1,221
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Defining Baseline Epigenetic Landscapes in the Rat Liver

, , , , &
Pages 1503-1527 | Received 24 Feb 2017, Accepted 30 Aug 2017, Published online: 13 Nov 2017

References

  • Chen M , SuzukiA , BorlakJ , AndradeRJ , LucenaMI . Drug-induced liver injury: interactions between drug properties and host factors . J. Hepatol.63 ( 2 ), 503 – 514 ( 2015 ).
  • Weiler S , MerzM , Kullak-UblickGA . Drug-induced liver injury: the dawn of biomarkers?F1000Prime Rep.7 , 34 ( 2015 ).
  • Harrill AH , WatkinsPB , SuSet al. Mouse population-guided resequencing reveals that variants in CD44 contribute to acetaminophen-induced liver injury in humans . Genome Res.19 ( 9 ), 1507 – 1515 ( 2009 ).
  • Daly AK . Pharmacogenetics and human genetic polymorphisms . Biochem. J.429 ( 3 ), 435 – 449 ( 2010 ).
  • Watson RE , GoodmanJI . Epigenetics and DNA methylation come of age in toxicology . Toxicol. Sci.67 ( 1 ), 11 – 16 ( 2002 ).
  • Thomson JP , MoggsJG , WolfCR , MeehanRR . Epigenetic profiles as defined signatures of xenobiotic exposure . Mutat. Res.764–765 , 3 – 9 ( 2014 ).
  • Terranova R , VitobelloA , Del Rio EspinolaAet al. Progress in identifying epigenetic mechanisms of xenobiotic-induced non-genotoxic carcinogenesis . Curr. Opin. Toxicol.3 , 62 – 70 ( 2017 ).
  • Watson RE , GoodmanJI . Effects of phenobarbital on DNA methylation in GC-rich regions of hepatic DNA from mice that exhibit different levels of susceptibility to liver tumorigenesis . Toxicol. Sci.68 ( 1 ), 51 – 58 ( 2002 ).
  • Pogribny IP , TryndyakVP , BoureikoAet al. Mechanisms of peroxisome proliferator-induced DNA hypomethylation in rat liver . Mutat. Res.644 ( 1–2 ), 17 – 23 ( 2008 ).
  • Thomson JP , HunterJM , LempiainenHet al. Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver . Nucleic Acids Res.41 ( 11 ), 5639 – 5654 ( 2013 ).
  • Lempiainen H , CouttetP , BolognaniFet al. Identification of Dlk1-Dio3 imprinted gene cluster noncoding RNAs as novel candidate biomarkers for liver tumor promotion . Toxicol. Sci.131 ( 2 ), 375 – 386 ( 2013 ).
  • Thomson JP , OttavianoR , UnterbergerEBet al. Loss of Tet1-associated 5-hydroxymethylcytosine is concomitant with aberrant promoter hypermethylation in liver cancer . Cancer Res.76 ( 10 ), 3097 – 3108 ( 2016 ).
  • Reik W , DeanW . DNA methylation and mammalian epigenetics . Electrophoresis22 ( 14 ), 2838 – 2843 ( 2001 ).
  • Lempiainen H , MullerA , BrasaSet al. Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice . PLoS ONE6 ( 3 ), e18216 ( 2011 ).
  • Thomson JP , LempiainenH , HackettJAet al. Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome . Genome Biol.13 ( 10 ), R93 ( 2012 ).
  • Zhuo H , TangJ , LinZet al. The aberrant expression of MEG3 regulated by UHRF1 predicts the prognosis of hepatocellular carcinoma . Mol. Carcinog.55 ( 2 ), 209 – 219 ( 2016 ).
  • Lian CG , XuS , GuoWet al. Decrease of 5-hydroxymethylcytosine in rat liver with subchronic exposure to genotoxic carcinogens riddelliine and aristolochic acid . Mol. Carcinog.54 ( 11 ), 1503 – 1507 ( 2014 ).
  • Ozden S , Turgut KaraN , SezermanOUet al. Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure . Toxicol. Appl. Pharmacol.289 ( 2 ), 203 – 212 ( 2015 ).
  • Dunican DS , CruickshanksHA , SuzukiMet al. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function . Genome Biol.14 ( 12 ), R146 ( 2013 ).
  • Rommer M , Ellinger-ZiegelbauerH , Grasl-KrauppB , SchwarzM , ZellA . MARCARviz: interactive web-platform for exploratory analysis of toxicogenomics data for nongenotoxic hepatocarcinogenesis . PeerJ Preprints4 , e2393v1 ( 2016 ).
  • Yu Y , FuscoeJC , ZhaoCet al. A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages . Nat. Commun.5 , 3230 ( 2014 ).
  • Bioinformatics Core at the Wellcome Trust Centre for Cell Biology . http://www.bioinformatics.ed.ac.uk/groups/bioinformatics-core-wellcome-trust-centre-cell-biology
  • Functional Annotation Tool DAVID Bioinformatics Resources 6.8, NIAID/NIH . https://david.ncifcrf.gov/summary.jsp
  • Thomson JP , FawkesA , OttavianoRet al. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures . Sci. Rep.5 , 9778 ( 2015 ).
  • Song CX , SzulwachKE , FuYet al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine . Nat. Biotechnol.29 ( 1 ), 68 – 72 ( 2011 ).
  • Hon GC , SongCX , DuTet al. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation . Mol. Cell56 ( 2 ), 286 – 297 ( 2014 ).
  • Putiri EL , TiedemannRL , ThompsonJJet al. Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells . Genome Biol.15 ( 6 ), R81 ( 2014 ).
  • Thomson JP , HunterJM , NestorCEet al. Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques . Nucleic Acids Res.41 ( 22 ), e206 ( 2013 ).
  • Serandour AA , AvnerS , OgerFet al. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers . Nucleic Acids Res.40 ( 17 ), 8255 – 8265 ( 2012 ).
  • Barski A , CuddapahS , CuiKet al. High-resolution profiling of histone methylations in the human genome . Cell129 ( 4 ), 823 – 837 ( 2007 ).
  • Gu J , StevensM , XingXet al. Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome . G3 (Bethesda)6 ( 4 ), 973 – 986 ( 2016 ).
  • Wen L , LiX , YanLet al. Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain . Genome Biol15 ( 3 ), R49 ( 2014 ).
  • Shen Y , YueF , McclearyDFet al. A map of the cis-regulatory sequences in the mouse genome . Nature488 ( 7409 ), 116 – 120 ( 2012 ).
  • Luisier R , LempiainenH , ScherbichlerNet al. Phenobarbital induces cell cycle transcriptional responses in mouse liver humanized for constitutive androstane and pregnane x receptors . Toxicol. Sci.139 ( 2 ), 501 – 511 ( 2014 ).
  • Moggs JG , MaclachlanT , MartusH-J , BentleyP . Derisking drug-induced carcinogenicity for novel therapeutics . Trends Cancer2 ( 8 ), 398 – 408 ( 2016 ).
  • Hardy T , ZeybelM , DayCPet al. Plasma DNA methylation: a potential biomarker for stratification of liver fibrosis in non-alcoholic fatty liver disease . Gut66 ( 7 ), 1321 – 1328 ( 2016 ).