연구동향 분석
박사

Study on DNA methylation patterns of the swine genome using RRBS : 돼지 유전체의 DNA 메틸화 양상 분석

최민경 2016년

논문상세정보
인용/피인용
' Study on DNA methylation patterns of the swine genome using RRBS : 돼지 유전체의 DNA 메틸화 양상 분석' 의 주제별 논문영향력
논문영향력 선정 방법
논문영향력 요약
주제
  • RRBS
  • dna methylation
  • epigenetics
  • gene expression regulation
  • pig
동일주제 총논문수 논문피인용 총횟수 주제별 논문영향력의 평균
304 0

0.0%

' Study on DNA methylation patterns of the swine genome using RRBS : 돼지 유전체의 DNA 메틸화 양상 분석' 의 참고문헌

  • Ziller MJ, Gu H, Muller F, Donaghey J, Tsai LTY, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, et al: Charting a dynamic DNA methylation landscape of the human genome. Nature 2013, 500:477- 481.
  • Zhuang J, Widschwendter M, Teschendorff AE: A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform. BMC Bioinformatics 2012, 13:59.
  • Zhu J-K: Active DNA demethylation mediated by DNA glycosylases. Annual Review of Genetics 2009, 43:143-166.
  • Zhu B, Zheng Y, Hess D, Angliker H, Schwarz S, Siegmann M, Thiry S, Jost J-P: 5-Methylcytosine-DNA glycosylase activity is present in a cloned G/T mismatch DNA glycosylase associated with the chicken embryo DNA demethylation complex. Proceedings of the National Academy of Sciences 2000, 97:5135-5139.
  • Zhang Y, Liu H, Lv J, Xiao X, Zhu J, Liu X, Su J, Li X, Wu Q, Wang F, Cui Y: QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Research 2011, 39:e58- e58.
  • Yu M, Hon Gary C, Szulwach Keith E, Song C-X, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, et al: Base-resolution analysis of 5- hydroxymethylcytosine in the mammalian genome. Cell 2012, 149:1368-1380.
  • Yamaguchi S: Tet1 controls meiosis by regulating meiotic gene expression. Nature 2012.
  • Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, Barbera AJ, Zheng L, Zhang H, Huang S, et al: Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Molecular Cell 2011, 42:451-464.
  • Xu J: Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc Natl Acad Sci USA 2007, 104:12377-12382.
  • Xie W, Barr Cathy L, Kim A, Yue F, Lee Ah Y, Eubanks J, Dempster Emma L, Ren B: Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 2012, 148:816-831.
  • Xie H: Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Res 2011, 39:4099-4108.
  • Xi Y, Li W: BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 2009, 10:232.
  • Xi Y, Bock C, M ller F, Sun D, Meissner A, Li W: RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. Bioinformatics 2012, 28:430-432.
  • Wu SC, Zhang Y: Active DNA demethylation: Many roads lead to Rome (Nature Reviews Molecular Cell Biology (2010) 11 (607-620)). Nature Reviews Molecular Cell Biology 2010, 11:750.
  • Wu H: Dual functions of TET1 in transcriptional regulation in mouse embryonic stem cells. Nature 2011, 473:389-393.
  • Wu H, Zhang Y: Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 2014, 156:45-68.
  • Wu H, Zhang Y: Mechanisms and functions of Tet protein-mediated 5- methylcytosine oxidation. Genes Dev 2011, 25:2436-2452.
  • Wu H, Wu X, Shen L, Zhang Y: Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing. Nat Biotech 2014, 32:1231-1240.
  • Wolf JB: Evolution of genomic imprinting as a coordinator of coadapted gene expression. Proceedings of the National Academy of Sciences 2013, 110:5085-5090.
  • Wolf JB, Hager R: A Maternal–offspring coadaptation theory for the evolution of genomic imprinting. PLoS Biol 2006, 4:e380.
  • Williamson CM, Turner MD, Ball ST, Nottingham WT, Glenister P, Fray M, Tymowska-Lalanne Z, Plagge A, Powles-Glover N, Kelsey G, et al: Identification of an imprinting control region affecting the expression of all transcripts in the Gnas cluster. Nat Genet 2006, 38:350-355.
  • Williams K: TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011, 473:343-348.
  • Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007, 39:457-466.
