Published in Nat Rev Genet on May 01, 2005
Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet (2010) 15.70
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One (2007) 7.34
Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A (2010) 7.30
Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol (2007) 5.86
DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci U S A (2007) 4.55
Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol (2007) 4.29
Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet (2010) 4.27
The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol (2007) 3.70
Active DNA demethylation mediated by DNA glycosylases. Annu Rev Genet (2009) 3.66
RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis. PLoS Genet (2006) 3.41
Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science (2009) 3.33
OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet (2010) 3.23
Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J (2006) 3.19
Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol (2006) 3.09
Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol (2010) 3.02
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet (2011) 2.98
Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell (2010) 2.92
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol (2009) 2.86
Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J (2007) 2.79
Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev (2009) 2.71
Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One (2008) 2.69
Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J (2006) 2.68
Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell (2006) 2.53
Bursts of retrotransposition reproduced in Arabidopsis. Nature (2009) 2.50
Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc Natl Acad Sci U S A (2006) 2.46
Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev (2008) 2.16
An effector of RNA-directed DNA methylation in arabidopsis is an ARGONAUTE 4- and RNA-binding protein. Cell (2009) 2.16
Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant J (2007) 2.11
On the presence and role of human gene-body DNA methylation. Oncotarget (2012) 2.10
Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J (2007) 2.05
VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. Genes Dev (2007) 2.01
Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics (2008) 2.01
An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J (2009) 2.00
Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell (2008) 1.94
Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell (2012) 1.91
Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell (2013) 1.83
An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature (2010) 1.82
ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature (2008) 1.78
Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell (2010) 1.77
Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics (2007) 1.69
Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol (2008) 1.68
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Genome Res (2008) 1.68
DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell (2006) 1.64
Arabidopsis relatives of the human lysine-specific Demethylase1 repress the expression of FWA and FLOWERING LOCUS C and thus promote the floral transition. Plant Cell (2007) 1.64
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS One (2007) 1.60
Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol Cell Biol (2008) 1.58
Transgenerational epigenetic inheritance in plants. Biochim Biophys Acta (2011) 1.58
Viral genome methylation as an epigenetic defense against geminiviruses. J Virol (2008) 1.58
SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet (2008) 1.57
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. PLoS Genet (2010) 1.56
Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet (2008) 1.54
Heritable epigenetic variation among maize inbreds. PLoS Genet (2011) 1.54
Daddy issues: paternal effects on phenotype. Cell (2012) 1.49
Loss of the DNA methyltransferase MET1 Induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana. PLoS Genet (2012) 1.48
A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes Dev (2009) 1.45
Abscisic acid-mediated epigenetic processes in plant development and stress responses. J Integr Plant Biol (2008) 1.44
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations. PLoS One (2011) 1.44
Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genet (2008) 1.43
MATERNALLY EXPRESSED PAB C-TERMINAL, a novel imprinted gene in Arabidopsis, encodes the conserved C-terminal domain of polyadenylate binding proteins. Plant Cell (2008) 1.39
In planta assays involving epigenetically silenced genes reveal inhibition of cytosine methylation by genistein. Plant Methods (2012) 1.38
Concern Enhancement of RNA-directed DNA methylation of a transgene by simultaneously downregulating a ROS1 ortholog using a virus vector in Nicotiana benthamiana. Front Genet (2013) 1.38
DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns. EMBO J (2012) 1.33
Regulation of seed size by hypomethylation of maternal and paternal genomes. Plant Physiol (2006) 1.33
RNA silencing in plants: yesterday, today, and tomorrow. Plant Physiol (2008) 1.32
Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. PLoS Genet (2008) 1.31
Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana. PLoS Genet (2008) 1.30
