87
Views
41
CrossRef citations to date
0
Altmetric
Article

Tet1 and Tet2 Protect DNA Methylation Canyons against Hypermethylation

, , , , , & ORCID Icon show all
Pages 452-461 | Received 11 Jun 2015, Accepted 12 Nov 2015, Published online: 17 Mar 2023

REFERENCES

  • Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. 2013. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153:1134–1148. http://dx.doi.org/10.1016/j.cell.2013.04.022.
  • Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A. 2013. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153:1149–1163. http://dx.doi.org/10.1016/j.cell.2013.04.037.
  • Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935. http://dx.doi.org/10.1126/science.1170116.
  • Wu H, Zhang Y. 2014. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 156:45–68. http://dx.doi.org/10.1016/j.cell.2013.12.019.
  • Huang Y, Rao A. 2014. Connections between TET proteins and aberrant DNA modification in cancer. Trends Genet 30:464–474. http://dx.doi.org/10.1016/j.tig.2014.07.005.
  • Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, Stojic L, Halim S, Vowler SL, Lynch AG, Delatte B, de Bony EJ, Colin L, Defrance M, Krueger F, Silva AL, Ten Hoopen R, Ibrahim AE, Fuks F, Murrell A. 2015. 5-Hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Genome Biol 16:69. http://dx.doi.org/10.1186/s13059-015-0605-5.
  • Dawlaty MM, Breiling A, Le T, Barrasa MI, Raddatz G, Gao Q, Powell BE, Cheng AW, Faull KF, Lyko F, Jaenisch R. 2014. Loss of Tet enzymes compromises proper differentiation of embryonic stem cells. Dev Cell 29:102–111. http://dx.doi.org/10.1016/j.devcel.2014.03.003.
  • Dawlaty MM, Breiling A, Le T, Raddatz G, Barrasa MI, Cheng AW, Gao Q, Powell BE, Li Z, Xu M, Faull KF, Lyko F, Jaenisch R. 2013. Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. Dev Cell 24:310–323. http://dx.doi.org/10.1016/j.devcel.2012.12.015.
  • Hackett JA, Dietmann S, Murakami K, Down TA, Leitch HG, Surani MA. 2013. Synergistic mechanisms of DNA demethylation during transition to ground-state pluripotency. Stem Cell Reports 1:518–531. http://dx.doi.org/10.1016/j.stemcr.2013.11.010.
  • Sérandour AA, Avner S, Oger F, Bizot M, Percevault F, Lucchetti-Miganeh C, Palierne G, Gheeraert C, Barloy-Hubler F, Péron CL, Madigou T, Durand E, Froguel P, Staels B, Lefebvre P, Métivier R, Eeckhoute J, Salbert G. 2012. Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic Acids Res 40:8255–8265. http://dx.doi.org/10.1093/nar/gks595.
  • Lu F, Liu Y, Jiang L, Yamaguchi S, Zhang Y. 2014. Role of Tet proteins in enhancer activity and telomere elongation. Genes Dev 28:2103–2119. http://dx.doi.org/10.1101/gad.248005.114.
  • Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, Ren B. 2014. 5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol Cell 56:286–297. http://dx.doi.org/10.1016/j.molcel.2014.08.026.
  • Schübeler D. 2015. Function and information content of DNA methylation. Nature 517:321–326. http://dx.doi.org/10.1038/nature14192.
  • Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. 2011. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480:490–495. http://dx.doi.org/10.1038/nature10716.
  • Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, Zhang X, Chavez L, Wang H, Hannah R, Kim SB, Yang L, Ko M, Chen R, Göttgens B, Lee JS, Gunaratne P, Godley LA, Darlington GJ, Rao A, Li W, Goodell MA. 2014. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet 46:17–23. http://dx.doi.org/10.1038/ng.2836.
  • Delatte B, Deplus R, Fuks F. 2014. Playing TETris with DNA modifications. EMBO J 33:1198–1211. http://dx.doi.org/10.15252/embj.201488290.
  • Ehrlich M, Ehrlich KC. 2014. DNA cytosine methylation and hydroxymethylation at the borders. Epigenomics 6:563–566. http://dx.doi.org/10.2217/epi.14.48.
  • Tuorto F, Liebers R, Musch T, Schaefer M, Hofmann S, Kellner S, Frye M, Helm M, Stoecklin G, Lyko F. 2012. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol 19:900–905. http://dx.doi.org/10.1038/nsmb.2357.
  • Raddatz G, Gao Q, Bender S, Jaenisch R, Lyko F. 2012. Dnmt3a protects active chromosome domains against cancer-associated hypomethylation. PLoS Genet 8:e1003146. http://dx.doi.org/10.1371/journal.pgen.1003146.
  • Xi Y, Li W. 2009. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10:232. http://dx.doi.org/10.1186/1471-2105-10-232.
  • Ernst J, Kellis M. 2012. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9:215–216. http://dx.doi.org/10.1038/nmeth.1906.
  • Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560. http://dx.doi.org/10.1038/nature06008.
  • Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. 2012. A map of the cis-regulatory sequences in the mouse genome. Nature 488:116–120. http://dx.doi.org/10.1038/nature11243.
  • Sun D, Xi Y, Rodriguez B, Park HJ, Tong P, Meong M, Goodell MA, Li W. 2014. MOABS: model based analysis of bisulfite sequencing data. Genome Biol 15:R38. http://dx.doi.org/10.1186/gb-2014-15-2-r38.
  • Bocker MT, Tuorto F, Raddatz G, Musch T, Yang FC, Xu M, Lyko F, Breiling A. 2012. Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster. Nat Commun 3:818. http://dx.doi.org/10.1038/ncomms1826.
  • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111. http://dx.doi.org/10.1093/bioinformatics/btp120.
  • Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11:R106. http://dx.doi.org/10.1186/gb-2010-11-10-r106.
  • Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. 2013. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31:46–53. http://dx.doi.org/10.1038/nbt.2450.
  • Hong EE, Okitsu CY, Smith AD, Hsieh CL. 2013. Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA. Mol Cell Biol 33:2683–2690. http://dx.doi.org/10.1128/MCB.00220-13.
  • Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. 2008. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40:897–903. http://dx.doi.org/10.1038/ng.154.
  • Zentner GE, Tesar PJ, Scacheri PC. 2011. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 21:1273–1283. http://dx.doi.org/10.1101/gr.122382.111.
  • Chen Y, Jørgensen M, Kolde R, Zhao X, Parker B, Valen E, Wen J, Sandelin A. 2011. Prediction of RNA polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics 12:544. http://dx.doi.org/10.1186/1471-2164-12-544.
  • Huang Y, Chavez L, Chang X, Wang X, Pastor WA, Kang J, Zepeda-Martínez JA, Pape UJ, Jacobsen SE, Peters B, Rao A. 2014. Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc Natl Acad Sci U S A 111:1361–1366. http://dx.doi.org/10.1073/pnas.1322921111.
  • Rosen ED, MacDougald OA. 2006. Adipocyte differentiation from the inside out. Nat Rev Mol Cell Biol 7:885–896. http://dx.doi.org/10.1038/nrm2066.
  • Omatsu Y, Seike M, Sugiyama T, Kume T, Nagasawa T. 2014. Foxc1 is a critical regulator of haematopoietic stem/progenitor cell niche formation. Nature 508:536–540. http://dx.doi.org/10.1038/nature13071.
  • Davis KE, Moldes M, Farmer SR. 2004. The forkhead transcription factor FoxC2 inhibits white adipocyte differentiation. J Biol Chem 279:42453–42461. http://dx.doi.org/10.1074/jbc.M402197200.
  • Thiery JP, Acloque H, Huang RY, Nieto MA. 2009. Epithelial-mesenchymal transitions in development and disease. Cell 139:871–890. http://dx.doi.org/10.1016/j.cell.2009.11.007.
  • Hader C, Marlier A, Cantley L. 2010. Mesenchymal-epithelial transition in epithelial response to injury: the role of Foxc2. Oncogene 29:1031–1040. http://dx.doi.org/10.1038/onc.2009.397.
  • Bard JB, Lam MS, Aitken S. 2008. A bioinformatics approach for identifying candidate transcriptional regulators of mesenchyme-to-epithelium transitions in mouse embryos. Dev Dyn 237:2748–2754. http://dx.doi.org/10.1002/dvdy.21652.
  • Hu X, Zhang L, Mao SQ, Li Z, Chen J, Zhang RR, Wu HP, Gao J, Guo F, Liu W, Xu GF, Dai HQ, Shi YG, Li X, Hu B, Tang F, Pei D, Xu GL. 2014. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 14:512–522. http://dx.doi.org/10.1016/j.stem.2014.01.001.
  • Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K. 2011. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473:343–348. http://dx.doi.org/10.1038/nature10066.
  • Tsai YP, Chen HF, Chen SY, Cheng WC, Wang HW, Shen ZJ, Song C, Teng SC, He C, Wu KJ. 2014. TET1 regulates hypoxia-induced epithelial-mesenchymal transition by acting as a co-activator. Genome Biol 15:513. http://dx.doi.org/10.1186/s13059-014-0513-0.
  • Jin C, Lu Y, Jelinek J, Liang S, Estecio MR, Barton MC, Issa JP. 2014. TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells. Nucleic Acids Res 42:6956–6971. http://dx.doi.org/10.1093/nar/gku372.
  • Nakamura R, Tsukahara T, Qu W, Ichikawa K, Otsuka T, Ogoshi K, Saito TL, Matsushima K, Sugano S, Hashimoto S, Suzuki Y, Morishita S, Takeda H. 2014. Large hypomethylated domains serve as strong repressive machinery for key developmental genes in vertebrates. Development 141:2568–2580. http://dx.doi.org/10.1242/dev.108548.
  • Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y. 2011. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev 25:679–684. http://dx.doi.org/10.1101/gad.2036011.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.