  • Waterston RH: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
  • Wang X, Clark AG: Using next-generation RNA sequencing to identify imprinted genes. Heredity 2014, 113:156-166.
  • Wang S: Method to detect differentially methylated loci with casecontrol designs using Illumina arrays. Genet Epidemiol 2011, 35:686- 694.
  • Wang L, Sun J, Wu H, Liu S, Wang J, Wu B, Huang S, Li N, Wang J, Zhang X: Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for largesample- scale epigenomic studies. J Biotechnol 2012, 157:1-6.
  • Wang J, Xia Y, Li L, Gong D, Yao Y, Luo H, Lu H, Yi N, Wu H, Zhang X, et al: Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing. BMC Genomics 2013, 14:11.
  • Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, et al: Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res 2013, 23:555-567.
  • Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy- Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, et al: From FastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. In Current Protocols in Bioinformatics. John Wiley & Sons, Inc.; 2013
  • Tumbleson S: Advances in Swine in Biomedical Research. Edited by M. E. Tumbleson and L. B. Schook. Plenum Publishing Corporation. Experimental Physiology 1997, 82:803-804.
  • Thorvaldsen JL, Duran KL, Bartolomei MS: Deletion of the H19 differentially methylated domain results in loss of imprinted expression of H19 and Igf2. Genes & Development 1998, 12:3693-3702.
  • Team RC: R: A language and environment for statistical computing. R Foundation for Statistical Computing; 2014.
  • Tahiliani M: Conversion of 5-methylcytosine to 5- hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935.
  • Szwagierczak A, Bultmann S, Schmidt CS, Spada F, Leonhardt H: Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Research 2010, 38:e181-e181.
  • Szulwach KE, Li X, Li Y, Song C-X, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, et al: Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells. PLoS Genet 2011, 7:e1002154.
  • Suzuki MM, Bird A: DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008, 9:465-476.
  • Susan JC, Harrison J, Paul CL, Frommer M: High sensitivity mapping of methylated cytosines. Nucleic Acids Research 1994, 22:2990-2997.
  • Surani MAH, Barton SC, Norris ML: Nuclear transplantation in the mouse: Heritable differences between parental genomes after activation of the embryonic genome. Cell 1986, 45:127-136.
  • Surani MAH, Barton SC, Norris ML: Influence of parental chromosomes on spatial specificity in androgenetic [harr] parthenogenetic chimaeras in the mouse. Nature 1987, 326:395-397.
  • Surani MAH, Barton SC, Norris ML: Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 1984, 308:548-550.
  • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences 2005, 102:15545-15550.
  • Su J, Wang Y, Xing X, Liu J, Zhang Y: Genome-wide analysis of DNA methylation in bovine placentas. BMC Genomics 2014, 15:12.
  • Su J, Shao X, Liu H, Liu S, Wu Q, Zhang Y: Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics 2012, 99:10-17.
  • Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen S: 5- Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biology 2011, 12:R54.
  • Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100:9440-9445.
  • Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schubeler D: DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 2011, 480:490-495.
  • Spencer HG, Clark AG: Non-conflict theories for the evolution of genomic imprinting. Heredity 2014, 113:112-118.
  • Song J, Rechkoblit O, Bestor TH, Patel DJ: Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 2011, 331:1036-1040.
  • Song C-X, Szulwach Keith E, Dai Q, Fu Y, Mao S-Q, Lin L, Street C, Li Y, Poidevin M, Wu H, et al: Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 2013, 153:678-691.
  • Song C-X, Clark TA, Lu X-Y, Kislyuk A, Dai Q, Turner SW, He C, Korlach J: Sensitive and specific single-molecule sequencing of 5- hydroxymethylcytosine. Nat Meth 2012, 9:75-77.
  • Smith ZD, Meissner A: DNA methylation: roles in mammalian development. Nat Rev Genet 2013, 14:204-220.
  • Smith ZD, Gu H, Bock C, Gnirke A, Meissner A: High-throughput bisulfite sequencing in mammalian genomes. Methods 2009, 48:226- 232.
  • Smith RJ, Dean W, Konfortova G, Kelsey G: Identification of novel imprinted genes in a genome-wide screen for maternal methylation. Genome Research 2003, 13:558-569.
  • Smallwood SA, Tomizawa S, Krueger F, Ruf N, Carli N, Segonds-Pichon A, Sato S, Hata K, Andrews SR, Kelsey G: Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 2011, 43:811-814.