Recent advances in the structural mechanisms of DNA glycosylases. Biochim Biophys Acta (2012) 1.30
Mapping the genome landscape using tiling array technology. Curr Opin Plant Biol (2007) 1.28
Genome-wide profiling of populus small RNAs. BMC Genomics (2009) 1.28
The impact of Arabidopsis on human health: diversifying our portfolio. Cell (2008) 1.27
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data. Nucleic Acids Res (2010) 1.27
Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA. Nucleic Acids Res (2010) 1.26
A metastable DWARF1 epigenetic mutant affecting plant stature in rice. Proc Natl Acad Sci U S A (2009) 1.26
The roles of polyamines during the lifespan of plants: from development to stress. Planta (2014) 1.26
Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize. Plant Cell (2008) 1.25
Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation. J Virol (2009) 1.25
HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable element silencing in Arabidopsis. Plant Physiol (2011) 1.24
Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J (2010) 1.23
The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics (2008) 1.22
RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics (2012) 1.19
The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. Cell Cycle (2012) 1.14
RNA-directed DNA methylation and demethylation in plants. Sci China C Life Sci (2009) 1.14
Proliferation and cell fate establishment during Arabidopsis male gametogenesis depends on the Retinoblastoma protein. Proc Natl Acad Sci U S A (2009) 1.14
Deficiency in DNA methylation increases meiotic crossover rates in euchromatic but not in heterochromatic regions in Arabidopsis. Proc Natl Acad Sci U S A (2012) 1.13
Genetic interactions between DNA demethylation and methylation in Arabidopsis. Plant Physiol (2007) 1.13
Transcriptionally silenced transgenes in maize are activated by three mutations defective in paramutation. Genetics (2006) 1.12
A robust and sensitive synthetic sensor to monitor the transcriptional output of the cytokinin signaling network in planta. Plant Physiol (2013) 1.12
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics (2012) 1.10
Promoter DNA hypermethylation and gene repression in undifferentiated Arabidopsis cells. PLoS One (2008) 1.09
ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell (2005) 1.09
The allotetraploid Arabidopsis thaliana-Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants. Mol Genet Genomics (2009) 1.08
Molecular regulation of fruit ripening. Front Plant Sci (2013) 1.08
Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.). PLoS One (2013) 1.07
Epigenetic mechanisms of plant stress responses and adaptation. Plant Cell Rep (2013) 1.06
Small RNAs originated from pseudogenes: cis- or trans-acting? PLoS Comput Biol (2009) 1.05
The Functions of RNA-Dependent RNA Polymerases in Arabidopsis. Arabidopsis Book (2011) 1.05
Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants. PLoS Genet (2008) 1.05
Domain structure of the DEMETER 5-methylcytosine DNA glycosylase. Proc Natl Acad Sci U S A (2010) 1.03
Tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum. Plant Physiol (2011) 1.03
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature (2008) 26.78
Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet (2010) 15.70
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell (2006) 15.24
Genetic and functional diversification of small RNA pathways in plants. PLoS Biol (2004) 12.21
ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science (2003) 9.54
Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature (2002) 9.51
Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature (2010) 8.84
UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science (2007) 7.90
Criteria for annotation of plant MicroRNAs. Plant Cell (2008) 7.49
Epigenetic inheritance in plants. Nature (2007) 7.40
Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A (2010) 7.30
Small interfering RNA-induced transcriptional gene silencing in human cells. Science (2004) 7.29
The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol (2008) 6.02
Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet (2006) 5.81
Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A (2002) 5.49
Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol (2002) 5.47
Relationship between nucleosome positioning and DNA methylation. Nature (2010) 5.27
An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell (2006) 5.22
Epigenetic reprogramming in plant and animal development. Science (2010) 5.18
RNA silencing genes control de novo DNA methylation. Science (2004) 5.11
One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science (2003) 5.00
The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell (2006) 4.82
DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci (2002) 4.72
DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell (2002) 4.31
Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol (2007) 4.30
Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol (2003) 4.27
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res (2006) 4.08
Applications of DNA tiling arrays for whole-genome analysis. Genomics (2005) 3.94
Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science (2006) 3.87
Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev (2007) 3.75
The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol (2007) 3.70
