Published in J Mol Biol on February 28, 2006
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature (2008) 3.28
Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev (2009) 2.41
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence. Nucleic Acids Res (2007) 1.60
Highlights of the DNA cutters: a short history of the restriction enzymes. Nucleic Acids Res (2013) 1.60
Structure, function and mechanism of exocyclic DNA methyltransferases. Biochem J (2006) 1.07
Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification. Bioessays (2015) 0.89
Dam it's good! DamID profiling of protein-DNA interactions. Wiley Interdiscip Rev Dev Biol (2015) 0.87
Establishing and maintaining sequestration of Dam target sites for phase variation of agn43 in Escherichia coli. J Bacteriol (2010) 0.87
Mutations within the catalytic motif of DNA adenine methyltransferase (Dam) of Aeromonas hydrophila cause the virulence of the Dam-overproducing strain to revert to that of the wild-type phenotype. Infect Immun (2006) 0.86
Modulation of Escherichia coli DNA methyltransferase activity by biologically derived GATC-flanking sequences. J Biol Chem (2008) 0.83
DamIP: a novel method to identify DNA binding sites in vivo. Nucl Recept Signal (2010) 0.83
Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest. Genome Res (2016) 0.83
DNA base flipping by both members of the PspGI restriction-modification system. Nucleic Acids Res (2008) 0.82
DNA Methylation. Ecosal Plus (2014) 0.82
Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila. Nucleic Acids Res (2016) 0.81
SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers. Mol Cell (2015) 0.81
The Caulobacter crescentus DNA-(adenine-N6)-methyltransferase CcrM methylates DNA in a distributive manner. Nucleic Acids Res (2011) 0.81
Research resource: The estrogen receptor α cistrome defined by DamIP. Mol Endocrinol (2011) 0.79
Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents. Br J Pharmacol (2013) 0.78
Escherichia coli DNA adenine methyltransferase: the structural basis of processive catalysis and indirect read-out. J Biol Chem (2009) 0.78
Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression. Nucleic Acids Res (2015) 0.77
Getting Down to Specifics: Profiling Gene Expression and Protein-DNA Interactions in a Cell Type-Specific Manner. Adv Genet (2015) 0.77
DamIP: using mutant DNA adenine methyltransferase to study DNA-protein interactions in vivo. Curr Protoc Mol Biol (2011) 0.77
DNA Methyltransferase Activity Assays: Advances and Challenges. Theranostics (2016) 0.76
N6-Methyladenine: A Conserved and Dynamic DNA Mark. Adv Exp Med Biol (2016) 0.75
Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles. MBio (2017) 0.75
Crystallization and X-ray diffraction studies of DNA-free and DNA-bound forms of EcoO109I DNA methyltransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.75
DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence. Front Microbiol (2017) 0.75
Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A (1991) 119.63
Protein production by auto-induction in high density shaking cultures. Protein Expr Purif (2005) 29.74
Eukaryotic cytosine methyltransferases. Annu Rev Biochem (2005) 15.45
Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu Rev Biochem (1996) 10.86
The role of DNA methylation in mammalian epigenetics. Science (2001) 9.26
HhaI methyltransferase flips its target base out of the DNA helix. Cell (1994) 8.72
Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation. J Mol Biol (1977) 6.55
Rotation function calculations with GLRF program. Methods Enzymol (1997) 3.99
An essential role for DNA adenine methylation in bacterial virulence. Science (1999) 3.80
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature (2005) 3.67
Sequence specificity of the P1 modification methylase (M.Eco P1) and the DNA methylase (M.Eco dam) controlled by the Escherichia coli dam gene. J Mol Biol (1978) 3.41
Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives. J Biol Chem (1969) 3.39
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature (2004) 3.30
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell (1995) 3.17
AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res (2001) 3.16
Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem (2002) 3.15
Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat Struct Biol (2001) 3.04
Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli. Mol Microbiol (2002) 2.50
Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature (2005) 2.44
Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect Immun (2001) 2.42
Timing and targeting: the biological functions of Dam methylation in E. coli. Cell (1988) 2.40
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell (1999) 2.14
Dam methylation: coordinating cellular processes. Curr Opin Microbiol (2005) 2.11
The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J Biol Chem (2004) 2.08
DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity. Proc Natl Acad Sci U S A (1999) 1.86
2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucleic Acids Res (1998) 1.83
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases. Nucleic Acids Res (1998) 1.60
Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis. Proc Natl Acad Sci U S A (2003) 1.58
Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry (1996) 1.46
Biotin-avidin microplate assay for the quantitative analysis of enzymatic methylation of DNA by DNA methyltransferases. Biol Chem (2000) 1.42
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase. Cell (2005) 1.36