  • Smallwood SA, Kelsey G: De novo DNA methylation: a germ cell perspective. Trends Genet 2012, 28:33-42.
  • Sibley CP, Coan PM, Ferguson-Smith AC, Dean W, Hughes J, Smith P, Reik W, Burton GJ, Fowden AL, Const ncia M: Placental-specific insulin-like growth factor 2 (Igf2) regulates the diffusional exchange characteristics of the mouse placenta. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:8204- 8208.
  • Shukla S: CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011, 479:74-79.
  • Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H: Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 2013, 9:e1003439.
  • Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B: A map of the cis-regulatory sequences in the mouse genome. Nature 2012, 488:116-120.
  • Shen L, Wu H, Diep D, Yamaguchi S, D’Alessio Ana C, Fung H-L, Zhang K, Zhang Y: Genome-wide analysis reveals TET- and TDG-Dependent 5- methylcytosine oxidation dynamics. Cell 2013, 153:692-706.
  • Sharif J: The SRA protein Np95 mediates epigenetic inheritance by recruiting DNMT1 to methylated DNA. Nature 2007, 450:908-912.
  • Serre D, Lee BH, Ting AH: MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res 2010, 38:391-399.
  • Seisenberger S: The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell 2012, 48:849- 862.
  • Saxonov S, Berg P, Brutlag D L: A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006, 103:1412-1417.
  • Savova V, Vigneau S, Gimelbrant AA: Autosomal monoallelic expression: genetics of epigenetic diversity? Current Opinion in Genetics & Development 2013, 23:642-648.
  • Sasaki H, Matsui Y: Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet 2008, 9:129- 140.
  • Sapienza C, Peterson AC, Rossant J, Balling R: Degree of methylation of transgenes is dependent on gamete of origin. Nature 1987, 328:251- 254.
  • Saitou M: Germ cell specification in mice. Curr Opin Genet Dev 2009, 19:386-395.
  • Saitou M, Barton SC, Surani MA: A molecular programme for the specification of germ cell fate in mice. Nature 2002, 418:293-300.
  • Rubin CJ, Megens HJ, Martinez Barrio A, Maqbool K, Sayyab S, Schwochow D, Wang C, Carlborg O, Jern P, Jorgensen CB, et al: Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci U S A 2012, 109:19529-19536.
  • Robinson MD: Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Res 2012.
  • Robertson KD: DNA methylation and human disease. Nat Rev Genet 2005, 6:597-610.
  • Riviere I, Sunshine MJ, Littman DR: Regulation of IL-4 expression by activation of individual alleles. Immunity 1998, 9:217-228.
  • Raval A: Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia. Cell 2007, 129:879-890.
  • Rauch TA, Wang Z, Wu X, Kernstine KH, Riggs AD, Pfeifer GP: DNA methylation biomarkers for lung cancer. Tumour Biol 2012, 33:287-296.
  • Poage GM: Identification of an epigenetic profile classifier that is associated with survival in head and neck cancer. Cancer Res 2012, 72:2728-2737.
  • Philippe Bardou JM, Fr d ric Escudi , Christophe Djemiel and Christophe Klopp: jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15.
  • Pfaffeneder T, Hackner B, Tru M, M nzel M, M ller M, Deiml CA, Hagemeier C, Carell T: The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA. Angewandte Chemie International Edition 2011, 50:7008-7012.
  • Peng Q, Ecker JR: Detection of allele-specific methylation through a generalized heterogeneous epigenome model. Bioinformatics 2012, 28:i163-i171.
  • Pedersen B, Hsieh TF, Ibarra C, Fischer RL: MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics 2011, 27:2435- 2436.
  • Paudel Y, Madsen O, Megens HJ, Frantz LA, Bosse M, Bastiaansen JW, Crooijmans RP, Groenen MA: Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication. BMC Genomics 2013, 14:449.
  • Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, et al: Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011, 473:394-397.
  • Pan H, Chen L, Dogra S, Teh AL, Tan JH, Lim YI, Lim YC, Jin S, Lee YK, Ng PY, et al: Measuring the methylome in clinical samples: improved processing of the Infinium Human Methylation450 BeadChip Array. Epigenetics 2012, 7:1173-1187.
  • Otto C, Stadler PF, Hoffmann S: Fast and sensitive mapping of bisulfitetreated sequencing data. Bioinformatics 2012, 28:1698-1704.
