Assessment of DNA Epigenetic Modifications.

Abstract:

:DNA molecules utilize adenine, thymine, cytosine, and guanine for coding genetic information. In addition to these four canonical nucleobases, DNA molecules also contain a variety of modified nucleobases that can control and regulate gene expression and chromosome structure. Elucidating the functions of DNA modifications relies on the sensitive detection, accurate quantification, and genome-wide mapping of these modifications in genomic DNA. The significant advances of techniques and methods in recent years have enabled the discovery and functional studies of a number of new modifications in DNA in both prokaryotes and eukaryotes. Mass spectrometry-based methods for analyzing DNA modifications have substantially advanced over the past decade, which has greatly stimulated the research of DNA epigenetic modifications. The emergence of next-generation sequencing technology provides complementary methodology to enable genome-wide mapping of modifications, which is very important to reveal the biological roles of DNA modifications. This perspective highlights the recent methodologies for the assessment of DNA modifications with focus on mass spectrometry and sequencing analytical strategies.

journal_name

Chem Res Toxicol

authors

Yuan BF

doi

10.1021/acs.chemrestox.9b00372

subject

Has Abstract

pub_date

2020-03-16 00:00:00

pages

695-708

issue

3

eissn

0893-228X

issn

1520-5010

journal_volume

33

pub_type

杂志文章
  • Metabolism of genistein by rat and human cytochrome P450s.

    abstract::The metabolism of genistein (4',5,7-trihydroxyisoflavone), a phytoestrogen derived from soy products, was investigated using rat and human liver microsomes and recombinant human cytochrome P450 enzymes. Metabolism of genistein by microsomes obtained from rats treated with pyridine, phenobarbital, beta-naphthoflavone, ...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx9802320

    authors: Roberts-Kirchhoff ES,Crowley JR,Hollenberg PF,Kim H

    更新日期:1999-07-01 00:00:00

  • Characterization of a lipid hydroperoxide-derived RNA adduct in rat intestinal epithelial cells.

    abstract::Five major products (adducts A(1a), A(1b), A(2), A(3,) and B) from the reaction of guanosine (Guo) with 4-oxo-2(E)-nonenal (ONE) were detected by liquid chromatography-mass spectrometry (LC-MS). Tandem MS (MS/MS) analysis of these compounds suggested that modifications to the nucleoside had been introduced. Adducts A(...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx0600189

    authors: Zhu P,Lee SH,Wehrli S,Blair IA

    更新日期:2006-06-01 00:00:00

  • Base sequence-dependent bends in site-specific benzo[a]pyrene diol epoxide-modified oligonucleotide duplexes.

    abstract::The site specifically modified oligonucleotides 5'-d(TCCTCCTG1G2CCTCTC) (I) and 5'-d(CTATG1G2G3TATC) (II) were synthesized with single modified guanine residues at positions G1, G2, or G3, derived from the covalent binding reaction of 7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene ((+)-anti-BPDE) with ...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx9501086

    authors: Liu T,Xu J,Tsao H,Li B,Xu R,Yang C,Amin S,Moriya M,Geacintov NE

    更新日期:1996-01-01 00:00:00

  • Low-density lipoprotein has an enormous capacity to bind (E)-4-hydroxynon-2-enal (HNE): detection and characterization of lysyl and histidyl adducts containing multiple molecules of HNE.

    abstract::( E)-4-Hydroxynon-2-enal (HNE), an electrophilic bifunctional cytotoxic lipid peroxidation product, forms covalent adducts with nucleophilic side chains of amino acid residues. HNE-derived adducts have been implicated in many pathophysiological processes including atherosclerosis, diabetes, and Alzheimer's disease. Tr...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx8000303

    authors: Annangudi SP,Deng Y,Gu X,Zhang W,Crabb JW,Salomon RG

    更新日期:2008-07-01 00:00:00

  • Biotransformation Mechanism of Pesticides by Cytochrome P450: A DFT Study on Dieldrin.