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol (2005) 3.54
Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol (2004) 3.54
Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J (2004) 3.51
DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J (2002) 3.50
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol (2011) 3.48
RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis. PLoS Genet (2006) 3.41
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature (2008) 3.28
Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol (2003) 3.11
Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol (2008) 3.10
Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol (2006) 3.09
Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A (2007) 3.05
Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell (2013) 3.02
Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma (2004) 3.00
Dysregulated humoral immunity to nontyphoidal Salmonella in HIV-infected African adults. Science (2010) 2.91
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol (2009) 2.86
Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One (2008) 2.69
Membrane protein architects: the role of the BAM complex in outer membrane protein assembly. Nat Rev Microbiol (2009) 2.52
Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res (2004) 2.28
Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell (2012) 2.19
Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proc Natl Acad Sci U S A (2009) 2.18
Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev (2008) 2.16
Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol (2009) 2.14
A novel dispersin protein in enteroaggregative Escherichia coli. J Clin Invest (2002) 2.14
Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase. J Biol Chem (2004) 2.09
LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc Natl Acad Sci U S A (2006) 2.08
A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J Bacteriol (2010) 2.08
DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol (2012) 2.07
A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol (2010) 1.99
Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes. Mol Microbiol (2008) 1.99
MORC family ATPases required for heterochromatin condensation and gene silencing. Science (2012) 1.97
Salmonella induces a switched antibody response without germinal centers that impedes the extracellular spread of infection. J Immunol (2007) 1.96
The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol (2007) 1.93
Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. PLoS One (2010) 1.90
ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol (2009) 1.85
A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin (2012) 1.82
Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature (2013) 1.82
UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells. Nucleic Acids Res (2008) 1.80
Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes. J Biol Chem (2011) 1.80
Genomic analysis of secretion systems. Curr Opin Microbiol (2003) 1.68
DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A (2012) 1.65
Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature (2010) 1.63
From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis. Nat Rev Microbiol (2012) 1.62
SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet (2011) 1.61
IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat Struct Mol Biol (2009) 1.59
SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet (2008) 1.57
The Pic protease of enteroaggregative Escherichia coli promotes intestinal colonization and growth in the presence of mucin. Infect Immun (2009) 1.55
Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol (2005) 1.55
The porin OmpD from nontyphoidal Salmonella is a key target for a protective B1b cell antibody response. Proc Natl Acad Sci U S A (2009) 1.51
Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc Natl Acad Sci U S A (2014) 1.50
RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee. Proc Natl Acad Sci U S A (2013) 1.49
Loss of the DNA methyltransferase MET1 Induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana. PLoS Genet (2012) 1.48
Plants regenerated from tissue culture contain stable epigenome changes in rice. Elife (2013) 1.48
Epigenetic modifications in plants: an evolutionary perspective. Curr Opin Plant Biol (2011) 1.45
Structure and function of BamE within the outer membrane and the β-barrel assembly machine. EMBO Rep (2011) 1.45
Genome sequence of the emerging pathogen Aeromonas caviae. J Bacteriol (2010) 1.44
A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes Dev (2011) 1.43
Discovery of an archetypal protein transport system in bacterial outer membranes. Nat Struct Mol Biol (2012) 1.41
Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell Stem Cell (2013) 1.40
Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci U S A (2012) 1.39
Regulation and function of Ag43 (flu). Annu Rev Microbiol (2008) 1.37
Weapons of mass destruction: virulence factors of the global killer enterotoxigenic Escherichia coli. FEMS Microbiol Lett (2006) 1.35
Catalytic properties and kinetic mechanism of human recombinant Lys-9 histone H3 methyltransferase SUV39H1: participation of the chromodomain in enzymatic catalysis. Biochemistry (2006) 1.34
Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana. PLoS Genet (2008) 1.30