  • Okano M, Xie S, Li E: Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat Genet 1998, 19:219-220.
  • Okano M, Bell DW, Haber DA, Li E: DNA methyltransferases DNMT3A and DNMT3B are essential for de novo methylation and mammalian development. Cell 1999, 99:247-257.
  • Okada Y, Yamagata K, Hong K, Wakayama T, Zhang Y: A role for the elongator complex in zygotic paternal genome demethylation. Nature 2010, 463:554-558.
  • Oakes CC, La Salle S, Smiraglia DJ, Robaire B, Trasler JM: Developmental acquisition of genome-wide DNA methylation occurs prior to meiosis in male germ cells. Dev Biol 2007, 307:368-379.
  • Nielsen R, Paul JS, Albrechtsen A, Song YS: Genotype and SNP calling from next-generation sequencing data. Nature Rev Genet 2011, 12:443- 451.
  • Niculescu MD, Zeisel SH: Diet, methyl donors and DNA methylation: Interactions between dietary folate, methionine and choline. Journal of Nutrition 2002, 132:2333s-2335s.
  • Nguyen DT, Lee K, Choi H, Choi MK, Le MT, Song N, Kim JH, Seo HG, Oh JW, Lee K, et al: The complete swine olfactory subgenome: expansion of the olfactory gene repertoire in the pig genome. BMC Genomics 2012, 13:584.
  • Nag A, Vigneau S, Savova V, Zwemer LM, Gimelbrant AA: Chromatin signature identifies monoallelic gene expression across mammalian cell types. G3: Genes|Genomes|Genetics 2015, 5:1713-1720.
  • Moyzis RK, Torney DC, Meyne J, Buckingham JM, Wu J-R, Burks C, Sirotkin KM, Goad WB: The distribution of interspersed repetitive DNA sequences in the human genome. Genomics 1989, 4:273-289.
  • Moser D: Functional analysis of a potassium-chloride co-transporter 3 (SLC12A6) promoter polymorphism leading to an additional DNA methylation site. Neuropsychopharmacology 2008, 34:458-467.
  • Morgan HD, Santos F, Green K, Dean W, Reik W: Epigenetic reprogramming in mammals. Hum Mol Genet 2005, 14 Spec No 1:R47- 58.
  • Morgan HD, Dean W, Coker HA, Reik W, Petersen-Mahrt SK: Activationinduced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent Tissues: Implications for epigenetic reprogramming. Journal of Biological Chemistry 2004, 279:52353-52360.
  • Moore GE, Oakey R: The role of imprinted genes in humans. Genome Biol 2011, 12:106.
  • Miyanari Y, Torres-Padilla M-E: Control of ground-state pluripotency by allelic regulation of Nanog. Nature 2012, 483:470-473.
  • Miller CA, Hampton O, Coarfa C, Milosavljevic A: ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS ONE 2011, 6:e16327.
  • Metivier R, Gallais R, Tiffoche C, Le Peron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, et al: Cyclical DNA methylation of a transcriptionally active promoter. Nature 2008, 452:45-50.
  • Mell n M, Ayata P, Dewell S, Kriaucionis S, Heintz N: MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 2012, 151:1417-1430.
  • Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454:766-770.
  • Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R: Reduced representation bisulfite sequencing for comparative highresolution DNA methylation analysis. Nucleic Acids Res 2005, 33:5868- 5877.
  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The genome analysis toolkit: A MapReduce framework for analyzing nextgeneration DNA sequencing data. Genome Research 2010, 20:1297- 1303.
  • Matsui T: Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 2010, 464:927-931.
  • Matarese F, Carrillo‐de Santa Pau E, Stunnenberg HG: 5‐Hydroxymethylcytosine: a new kid on the epigenetic block? Molecular Systems Biology 2011, 7.
  • Magklara A, Lomvardas S: Stochastic gene expression in mammals: lessons from olfaction. Trends in Cell Biology 2013, 23:449-456.
  • Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ: Computational and experimental identification of novel human imprinted genes. Genome Research 2007, 17:1723-1730.
  • Long Hannah K, Blackledge Neil P, Klose Robert J: ZF-CxxC domaincontaining proteins, CpG islands and the chromatin connection. Biochemical Society Transactions 2013, 41:727-740.
  • Liu Y, Siegmund KD, Laird PW, Berman BP: Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol 2012, 13:R61.
