6, RPD3B, RTS1, SIL1, AT5G63110) physically interacts with METHYLTRANSFERASE 1 (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160)
(ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) is required for DNA methylation of transposable elements Arabidopsis thaliana
plant methylation is found in transposable elements (TEs)
(ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) and RdDM affect transposable elements Arabidopsis thaliana
RdDM mostly targets short transposable elements and transposable element edges Arabidopsis thaliana
loss of H1 greatly ameliorates reduction of TE CG methylation in (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) Arabidopsis thaliana
46% (n = 451) of DMS3-ZF loci producing siRNAs were called as differentially hypermethylated regions (hyperDMRs) Arabidopsis thaliana
6mA sites have most two significantly enriched motifs of AMBGA and ARGYA Casuarina equisetifolia
ZMET2 is functional homolog of (CMT3, AT1G69770) Zea mays
SLMs do not overlap with columella DMRs
DNA methylation occurs in CG sequence context Arabidopsis thaliana
sequence-specific DNA binding proteins are used DNA methylation patterning
DOMAINS REARRANGED METHYLTRANSFERASE 2 (DMT7, DRM2, AT5G14620) is major de novo DNA methyltransferase
rdm3-3 mutant shows dramatically reduced DNA methylation at AtSN1 Arabidopsis thaliana
(ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) mutation disrupted CHH methylation
(SDG13, SUVR1, AT1G04050) /2/3/4/5 quintuple mutant does not show additional methylation loss compared with (SDG18, SUVR2, AT5G43990) alone Arabidopsis thaliana
(ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) cooperates with RdDM pathway Arabidopsis thaliana
euchromatic (ATNACK2, NACK2, TES, AT3G43210) with low H3K9me2 lose DNA methylation in h1 plants Arabidopsis thaliana
H1 plants causes heterochromatic TEs to lose less DNA methylation than euchromatic (ATNACK2, NACK2, TES, AT3G43210) Arabidopsis thaliana
mammalian Dnmt3a and Dnmt3L form Dnmt3L-Dnmt3a-Dnmt3a-Dnmt3L tetramer
ZF-SUVH9 targeted methylation in (NRPD1, NRPD1A, POL IVA, SDE4, SMD2, AT1G63020) mutant
paternal FWA-GFP allele ectopically expressed in 50% developing endosperm Arabidopsis thaliana
bisulfite sequencing of six rdd-downregulated genes showed that TE and surrounding sequences are methylated Arabidopsis thaliana
bm allele becomes methylated at overall levels between 7 and 12.8% Arabidopsis thaliana
re-methylation can occur in absence of homologous methylated allele Arabidopsis thaliana
DNA methylation of MAT4-FLAG line was consistently restored to L119 level Arabidopsis thaliana
CHG DNA methylation in Pro35S-NPTII transgene was only moderately reduced in (AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant Arabidopsis thaliana
(AtSAMS3, MAT4, MTO3, SAMS3, AT3G17390) mutant reduces genomic-wide DNA methylation, especially CHG and CHH methylation at pericentromeric heterochromatin regions Arabidopsis thaliana
(LBD26, AT3G27940) showed no change in CG methylation Arabidopsis thaliana
siRNAs might originate from maternal ovule tissues Arabidopsis thaliana
CNG methylation is maintained primarily by CMT3-KYP pathway Arabidopsis thaliana
bisulfite sequencing analysis detected only subtle changes in methylation around the promoter TE sequences upon Fo infection Arabidopsis thaliana
whole-genome bisulphite sequencing identified methylated cytosines Populus trichocarpa
methylated cytosines in male flower libraries account for 14.7% of all covered cytosines Populus trichocarpa
smaller gene size might be main reason for low methylation levels in gene bodies of miRNA genes
(AT5G38550) (jacalin lectin) showed slight reduction in CG and CHG methylation in Col-0 Arabidopsis thaliana
AtDRM1-HsDNMT3A orthology pair encodes de novo DNA methyltransferases Arabidopsis thaliana; Homo sapiens
genes epigenetically silenced by DNA methylation are stably transmitted over several generations Arabidopsis thaliana
targets of methyltransferases include MuDR DNA transposons Arabidopsis thaliana
CG methylation is highly enriched in H3K4me1-containing regions Arabidopsis thaliana
hypermethylated loci in (IBM1, AT3G07610) and (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) mutants show no apparent correlation between (IBM1, AT3G07610) and (ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) mutants Arabidopsis thaliana
bisulfite sequencing PCR (BSP) confirmed methylation level of AtCO promoter Arabidopsis thaliana
(KYP, SDG33, SUVH4, AT5G13960) mutants show loss of non-CpG methylation Arabidopsis thaliana
(ATDDM1, CHA1, CHR01, CHR1, DDM1, SOM1, SOM4, AT5G66750) mutants show loss of DNA methylation at non-CpG sites in (ATNACK2, NACK2, TES, AT3G43210) Arabidopsis thaliana
(ATFOLT1, FOLT1, AT5G66380) DNA methylation affects CHG sites Arabidopsis thaliana
(DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) mutant does not change significantly DNA methylation levels at non-CG targets Arabidopsis thaliana
overall CNN methylation level in non-silenced Col-0 plants was 4.5-5.5%
methylation in genomic target sequence of (CAT2, AT4G35090) was scattered throughout genomic target sequence
METHYLTRANSFERASE1 (DDM2, DMT01, DMT1, MET1, MET2, METI, AT5G49160) is homologous to mammalian DNA methyltransferase DNMT1 Arabidopsis thaliana
knockout mutation of (MEM1, ZC2HC1, AT1G48950) leads to 1793 CHG hyper-DMRs Arabidopsis thaliana
(IBM1, AT3G07610) mutation in Arabidopsis affected DNA methylation level in non-CG cytosine Arabidopsis thaliana
TE body methylation has CG and CHG more abundant than CHH (>80% CG and CHG, >40% CHH) Physcomitrella patens
RLG3 shows broadest pattern with no discernible body peak Physcomitrella patens