Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA

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Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA is …
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scholarly articleQ13442814
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P356DOI10.1021/ACS.CHEMREV.6B00191
P932PMC publication ID5299066
P698PubMed publication ID27501078

P50authorAlexander C DrohatQ47503014
P2093author name stringChristopher T Coey
P2860cites workMED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1Q22009114
DNA methylation patterns and epigenetic memoryQ22065780
Instability and decay of the primary structure of DNAQ22122361
Definitive identification of mammalian 5-hydroxymethyluracil DNA N-glycosylase activity as SMUG1Q24291615
Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brainQ24299862
Mammalian 5-Formyluracil−DNA Glycosylase. 2. Role of SMUG1 Uracil−DNA Glycosylase in Repair of 5-Formyluracil and Other Oxidized and Deaminated Base LesionsQ24300667
Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNAQ24305161
Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repairQ24309357
Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidationQ24311603
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1Q24316558
Genome demethylation and imprinting in the endospermQ34856775
Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylationQ34984573
DNA demethylation in hormone-induced transcriptional derepressionQ35008010
Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosineQ35076369
A mechanistic perspective on the chemistry of DNA repair glycosylasesQ35171800
Chemistry and biology of DNA repairQ35173709
Gadd45a promotes DNA demethylation through TDG.Q35562151
GADD45A protein plays an essential role in active DNA demethylation during terminal osteogenic differentiation of adipose-derived mesenchymal stem cellsQ35562615
Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2.Q35699206
DNA demethylation in the Arabidopsis genome.Q35741567
Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved MethionineQ35747955
DNA charge transport as a first step in coordinating the detection of lesions by repair proteinsQ35751064
A DNA 3' phosphatase functions in active DNA demethylation in ArabidopsisQ35754674
The mammalian de novo DNA methyltransferases DNMT3A and DNMT3B are also DNA 5-hydroxymethylcytosine dehydroxymethylasesQ36286073
Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3AQ36298528
Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G.Q36305701
Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA.Q36370892
Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transferQ36389665
Uracil-DNA Glycosylase UNG Promotes Tet-mediated DNA DemethylationQ36442386
Nucleic acid modifications with epigenetic significanceQ36456771
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNAQ24319667
Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sitesQ24328865
Modification of the human thymine-DNA glycosylase by ubiquitin-like proteins facilitates enzymatic turnoverQ24534803
Identification of 5-formyluracil DNA glycosylase activity of human hNTH1 proteinQ24537479
Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylaseQ24562354
Mutational analysis of the damage-recognition and catalytic mechanism of human SMUG1 DNA glycosylaseQ24563901
Reprogramming towards pluripotency requires AID-dependent DNA demethylationQ24607262
A decade of exploring the cancer epigenome - biological and translational implicationsQ24614467
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosineQ24614582
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNAQ24632387
Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cellsQ24650179
5-halogenated pyrimidine lesions within a CpG sequence context mimic 5-methylcytosine by enhancing the binding of the methyl-CpG-binding domain of methyl-CpG-binding protein 2 (MeCP2).Q24794741
Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylaseQ24812802
Mechanism and function of oxidative reversal of DNA and RNA methylationQ27002361
Overview of base excision repair biochemistryQ27021659
The Fpg/Nei family of DNA glycosylases: substrates, structures, and search for damageQ27021912
Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187Q27619846
Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNAQ27621681
Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylaseQ27640474
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylaseQ27643123
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylaseQ27657850
Separation-of-function mutants unravel the dual-reaction mode of human 8-oxoguanine DNA glycosylaseQ27666499
Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylationQ27670542
Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNAQ27670999
Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylationQ27672864
Crystal Structure of Human Methyl-Binding Domain IV Glycosylase Bound to Abasic DNAQ27678915
Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylaseQ27679377
Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNAQ27681187
Postreplicative mismatch repairQ27690911
Structural insight into substrate preference for TET-mediated oxidationQ27702550
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNAQ27733802
MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamilyQ27766319
Mismatch-specific thymine DNA glycosylase and DNA polymerase beta mediate the correction of G.T mispairs in nuclear extracts from human cellsQ33721136
A mammalian protein with specific demethylase activity for mCpG DNA.Q33853552
An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA geneQ33906087
Base excision repair: a critical player in many gamesQ33908163
DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation.Q33931372
X inactivation, differentiation, and DNA methylationQ33999850
Methylation-independent DNA binding modulates specificity of Repressor of Silencing 1 (ROS1) and facilitates demethylation in long substratesQ34003906
The discovery of 5-formylcytosine in embryonic stem cell DNA.Q34027511
An N -Glycosidase from Escherichia coli That Releases Free Uracil from DNA Containing Deaminated Cytosine ResiduesQ34052545
E2-mediated small ubiquitin-like modifier (SUMO) modification of thymine DNA glycosylase is efficient but not selective for the enzyme-product complexQ34076047
Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.Q34249450
Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease IIIQ34256473
Mechanism of stimulation of the DNA glycosylase activity of hOGG1 by the major human AP endonuclease: bypass of the AP lyase activity stepQ34286685
Recent advances in the structural mechanisms of DNA glycosylasesQ34306735
AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in ArabidopsisQ34313038
Domain structure of the DEMETER 5-methylcytosine DNA glycosylaseQ34320211
Mammalian base excision repair: the forgotten archangelQ34327812
AID enzymatic activity is inversely proportional to the size of cytosine C5 orbital cloudQ34391465
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsisQ34562910
DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases.Q34598249
CpG-rich islands and the function of DNA methylationQ28131800
The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sitesQ28145111
Uracil-DNA glycosylase acts by substrate autocatalysisQ28199337
Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sitesQ28262535
DNA Methylation and Gene FunctionQ28263722
The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cellsQ28264721
Purification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. Direct identification of Lys-212 as the active nucleophilic residueQ28279728
Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogrammingQ28284694
Base excision repairQ28288115
DNA mismatch repair: functions and mechanismsQ28296096
CpG islands and the regulation of transcriptionQ28315762
Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specificationQ28504641
Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stabilityQ28508931
Mammalian 5-formyluracil-DNA glycosylase. 1. Identification and characterization of a novel activity that releases 5-formyluracil from DNAQ28577035
Quality control by DNA repairQ28608962
Stimulation of human 8-oxoguanine-DNA glycosylase by AP-endonuclease: potential coordination of the initial steps in base excision repairQ28645611
Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairsQ28740645
Crystal structure of thymine DNA glycosylase conjugated to SUMO-1Q28910402
Base-excision repair of oxidative DNA damageQ29615373
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterningQ29615977
Cancer epigenetics comes of ageQ29617275
The DNA methyltransferases of mammalsQ29617317
The role of DNA methylation in mammalian epigeneticsQ29617979
Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brainQ30433875
Role of electrophilic and general base catalysis in the mechanism of Escherichia coli uracil DNA glycosylase.Q30582190
Conformation and proton configuration of pyrimidine deoxynucleoside oxidation damage products in waterQ30597717
Escherichia coli uracil DNA glycosylase: NMR characterization of the short hydrogen bond from His187 to uracil O2.Q30614512
Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNAQ30992958
Transition-state analysis of the DNA repair enzyme MutY.Q31151684
5-methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complexQ33180228