    abstract::Pesticide biotransformation, especially by cytochrome P450 enzymes (CYPs), may produce metabolites with substantially altered toxicological and physicochemical profiles, which has drawn great attention as a basis for environmental risk assessment. CYPs are active in the metabolism of various reactions of pesticides, a...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/acs.chemrestox.0c00013

    authors: Chai L,Ji S,Zhang S,Yu H,Zhao M,Ji L

    更新日期:2020-06-15 00:00:00

  • Characterization of the transient oxaphosphetane BChE inhibitor formed from spontaneously activated ethephon.

    abstract::The major plant growth regulator ethephon degrades to ethylene and phosphate in aqueous solutions and plants and is spontaneously activated to a butyrylcholinesterase (BChE) inhibitor in alkaline solutions and animal tissues. In the present (31)P NMR kinetic study of the reactions of ethephon in pH 7.4 carbonate buffe...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx4002429

    authors: Lantz SR,Casida JE

    更新日期:2013-09-16 00:00:00

  • Conversion of a hemoglobin alpha chain aspartate(47) ester to N-(2,3-dihydroxypropyl)asparagine as a method for identification of the principal binding site for benzo[a]pyrene anti-diol epoxide.

    abstract::Human hemoglobin was alkylated with (+/-)-7 beta,8 alpha-dihydroxy-9 alpha,10 alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE) and then treated with aqueous (+/-)-3-amino-1,2-propanediol to convert alkylated carboxyl side chains to N-(2,3-dihydroxypropyl) amides. Tryptic peptides produced from the modified protein...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx00021a016

    authors: Day BW,Skipper PL,Rich RH,Naylor S,Tannenbaum SR

    更新日期:1991-05-01 00:00:00

  • Enzymatic methylation of DNA in cultured human cells studied by stable isotope incorporation and mass spectrometry.

    abstract::Enzymatic methylation of cytosine residues in DNA, in conjunction with covalent histone modifications, establishes an epigenetic code essential for the proper control of gene expression in higher organisms. Once established during cellular differentiation, the epigenetic code must be faithfully transmitted to progeny ...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx900027w

    authors: Herring JL,Rogstad DK,Sowers LC

    更新日期:2009-06-01 00:00:00

  • Reduced Transcriptomic Approach for Screening and Prediction of Chemical Toxicity.

    abstract::The reduced transcriptomic approach allows full dose range testing of hundreds of chemicals or mixtures using human cells or zebrafish embryos. Points of departure of genes and pathways can be used for potency ranking and to classify chemicals by disrupted biological pathways. ...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/acs.chemrestox.8b00104

    authors: Dai J

    更新日期:2018-07-16 00:00:00

  • Detection of Carbofuran-Protein Adducts in Serum of Occupationally Exposed Pesticide Factory Workers in Pakistan.

    abstract::This study was conducted to investigate the protein adducts with pesticides in a cohort of 172 factory workers that were exposed to a mixture of pesticides. The 35 samples showing considerable variation in biochemical parameters, i.e., butyrylcholinestrase (BChE), serum glutamic pyruvic transaminase (SGPT), serum glut...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/acs.chemrestox.6b00222

    authors: Rehman T,Khan MM,Shad MA,Hussain M,Oyler BL,Goo YA,Goodlett DR

    更新日期:2016-10-17 00:00:00

  • Reevaluation of the effect of ellagic acid on N-methyl-N-nitrosourea DNA alkylation and mutagenicity.

    abstract::N-Methyl-N-nitrosourea (MNU) is a reactive, mutagenic methylating agent. MNU methylates DNA at various sites, including guanine N7, guanine O6, and adenine N3. Dixit and Gold [(1986) Proc. Natl. Acad. Sci. U.S.A. 83, 8039-8043] reported that ellagic acid, a phenolic natural product, inhibited the mutagenicity of MNU i...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx00015a002

    authors: Lord HL,Josephy PD,Snieckus VA

    更新日期:1990-05-01 00:00:00

  • Mode of action of poly(vinylpyridine-N-oxide) in preventing silicosis: effective scavenging of carbonate anion radical.