Salmonella DNA adenine methylase mutants elicit protective immune responses to homologous and heterologous serovars in chickens. Infect Immun (2001) 1.31
The mechanism by which DNA adenine methylase and PapI activate the pap epigenetic switch. Mol Cell (2003) 1.29
MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage. Mol Cell (2005) 1.18
Site-directed mutagenesis by polymerase chain reaction. Methods Mol Biol (2002) 1.15
Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine. Structure (1998) 1.15
Direct real time observation of base flipping by the EcoRI DNA methyltransferase. J Biol Chem (1998) 1.11
Flipping duplex DNA inside out: a double base-flipping reaction mechanism by Escherichia coli MutY adenine glycosylase. J Biol Chem (2002) 1.09
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res (2004) 1.03
Inactivation of deoxyadenosine methyltransferase (dam) attenuates Haemophilus influenzae virulence. Mol Microbiol (2004) 1.03
Structure of the bacteriophage T4 DNA adenine methyltransferase. Nat Struct Biol (2003) 1.02
Salmonella DNA adenine methylase mutants prevent colonization of newly hatched chickens by homologous and heterologous serovars. Int J Food Microbiol (2003) 0.96
Stopped-flow and mutational analysis of base flipping by the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase. J Mol Biol (2004) 0.95
Bacteriophage T2Dam and T4Dam DNA-[N6-adenine]-methyltransferases. Prog Nucleic Acid Res Mol Biol (2004) 0.84
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature (2007) 11.14
Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature (2007) 8.33
Cyclical DNA methylation of a transcriptionally active promoter. Nature (2008) 7.62
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res (2003) 7.56
Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci (2003) 5.65
Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet (2003) 4.56
Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature (2007) 4.49
Structural basis for the product specificity of histone lysine methyltransferases. Mol Cell (2003) 4.42
5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat Neurosci (2011) 4.15
The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol (2005) 3.93
Protein lysine methyltransferase G9a acts on non-histone targets. Nat Chem Biol (2008) 3.53
The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin. Cell (2006) 3.46
Fluorescent indicators of cAMP and Epac activation reveal differential dynamics of cAMP signaling within discrete subcellular compartments. Proc Natl Acad Sci U S A (2004) 3.31
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature (2008) 3.28
The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules. Nat Struct Mol Biol (2008) 3.20
The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J Biol Chem (2010) 3.03
Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma (2004) 3.00
Structure of the Neurospora SET domain protein DIM-5, a histone H3 lysine methyltransferase. Cell (2002) 2.94
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol (2009) 2.87
In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases. J Biol Chem (2004) 2.86
BISMA--fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics (2010) 2.60
Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res (2012) 2.55
Synergy among nuclear receptor coactivators: selective requirement for protein methyltransferase and acetyltransferase activities. Mol Cell Biol (2002) 2.51
Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294. Nat Struct Mol Biol (2009) 2.50
Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res (2010) 2.39
Structure and function of mammalian DNA methyltransferases. Chembiochem (2010) 2.39
DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet (2009) 2.37
Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Mol Cell (2008) 2.35
Oncogenic KRAS activates hedgehog signaling pathway in pancreatic cancer cells. J Biol Chem (2007) 2.34
Structure of the predominant protein arginine methyltransferase PRMT1 and analysis of its binding to substrate peptides. Structure (2003) 2.30
A common mode of recognition for methylated CpG. Trends Biochem Sci (2013) 2.28
Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J Biol Chem (2005) 2.28
The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat Struct Biol (2002) 2.24
The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J Biol Chem (2004) 2.08
Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling. Nat Immunol (2010) 2.07
Differential signaling of cyclic AMP: opposing effects of exchange protein directly activated by cyclic AMP and cAMP-dependent protein kinase on protein kinase B activation. J Biol Chem (2002) 2.06
Chromatin targeting of de novo DNA methyltransferases by the PWWP domain. J Biol Chem (2004) 2.02
Nab2p is required for poly(A) RNA export in Saccharomyces cerevisiae and is regulated by arginine methylation via Hmt1p. J Biol Chem (2002) 1.99
Cell cycle-dependent subcellular localization of exchange factor directly activated by cAMP. J Biol Chem (2002) 1.94
Mutational analysis of the catalytic domain of the murine Dnmt3a DNA-(cytosine C5)-methyltransferase. J Mol Biol (2006) 1.93
Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases. J Biol Chem (2002) 1.85
Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism. RNA (2008) 1.76
Structure of the SET domain histone lysine methyltransferase Clr4. Nat Struct Biol (2002) 1.70
Direct suppression of CNS autoimmune inflammation via the cannabinoid receptor CB1 on neurons and CB2 on autoreactive T cells. Nat Med (2007) 1.69