  • Liu XJ, Wang JQ, Li RS, Yang XJ, Sun QW, Albrecht E, Zhao RQ: Maternal dietary protein affects transcriptional regulation of myostatin gene distinctively at weaning and finishing stages in skeletal muscle of Meishan pigs. Epigenetics 2011, 6:899-907.
  • Liu L ZJ, Bates S, Li JJ, Peehl DM, Rhim JS, Pfeifer GP: A methylation profile of in vitro immortalized human cell lines. International Journal of Oncology 2005, 26:275-285.
  • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322.
  • Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, et al: Global epigenomic reconfiguration during mammalian brain development. Science 2013, 341.
  • Lin S-P, Youngson N, Takada S, Seitz H, Reik W, Paulsen M, Cavaille J, Ferguson-Smith AC: Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12. Nat Genet 2003, 35:97-102.
  • Liang P, Song F, Ghosh S, Morien E, Qin M, Mahmood S, Fujiwara K, Igarashi J, Nagase H, Held WA: Genome-wide survey reveals dynamic widespread tissue-specific changes in DNA methylation during development. BMC Genomics 2011, 12:231.
  • Li M, Wu H, Luo Z, Xia Y, Guan J, Wang T, Gu Y, Chen L, Zhang K, Ma J, et al: An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun 2012, 3:850.
  • Li M, Wang T, Wu H, Zhang J, Zhou C, Jiang A, Li R, Li X: Genome-Wide DNA methylation changes between the superficial and deep backfat tissues of the pig. Int J Mol Sci 2012, 13:7098-7108.
  • Li H, Durbin R: Fast and accurate short read alignment with Burrows– Wheeler transform. Bioinformatics 2009, 25:1754-1760.
  • Lehnertz B: SUV39H-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol 2003, 13:1192-1200.
  • Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, et al: Genome-wide analysis of DNA methylation patterns in horse. BMC Genomics 2014, 15:598.
  • Law JA, Jacobsen SE: Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 2010, 11:204-220.
  • Larsen F, Gundersen G, Lopez R, Prydz H: CpG islands as gene markers in the human genome. Genomics 1992, 13:1095-1107.
  • Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359.
  • Laird PW: Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 2010, 11:191-203.
  • Kwak W, Kim JN, Kim D, Hong JS, Jeong JH, Kim H, Cho S, Kim YY: Genome-wide DNA methylation profiles of small intestine and liver in fast-growing and slow-growing weaning piglets. Asian-Australas J Anim Sci 2014, 27:1532-1539.
  • Krueger F, Kreck B, Franke A, Andrews SR: DNA methylome analysis using short bisulfite sequencing data. Nature Methods 2012, 9:145-151.
  • Krueger F, Andrews SR: Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011, 27:1571-1572.
  • Kriaucionis S, Heintz N: The nuclear DNA base 5- hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324:929-930.
  • Kohli RM, Zhang Y: TET enzymes, TDG and the dynamics of DNA demethylation. Nature 2013, 502:472-479.
  • Kobayashi Y, Absher DM, Gulzar ZG, Young SR, McKenney JK, Peehl DM, Brooks JD, Myers RM, Sherlock G: DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res 2011, 21:1017-1027.
  • Ko M, An J, Bandukwala HS, Chavez L, Aijo T, Pastor WA, Segal MF, Li H, Koh KP, Lahdesmaki H, et al: Modulation of TET2 expression and 5- methylcytosine oxidation by the CXXC domain protein IDAX. Nature 2013, 497:122-126.
  • Knoll JHM, Nicholls RD, Magenis RE, Graham JM, Lalande M, Latt SA, Opitz JM, Reynolds JF: Angelman and Prader-Willi syndromes share a common chromosome 15 deletion but differ in parental origin of the deletion. American Journal of Medical Genetics 1989, 32:285-290.
  • Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler, David: The human genome browser at UCSC. Genome Research 2002, 12:996-1006.
  • Kellinger MW, Song C-X, Chong J, Lu X-Y, He C, Wang D: 5- formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nat Struct Mol Biol 2012, 19:831-833.
  • Karimi MM: DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 2011, 8:676-687.
  • Kaie Lokk VM, Balaji Rajashekar, Kaspar M rtens, Reedik M gi, Raivo Kolde, Marina Koltšina, Torbj rn K Nilsson, Jaak Vilo, Andres Salumets and Neeme T nisson: DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biology 2014, 15.