    abstract::Small particles of crystalline silicon dioxide (crystallites) are exceptionally toxic. Inhalation of quartz crystallites causes silicosis, a devastating lung disease afflicting miners, particularly coal and stone workers. Poly(vinylpyridine-N-oxide)s (PVPNOs) have been applied in the prevention and treatment of silico...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx050271t

    authors: Goldstein S,Czapski G,Heller A

    更新日期:2006-01-01 00:00:00

  • 42,43,44,45,46,47,55-Heptanor-41-oxohomoyessotoxin, a new biotoxin from mussels of the northern Adriatic sea.

    abstract::The diarrhetic shellfish toxin composition in the digestive glands of mussels from the northern Adriatic sea was investigated. Along with known yessotoxins, identified by comparison of their chromatographic and spectral properties with those reported in the literature, we isolated a new analogue of yessotoxin, 42,43,4...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx000259v

    authors: Ciminiello P,Fattorusso E,Forino M,Poletti R

    更新日期:2001-05-01 00:00:00

  • Genotoxicity evaluation of nanomaterials: dna damage, micronuclei, and 8-hydroxy-2-deoxyguanosine induced by magnetic doped CdSe quantum dots in male mice.

    abstract::Quantum dots (QDs) are a novel class of inorganic fluorophores which are gaining widespread recognition as a result of their exceptional photophysical properties and their applications as a biomarker and in molecular biomedical imaging. The aim of this study was to evaluate the in vivo genotoxicity in mice exposed to ...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx2000015

    authors: Khalil WK,Girgis E,Emam AN,Mohamed MB,Rao KV

    更新日期:2011-05-16 00:00:00

  • Use of Zebrafish in Drug Discovery Toxicology.

    abstract::Unpredicted human safety events in clinical trials for new drugs are costly in terms of human health and money. The drug discovery industry attempts to minimize those events with diligent preclinical safety testing. Current standard practices are good at preventing toxic compounds from being tested in the clinic; howe...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章,评审

    doi:10.1021/acs.chemrestox.9b00335

    authors: Cassar S,Adatto I,Freeman JL,Gamse JT,Iturria I,Lawrence C,Muriana A,Peterson RT,Van Cruchten S,Zon LI

    更新日期:2020-01-21 00:00:00

  • Chronic Cocaine Use Causes Changes in the Striatal Proteome Depending on the Endogenous Expression of Pleiotrophin.

    abstract::The neurotrophic factor pleiotrophin (PTN) is upregulated in different brain areas after the administration of different drugs of abuse, including psychostimulants. PTN has been shown to prevent cocaine-induced cytotoxicity in NG108-15 and PC12 cells. We previously demonstrated that specific phosphoproteins related to...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/acs.chemrestox.5b00130

    authors: Vicente-Rodríguez M,Herradón G,Ferrer-Alcón M,Uribarri M,Pérez-García C

    更新日期:2015-07-20 00:00:00

  • Endocrine disruption screening by protein and gene expression of vitellogenin in freshly isolated and cryopreserved rainbow trout hepatocytes.

    abstract::Xenobiotics may activate the estrogen receptor, resulting in alteration of normal endocrine functions in animals and humans. Consequently, this necessitates development of assay end points capable of identifying estrogenic xenobiotics. In the present study, we screened the potential estrogenicity of chemicals via thei...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx5002089

    authors: Markell LK,Mingoia RT,Peterson HM,Yao J,Waters SM,Finn JP,Nabb DL,Han X

    更新日期:2014-08-18 00:00:00

  • Disproportionation of clozapine radical: a link between one-electron oxidation of clozapine and formation of its nitrenium cation.

