(Q27672864)

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Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation

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scholarly article

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Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation (English)

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author name string

Hideharu Hashimoto

1

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Samuel Hong

2

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Ashok S Bhagwat

3

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Xing Zhang

4

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Xiaodong Cheng

5

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language of work or name

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publication date

1 November 2012

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Nucleic Acids Research

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40

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20

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10203-14

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copyright license

Creative Commons Attribution 3.0 Unported

8 November 2016

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April 2022 Public Data File from Crossref

copyright status

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describes a project that uses

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Europe PubMed Central

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3488261/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

DNA demethylation dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

PHENIX: a comprehensive Python-based system for macromolecular structure solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Reprogramming towards pluripotency requires AID-dependent DNA demethylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Enzymatic capture of an extrahelical thymine in the search for uracil in DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Modification of the human thymine-DNA glycosylase by ubiquitin-like proteins facilitates enzymatic turnover

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Crystal structure of a thwarted mismatch glycosylase DNA repair complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Coot: model-building tools for molecular graphics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Lessons learned from structural results on uracil-DNA glycosylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Biphasic kinetics of the human DNA repair protein MED1 (MBD4), a mismatch-specific DNA N-glycosylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

20 March 2017

Base-excision repair of oxidative DNA damage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

7 April 2017

Multiparametric scaling of diffraction intensities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

7 April 2017

Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Stoichiometry and affinity for thymine DNA glycosylase binding to specific and nonspecific DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Role of two strictly conserved residues in nucleotide flipping and N-glycosylic bond cleavage by human thymine DNA glycosylase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Active DNA demethylation mediated by DNA glycosylases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

ROS1 5-methylcytosine DNA glycosylase is a slow-turnover catalyst that initiates DNA demethylation in a distributive fashion

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

The versatile thymine DNA-glycosylase: a comparative characterization of the human, Drosophila and fission yeast orthologs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Synthesis of stable-isotope enriched 5-methylpyrimidines and their use as probes of base reactivity in DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Escherichia coli DNA glycosylase Mug: a growth-regulated enzyme required for mutation avoidance in stationary-phase cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Synthesis and properties of oligonucleotides containing 5-formyl-2'-deoxycytidine: in vitro DNA polymerase reactions on DNA templates containing 5-formyl-2'-deoxycytidine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

29 September 2017

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

2 June 2018

Substrate specificity of human thymine-DNA glycosylase on exocyclic cytosine adducts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

2 June 2018

Specificity of human thymine DNA glycosylase depends on N-glycosidic bond stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3488261

2 June 2018

Separating substrate recognition from base hydrolysis in human thymine DNA glycosylase by mutational analysis

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS845

21 January 2018

Mismatch uracil glycosylase from Escherichia coli: a general mismatch or a specific DNA glycosylase?

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https://api.crossref.org/works/10.1093%2FNAR%2FGKS845

21 January 2018

Kinetics of the action of thymine DNA glycosylase

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS845

21 January 2018

Synthesis and properties of oligodeoxynucleotides containing 5-carboxy-2'-deoxycytidines.

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS845

21 January 2018

Mutagenicity of 5-formylcytosine, an oxidation product of 5-methylcytosine, in DNA in mammalian cells

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS845

21 January 2018

Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS845

21 January 2018

Improved Synthesis and Mutagenicity of Oligonucleotides Containing 5-Hydroxymethylcytosine, 5-Formylcytosine and 5-Carboxylcytosine

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS845

21 January 2018

Mutagenicity of 5-formyluracil in mammalian cells

1 reference

https://pubmed.ncbi.nlm.nih.gov/22962365

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Aromatic substituent constants for structure-activity correlations

1 reference

https://pubmed.ncbi.nlm.nih.gov/22962365

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKS845

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

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