  • Kagiwada S, Kurimoto K, Hirota T, Yamaji M, Saitou M: Replicationcoupled passive DNA demethylation for the erasure of genome imprints in mice. EMBO J 2012.
  • Jones PA: Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012, 13:484-492.
  • Ji H: Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 2010, 467:338-342.
  • Jaffe AE: Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol 2012, 41:200-209.
  • Jaenisch R, Bird A: Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003.
  • Jackson M: Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells. Mol Cell Biol 2004, 24:8862-8871.
  • J rgensen HF, Ben-Porath I, Bird AP: Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains. Molecular and Cellular Biology 2004, 24:3387-3395.
  • Iyer LM, Tahiliani M, Rao A, Aravind L: Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle 2009, 8:1698-1710.
  • Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y: Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5- carboxylcytosine. Science 2011, 333:1300-1303.
  • Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, et al: The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009, 41:178-186.
  • Igarashi J, Muroi S, Kawashima H, Wang X, Shinojima Y, Kitamura E, Oinuma T, Nemoto N, Song F, Ghosh S, et al: Quantitative analysis of human tissue-specific differences in methylation. Biochem Biophys Res Commun 2008, 376:658-664.
  • Huang YZ, Sun JJ, Zhang LZ, Li CJ, Womack JE, Li ZJ, Lan XY, Lei CZ, Zhang CL, Zhao X, Chen H: Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in Bovine Muscle Tissue (Bos taurine). Scientific Reports 2014, 4:1-17.
  • Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG, Zhu J, Wang P, Xu Y: Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation. Cell 2013, 155:1545-1555.
  • Houseman EA: DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 2012, 13:86.
  • Hornshoj H, Conley LN, Hedegaard J, Sorensen P, Panitz F, Bendixen C: Microarray expression profiles of 20.000 genes across 23 healthy porcine tissues. PLoS One 2007, 2:e1203.
  • Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, et al: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 2012, 22:246-258.
  • Holliday R, Pugh JE: DNA modification mechanisms and gene activity during development. Science 1975, 187:226-232.
  • Heyn H, Sayols S, Moutinho C, Vidal E, Sanchez-Mut JV, Stefansson OA, Nadal E, Moran S, Eyfjord JE, Gonzalez-Suarez E, et al: Linkage of DNA methylation quantitative trait loci to human cancer risk. Cell Rep 2014, 7:331-338.
  • Hermann A, Goyal R, Jeltsch A: The Dnmt1 DNA-(cytosine-C5)- methyltransferase methylates DNA processively with high preference for hemimethylated target sites. Journal of Biological Chemistry 2004, 279:48350-48359.
  • Henckel A, Arnaud P: Genome-wide identification of new imprinted genes. Briefings in Functional Genomics 2010.
  • Hellman A, Chess A: Gene body-specific methylation on the active X chromosome. Science 2007, 315:1141-1143.
  • He Y-F, Li B-Z, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, et al: Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA. Science 2011, 333:1303-1307.
  • Hashimoto H, Pais JE, Zhang X, Saleh L, Fu Z-Q, Dai N, Correa IR, Zheng Y, Cheng X: Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature 2014, 506:391-395.
  • Hartung T, Zhang L, Kanwar R, Khrebtukova I, Reinhardt M, Wang C, Therneau TM, Banck MS, Schroth GP, Beutler AS: Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue. Epigenetics 2012, 7:421-428.
  • Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, et al: Comparison of sequencingbased methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 2010, 28:1097- 1105.
  • Harris EY, Ponts N, Le Roch KG, Lonardi S: BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics 2012, 28:1795-1796.
  • Hansen KD: Increased methylation variation in epigenetic domains across cancer types. Nature Genet 2011, 43:768-775.
  • Halachev K, Bast H, Albrecht F, Lengauer T, Bock C: EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol 2012.
  • Haig D: Genomic imprinting and kinship: How good is the evidence? Annual Review of Genetics 2004, 38:553-585.
  • Haig D, Westoby M: Parent-specific gene expression and the triploid endosperm. The American Naturalist 1989, 134:147-155.
  • Hadchouel M, Farza H, Simon D, Tiollais P, Pourcel C: Maternal inhibition of hepatitis B surface antigen gene expression in transgenic mice correlates with de novo methylation. Nature 1987, 329:454-456.
  • Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M: BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics 2013, 14:774.
  • Guo JU, Su Y, Shin JH, Shin J, Li H, Xie B, Zhong C, Hu S, Le T, Fan G, et al: Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci 2014, 17:215-222.
  • Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y, Yan J, Ren X, Lin S, Li J, et al: The DNA methylation landscape of human early embryos. Nature 2014, 511:606-610.
  • Guibert S, Forne T, Weber M: Global profiling of DNA methylation erasure in mouse primordial germ cells. Genome Res 2012, 22:633-641.
  • Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A: Preparation of reduced representation bisulfite sequencing libraries for genomescale DNA methylation profiling. Nat Protoc 2011, 6:468-481.
  • Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, et al: Analyses of pig genomes provide insight into porcine demography and evolution. Nature 2012, 491:393-398.
  • Gordon K, Clouaire T, Bao XX, Kemp SE, Xenophontos M, de Las Heras JI, Stancheva I: Immortality, but not oncogenic transformation, of primary human cells leads to epigenetic reprogramming of DNA methylation and gene expression. Nucleic Acids Res 2014, 42:3529- 3541.
  • Goldberg AD, Allis CD, Bernstein E: Epigenetics: a landscape takes shape. Cell 2007, 128:635-638.
  • Gloss BS, Patterson KI, Barton CA, Gonzalez M, Scurry JP, Hacker NF, Sutherland RL, O'Brien PM, Clark SJ: Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers. Cancer Lett 2012, 318:76-85.
  • Ghosh S, Yates AJ, Fr hwald MC, Miecznikowski JC, Plass C, Smiraglia D: Tissue specific DNA methylation of CpG islands in normal human adult somatic tissues distinguishes neural from non-neural tissues. Epigenetics 2010, 5:527-538.
  • Gertz J: Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet 2011, 7:e1002228.
  • Gardiner-Garden M, Frommer M: CpG islands in vertebrate genomes. J Mol Biol 1987, 196:261-282.
  • Gao F, Zhang J, Jiang P, Gong D, Wang JW, Xia Y, Ostergaard MV, Wang J, Sangild PT: Marked methylation changes in intestinal genes during the perinatal period of preterm neonates. BMC Genomics 2014, 15:716.
  • Frith MC, Mori R, Asai K: A mostly traditional approach improves alignment of bisulfite-converted DNA. Nucleic Acids Res 2012, 40:e100.
  • Fitzpatrick GV, Soloway PD, Higgins MJ: Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet 2002, 32:426-431.
  • Ficz G: Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011, 473:398-402.
  • Feldman N: G9A-mediated irreversible epigenetic inactivation of Oct- 3/4 during early embryogenesis. Nature Cell Biol 2006, 8:188-194.
  • Elango N, Yi SV: DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 2008, 25:1602-1608.
  • Ehrlich M: DNA hypomethylation in cancer cells. Epigenomics 2009, 1:239-259.
  • Dunican DS, Pennings S, Meehan RR: The CXXC-TET bridge - mind the methylation gap! Cell Res 2013, 23:973-974.
  • Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J, Tomazou EM, et al: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008, 26:779-785.
  • Dong KB: DNA methylation in ES cells requires the lysine methyltransferase G9A but not its catalytic activity. EMBO J 2008, 27:2691-2701.
  • Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd- Acosta C, Rho J, Loewer S, et al: Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 2009, 41:1350-1353.
  • Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F: Evaluation of the infinium methylation 450K technology. Epigenomics 2011, 3:771-784.
  • Deaton AM, Webb S, Kerr AR, Illingworth RS, Guy J, Andrews R, Bird A: Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res 2011, 21:1074-1086.
  • DeVeale B, van der Kooy D, Babak T: Critical evaluation of imprinted gene expression by RNA–Seq: A new perspective. PLoS Genet 2012, 8:e1002600.
  • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43:491-498.
  • De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, et al: Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci 2014, 17:1156-1163.
  • Day T, Bonduriansky R: Intralocus sexual conflict can drive the evolution of genomic imprinting. Genetics 2004, 167:1537-1546.
  • Dawlaty Meelad M, Ganz K, Powell Benjamin E, Hu Y-C, Markoulaki S, Cheng Albert W, Gao Q, Kim J, Choi S-W, Page David C, Jaenisch R: Tet1 Is Dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. Cell Stem Cell 2011, 9:166-175.