    abstract::The primary products of one-electron oxidation of clozapine and olanzapine, very effective atypical antipsychotic drugs, have been spectroscopically characterized. The oxidation process has been studied under glassy matrix conditions and by a pulse radiolysis technique in aqueous solution. The rate constants for the o...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx700128c

    authors: Sikora A,Adamus J,Marcinek A

    更新日期:2007-08-01 00:00:00

  • Biochemical investigations into the mutagenic potential of 8-oxo-2'-deoxyguanosine using nucleotide analogues.

    abstract::8-Oxo-2'-deoxyguanosine (OdG) is an abundant DNA lesion produced during oxidative damage to DNA. It can form relatively stable base pairs with both dC and dA that mimic natural dG:dC and dT:dA base pairs, respectively. Thus, when in the template strand, OdG can direct the insertion of either dCTP or dATP during replic...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx300365g

    authors: Hamm ML,Crowley KA,Ghio M,Lindell MA,McFadden EJ,Silberg JS,Weaver AM

    更新日期:2012-11-19 00:00:00

  • Chemical analysis and hemolytic activity of the fava bean aglycon divicine.

    abstract::Divicine is an unstable aglycon metabolite of the fava bean pyrimidine beta-glucoside vicine. Divicine has long been thought to be a mediator of an acute hemolytic crisis, known as favism, in susceptible individuals who ingest fava beans (Vicia faba). However, a recent report has questioned the chemical identity of th...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx00034a009

    authors: McMillan DC,Schey KL,Meier GP,Jollow DJ

    更新日期:1993-07-01 00:00:00

  • Enzyme induction by L-buthionine (S,R)-sulfoximine in cultured mouse hepatoma cells.

    abstract::Induction of Phase II enzymes of the [Ah] gene battery by L-buthionine (S,R)-sulfoximine (BSO) and other agents was examined in mouse hepatoma Hepa-1c1c7 cells. BSO, a nonelectrophilic inhibitor of gamma-glutamylcysteine synthetase (GCS), is routinely used to examine the toxicological implications of GSH depletion. Ex...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx00045a015

    authors: Shertzer HG,Vasiliou V,Liu RM,Tabor MW,Nebert DW

    更新日期:1995-04-01 00:00:00

  • The detection and identification of 42,43,44,45,46,47,55-heptanor-41-oxoyessotoxin, a new marine toxin from adriatic shellfish, by liquid chromatography-mass spectrometry.

    abstract::The diarrhetic shellfish toxin composition in the digestive glands of mussels collected in June 2001 from the Northern Adriatic sea was investigated by high-performance liquid chromatography coupled with electrospray ion trap mass spectrometry. Along with known yessotoxins (1, 3-6), identified by comparison of their r...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx025527z

    authors: Ciminiello P,Dell'Aversano C,Fattorusso E,Forino M,Magno S,Poletti R

    更新日期:2002-07-01 00:00:00

  • Virtual Cross-Linking of the Active Nemorubicin Metabolite PNU-159682 to Double-Stranded DNA.

    abstract::The DNA alkylating mechanism of PNU-159682 (PNU), a highly potent metabolite of the anthracycline nemorubicin, was investigated by gel-electrophoretic, HPLC-UV, and micro-HPLC/mass spectrometry (MS) measurements. PNU quickly reacted with double-stranded oligonucleotides, but not with single-stranded sequences, to form...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/acs.chemrestox.6b00362

    authors: Scalabrin M,Quintieri L,Palumbo M,Riccardi Sirtori F,Gatto B

    更新日期:2017-02-20 00:00:00

  • Contrasting effects of metal ions on S-nitrosoglutathione, related to coordination equilibria: GSNO decomposition assisted by Ni(II) vs stability Increase in the presence of Zn(II) and Cd(II).