Genes of the thymidine salvage pathway: thymine-7-hydroxylase from a Rhodotorula glutinis cDNA library and iso-orotate decarboxylase from Neurospora crassaQ33213312
GADD45A does not promote DNA demethylationQ33325901
Base excision repair of tandem modifications in a methylated CpG dinucleotide.Q33619413
Active DNA demethylation in plant companion cells reinforces transposon methylation in gametesQ33668697
TET enzymes, TDG and the dynamics of DNA demethylation.Q33715010
Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stabilityQ36627544
Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanismQ36651017
The mechanics of base excision repair, and its relationship to aging and diseaseQ36656724
Weakened N3 Hydrogen Bonding by 5-Formylcytosine and 5-Carboxylcytosine Reduces Their Base-Pairing StabilityQ36662987
Selective excision of 5-carboxylcytosine by a thymine DNA glycosylase mutant.Q36674636
DNA-mediated charge transport for DNA repairQ36689389
Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic primingQ36853522
Active DNA demethylation in plants and animals.Q36854300
Characterizing Requirements for Small Ubiquitin-like Modifier (SUMO) Modification and Binding on Base Excision Repair Activity of Thymine-DNA Glycosylase in VivoQ36884795
Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNAQ36970371
The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesionsQ36977957
DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45.Q37068711
Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G.Q37140478
The AID/APOBEC family of nucleic acid mutators.Q37206307
Mechanisms of base selection by human single-stranded selective monofunctional uracil-DNA glycosylaseQ37257364
ROS1 5-methylcytosine DNA glycosylase is a slow-turnover catalyst that initiates DNA demethylation in a distributive fashionQ37273644
Redox signaling between DNA repair proteins for efficient lesion detectionQ37340789
Role of two strictly conserved residues in nucleotide flipping and N-glycosylic bond cleavage by human thymine DNA glycosylaseQ37479458
Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA.Q37595036
A TET homologue protein from Coprinopsis cinerea (CcTET) that biochemically converts 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosineQ37701368
5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3Q37731556
Detection of damaged DNA bases by DNA glycosylase enzymesQ37752315
The curious chemical biology of cytosine: deamination, methylation, and oxidation as modulators of genomic potential.Q37946460
Advances in understanding the coupling of DNA base modifying enzymes to processes involving base excision repair.Q38122803
Mechanisms for enzymatic cleavage of the N-glycosidic bond in DNA.Q38245504
Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis.Q38291765
5-Methylcytosine DNA glycosylase activity is also present in the human MBD4 (G/T mismatch glycosylase) and in a related avian sequenceQ38307104
Substrate specificity and reaction mechanism of murine 8-oxoguanine-DNA glycosylaseQ38310719
Functionality of human thymine DNA glycosylase requires SUMO-regulated changes in protein conformationQ38328146
Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1.Q38330113
A mammalian DNA repair enzyme that excises oxidatively damaged guanines maps to a locus frequently lost in lung cancerQ38345459
Repair of the mutagenic DNA oxidation product, 5-formyluracilQ38358598
Tet2 Catalyzes Stepwise 5-Methylcytosine Oxidation by an Iterative and de novo Mechanism.Q38587746
Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation.Q38804981
An ONIOM and MD Investigation of Possible Monofunctional Activity of Human 8-Oxoguanine-DNA Glycosylase (hOgg1).Q39001898
DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for genomic integrityQ39494713
Cyclical DNA methylation of a transcriptionally active promoterQ40005351
The DNA N-glycosylase MED1 exhibits preference for halogenated pyrimidines and is involved in the cytotoxicity of 5-iododeoxyuridine.Q40248506
GADD45a physically and functionally interacts with TET1Q40347085
Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THFQ41077567
DNA charge transport for sensing and signalingQ41233751
Transition state analysis of thymidine hydrolysis by human thymidine phosphorylaseQ41906991
AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation.Q41917830
Coordinating the initial steps of base excision repair. Apurinic/apyrimidinic endonuclease 1 actively stimulates thymine DNA glycosylase by disrupting the product complexQ41952309
Specificity of human thymine DNA glycosylase depends on N-glycosidic bond stabilityQ42161686
The DNA repair protein XRCC1 functions in the plant DNA demethylation pathway by stimulating cytosine methylation (5-meC) excision, gap tailoring, and DNA ligationQ42182040
Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylaseQ42182897
A discontinuous DNA glycosylase domain in a family of enzymes that excise 5-methylcytosineQ42567554
Fe(II)/alpha-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolismQ42719732
Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamicsQ42738710
TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivationQ42761123
5-Formylcytosine alters the structure of the DNA double helixQ43096431
Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.Q43121080
Uracil and thymine reactivity in the gas phase: the S(N)2 reaction and implications for electron delocalization in leaving groupsQ43237888
Kinetics and binding of the thymine-DNA mismatch glycosylase, Mig-Mth, with mismatch-containing DNA substratesQ44267635
ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyaseQ44277312
Rational Engineering of a DNA Glycosylase Specific for an Unnatural Cytosine:Pyrene Base PairQ44426214
Product inhibition and magnesium modulate the dual reaction mode of hOgg1.Q45231852
Genetic interactions between DNA demethylation and methylation in Arabidopsis.Q45962529
DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis.Q45981966
Cytosine-5-methyltransferases add aldehydes to DNA.Q46017177
Synthesis and characterization of isotopically enriched pyrimidine deoxynucleoside oxidation damage productsQ46082221
Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks.Q46584490
Synthesis and properties of oligodeoxynucleotides containing 5-carboxy-2'-deoxycytidines.Q46893221
Deamination, oxidation, and C-C bond cleavage reactivity of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosineQ47691191
Establishment of methylation patterns in ES cells.Q50703085
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.Q53013759
Direct decarboxylation of 5-carboxylcytosine by DNA C5-methyltransferases.Q53058810
Transition state analysis of acid-catalyzed dAMP hydrolysis.Q53553616
Crystallization and crystallographic characterization of the iron-sulfur-containing DNA-repair enzyme endonuclease III from Escherichia coli.Q54673167
Mechanism and Stem-Cell Activity of 5-Carboxycytosine Decarboxylation Determined by Isotope TracingQ57376743
Improved Synthesis and Mutagenicity of Oligonucleotides Containing 5-Hydroxymethylcytosine, 5-Formylcytosine and 5-CarboxylcytosineQ57376757
Acidic hydrolysis of deoxycytidine and deoxyuridine derivatives. The general mechanism of deoxyribonucleoside hydrolysisQ67278441
Aromatic substituent constants for structure-activity correlationsQ69600149
Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediateQ73212716
The critical active-site amine of the human 8-oxoguanine DNA glycosylase, hOgg1: direct identification, ablation and chemical reconstitutionQ73790587
PYRIMIDINES. I. THE SYNTHESIS OF 6-FLUOROCYTOSINE AND RELATED COMPOUNDSQ76892774
Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation DynamicsQ86688630
P433issue20
P407language of work or nameEnglishQ1860
P304page(s)12711-12729
P577publication date2016-08-08
P1433published inChemical ReviewsQ900502
P1476titleRole of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA
P478volume116

Reverse relations

cites work (P2860)
Q41510570APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA.
Q58716914APURINIC/APYRIMIDINIC ENDONUCLEASE2 and ZINC FINGER DNA 3'-PHOSPHOESTERASE Play Overlapping Roles in the Maintenance of Epigenome and Genome Stability
Q55321915Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process.
Q90350691Comparison of DNA and RNA substrate effects on TET2 structure
Q92174412Defining the Role of Nucleotide Flipping in Enzyme Specificity Using 19F NMR
Q55446744Defining the impact of sumoylation on substrate binding and catalysis by thymine DNA glycosylase.
Q49170182Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process
Q49917892Harnessing natural DNA modifying activities for editing of the genome and epigenome.
Q64255145High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean
Q92122417Mitochondrial DNA: Epigenetics and environment
Q92809345Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase
Q39200289Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics
Q52720777Simultaneous sensitive detection of multiple DNA glycosylases from lung cancer cells at the single-molecule level.
Q38290315Structural Basis for Excision of 5-Formylcytosine by Thymine DNA Glycosylase
Q58760147The effect of dietary level of two inulin types differing in chain length on biogenic amine concentration, oxidant-antioxidant balance and DNA repair in the colon of piglets

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