The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9. Hum Mol Genet (2011) 1.67
Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome. J Mol Biol (2005) 1.65
Non-imprinted allele-specific DNA methylation on human autosomes. Genome Biol (2009) 1.64
Protein arginine methyltransferase 1: positively charged residues in substrate peptides distal to the site of methylation are important for substrate binding and catalysis. Biochemistry (2007) 1.55
A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability. Nat Struct Mol Biol (2010) 1.52
Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes. Nucleic Acids Res (2006) 1.52
Antiapoptotic effect of serum and glucocorticoid-inducible protein kinase is mediated by novel mechanism activating I{kappa}B kinase. Cancer Res (2005) 1.48
Comprehensive alanine-scanning mutagenesis of Escherichia coli CsrA defines two subdomains of critical functional importance. J Biol Chem (2006) 1.47
Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res (2008) 1.46
A novel EPAC-specific inhibitor suppresses pancreatic cancer cell migration and invasion. Mol Pharmacol (2012) 1.46
The human Dnmt2 has residual DNA-(cytosine-C5) methyltransferase activity. J Biol Chem (2003) 1.46
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics (2009) 1.45
Molecular coupling of DNA methylation and histone methylation. Epigenomics (2010) 1.43
Follicle-stimulating hormone induces multiple signaling cascades: evidence that activation of Rous sarcoma oncogene, RAS, and the epidermal growth factor receptor are critical for granulosa cell differentiation. Mol Endocrinol (2007) 1.42
Activation of antioxidant pathways in ras-mediated oncogenic transformation of human surface ovarian epithelial cells revealed by functional proteomics and mass spectrometry. Cancer Res (2004) 1.41
Reduced expression of NDUFS3 and its clinical significance in serous ovarian cancer. Int J Gynecol Cancer (2013) 1.40
High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell Rep (2013) 1.40
Phosphorylation-mediated inactivation of coactivator-associated arginine methyltransferase 1. Proc Natl Acad Sci U S A (2007) 1.40
Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA. Eur J Biochem (2002) 1.39
An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence. Genes Dev (2012) 1.38
Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase. J Biol Chem (2004) 1.38
Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases. J Mol Biol (2010) 1.37
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase. Cell (2005) 1.36
Accuracy of DNA methylation pattern preservation by the Dnmt1 methyltransferase. Nucleic Acids Res (2006) 1.36
Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation. Nucleic Acids Res (2012) 1.35
Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays. Chem Biol (2008) 1.34
Specificity analysis-based identification of new methylation targets of the SET7/9 protein lysine methyltransferase. Chem Biol (2011) 1.33
The structure of RalF, an ADP-ribosylation factor guanine nucleotide exchange factor from Legionella pneumophila, reveals the presence of a cap over the active site. J Biol Chem (2004) 1.33
Mechanism of intracellular cAMP sensor Epac2 activation: cAMP-induced conformational changes identified by amide hydrogen/deuterium exchange mass spectrometry (DXMS). J Biol Chem (2011) 1.32
Isoform-specific antagonists of exchange proteins directly activated by cAMP. Proc Natl Acad Sci U S A (2012) 1.27
DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones. Methods Mol Biol (2009) 1.26
De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases. Biochemistry (2005) 1.26
Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays. Epigenetics (2011) 1.26
Prevalence and risk profile of cervical Human papillomavirus infection in Zhejiang Province, southeast China: a population-based study. Virol J (2010) 1.25
Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase. Cell Res (2011) 1.24
Interplay between exchange protein directly activated by cAMP (Epac) and microtubule cytoskeleton. Mol Biosyst (2005) 1.21
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Nucleic Acids Res (2006) 1.20
Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis. Nucleic Acids Res (2008) 1.19
Targeted methylation and gene silencing of VEGF-A in human cells by using a designed Dnmt3a-Dnmt3L single-chain fusion protein with increased DNA methylation activity. J Mol Biol (2012) 1.17
Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4. J Biol Chem (2002) 1.16
Oligomerization and binding of the Dnmt3a DNA methyltransferase to parallel DNA molecules: heterochromatic localization and role of Dnmt3L. J Biol Chem (2011) 1.14
Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails. BMC Biochem (2011) 1.13
On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PLoS One (2011) 1.13
Discovery and structural characterization of a small molecule 14-3-3 protein-protein interaction inhibitor. Proc Natl Acad Sci U S A (2011) 1.12
Mechanism of Epac activation: structural and functional analyses of Epac2 hinge mutants with constitutive and reduced activities. J Biol Chem (2009) 1.12
hNaa10p contributes to tumorigenesis by facilitating DNMT1-mediated tumor suppressor gene silencing. J Clin Invest (2010) 1.11
Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Nucleic Acids Res (2012) 1.11
Matched-case comparison of neoadjuvant chemotherapy in patients with FIGO stage IB1-IIB cervical cancer to establish selection criteria. Eur J Cancer (2012) 1.10