    abstract::Complex formation between nitrosoglutathione (GSNO) and Zn(II), Cd(II), and Ni(II) ions was studied by potentiometry and spectroscopic techniques. GSNO forms simple ML and ML2 type complexes (L = GSNO) with these ions. The stability of GSNO in HEPES buffer solution, pH 7.4, increased in the presence of both Zn(II) and...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx034194i

    authors: Krezel A,Bal W

    更新日期:2004-03-01 00:00:00

  • Reaction of chromium (VI) with hydrogen peroxide in the presence of glutathione: reactive intermediates and resulting DNA damage.

    abstract::The reaction of chromium(VI) with hydrogen peroxide was studied in the presence of glutathione. In vitro, reaction of chromium(VI) with hydrogen peroxide alone led to production of hydroxyl radical as the significant reactive intermediate, while reaction of chromium(VI) with glutathione led to formation of two chromiu...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx00018a016

    authors: Aiyar J,Berkovits HJ,Floyd RA,Wetterhahn KE

    更新日期:1990-11-01 00:00:00

  • Synthesis and characterization of DNA minor groove binding alkylating agents.

    abstract::Derivatives of methyl 3-(1-methyl-5-(1-methyl-5-(propylcarbamoyl)-1H-pyrrol-3-ylcarbamoyl)-1H-pyrrol-3-ylamino)-3-oxopropane-1-sulfonate (1), a peptide-based DNA minor groove binding methylating agent, were synthesized and characterized. In all cases, the N-terminus was appended with an O-methyl sulfonate ester, while...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx300437x

    authors: Iyer P,Srinivasan A,Singh SK,Mascara GP,Zayitova S,Sidone B,Fouquerel E,Svilar D,Sobol RW,Bobola MS,Silber JR,Gold B

    更新日期:2013-01-18 00:00:00

  • Benzo[a]pyrene-induced changes in microRNA-mRNA networks.

    abstract::Toxicological studies assessing the safety of compounds for humans frequently use in vitro systems to characterize toxic responses in combination with transcriptomic analyses. Thus far, changes have mostly been investigated at the mRNA level. Recently, microRNAs have attracted attention because they are powerful negat...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx2003799

    authors: Lizarraga D,Gaj S,Brauers KJ,Timmermans L,Kleinjans JC,van Delft JH

    更新日期:2012-04-16 00:00:00

  • Sustained systemic delivery of green tea polyphenols by polymeric implants significantly diminishes benzo[a]pyrene-induced DNA adducts.

    abstract::The polyphenolics in green tea are believed to be the bioactive components. However, poor bioavailability following ingestion limits their efficacy in vivo. In this study, polyphenon E (poly E), a standardized green tea extract, was administered by sustained-release polycaprolactone implants (two, 2-cm implants; 20% d...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx2000625

    authors: Cao P,Vadhanam MV,Spencer WA,Cai J,Gupta RC

    更新日期:2011-06-20 00:00:00

  • Metabolism and disposition of O6-benzyl-2'-deoxyguanosine in Sprague-Dawley rats.

    abstract::O6-Benzyl-2'-deoxyguanosine is a potential antitumor drug modulator that is intended to reduce or eliminate O6-alkylguanine-DNA alkyltransferase activity in tumors prior to treatment with genotoxic chemotherapeutic alkylating agents. The rationale for using this compound instead of the more active O6-benzylguanine and...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx00042a008

    authors: Kokkinakis DM,Moschel RC,Pegg AE,Dolan ME,Schold SC Jr

    更新日期:1994-11-01 00:00:00

  • Peroxynitrite-dependent tryptophan nitration.

    abstract::Peroxynitrite (ONOO-), the reaction product of superoxide (O2.-) and nitric oxide (.NO), nitrates tyrosine and other phenolics. We report herein that tryptophan is also nitrated by peroxynitrite in the absence of transition metals to one predominant isomer of nitrotryptophan, as determined from spectral characteristic...

    journal_title:Chemical research in toxicology

    pub_type: 杂志文章

    doi:10.1021/tx950133b

    authors: Alvarez B,Rubbo H,Kirk M,Barnes S,Freeman BA,Radi R

    更新日期:1996-03-01 00:00:00