  • Cross SH, Charlton JA, Nan X, Bird AP: Purification of CpG islands using a methylated DNA binding column. Nat. Genet. 1994, 6:236–244.
  • Couldrey C, Brauning R, Bracegirdle J, Maclean P, Henderson HV, McEwan JC: Genome-wide DNA methylation patterns and transcription analysis in sheep muscle. PLoS One 2014, 9:e101853.
  • Cortellino S: Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 2011, 146:67-79.
  • Cortazar D: Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Nature 2011, 470:419-423.
  • Cordaux R, Batzer MA: The impact of retrotransposons on human genome evolution. Nature Reviews Genetics 2009, 10:691-703.
  • Coarfa C: Pash 3.0: a versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. BMC Bioinformatics 2011, 11:572.
  • Chow JC, Yen Z, Ziesche SM, Brown CJ: Silencing of the mammalian X chromosome. Annual Review of Genomics and Human Genetics 2005, 6:69-92.
  • Chotalia M, Smallwood SA, Ruf N, Dawson C, Lucifero D, Frontera M, James K, Dean W, Kelsey G: Transcription is required for establishment of germline methylation marks at imprinted genes. Genes & Development 2009, 23:105-117.
  • Choi M, Lee J, Le MT, Nguyen DT, Park S, Soundrarajan N, Schachtschneider KM, Kim J, Park J-K, Kim J-H, Park C: Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing. DNA Research 2015, 22:343-355.
  • Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhart DJ: Transcriptional regulation and function during the human cell cycle. Nat Genet 2001, 27:48-54.
  • Chen WV, Maniatis T: Clustered protocadherins. Development (Cambridge, England) 2013, 140:3297-3302.
  • Chen C-C, Wang K-Y, Shen C-KJ: The mammalian de novo DNA methyltransferases DNMT3A and DNMT3B are also DNA 5- hydroxymethylcytosine dehydroxymethylases. Journal of Biological Chemistry 2012, 287:33116-33121.
  • Cedar H, Bergman Y: Choreography of Ig allelic exclusion. Current Opinion in Immunology 2008, 20:308-317.
  • Buiting K, Saitoh S, Gross S, Dittrich B, Schwartz S, Nicholls RD: Inherited microdeletions in the Angelman and Prader-Willi syndromes define an imprinting centre on human chromosome 15. Nat Genet 1995, 9:395- 400.
  • Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG: Wholegenome DNA methylation profiling using MethylCap-seq. Methods 2010, 52:232-236.
  • Bostick M: UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007, 317:1760-1764.
  • Booth MJ: Quantitative sequencing of 5-methylcytosine and 5- hydroxymethylcytosine at single-base resolution. Science 2012, 336:934-937.
  • Bolado-Carrancio A, Riancho JA, Sainz J, Rodriguez-Rey JC: Activation of nuclear receptor NR5A2 increases Glut4 expression and glucose metabolism in muscle cells. Biochem Biophys Res Commun 2014, 446:614-619.
  • Bock C, Walter J, Paulsen M, Lengauer T: Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res 2008, 36:e55.
  • Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H, Jager N, Gnirke A, Stunnenberg HG, Meissner A: Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 2010, 28:1106-1114.
  • Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A: DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell 2012, 47:633-647.
  • Bjornsson HT: Intra-individual change over time in DNA methylation with familial clustering. JAMA 2008, 299:2877-2883.
  • Bix M, Locksley RM: Independent and epigenetic regulation of the interleukin-4 alleles in CD4+ T cells. Science 1998, 281:1352-1354.
  • Bischoff SR, Tsai S, Hardison N, Motsinger-Reif AA, Freking BA, Nonneman D, Rohrer G, Piedrahita JA: Characterization of conserved and nonconserved imprinted genes in swine. Biology of Reproduction 2009, 81:906-920.
  • Bird A: DNA methylation patterns and epigenetic memory. Genes Dev 2002, 16:6-21.
  • Barlow DP, Stoger R, Herrmann BG, Saito K, Schweifer N: The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus. Nature 1991, 349:84-87.
  • Altmann S, Murani E, Schwerin M, Metges CC, Wimmers K, Ponsuksili S: Maternal dietary protein restriction and excess affects offspring gene expression and methylation of non-SMC subunits of condensin I in liver and skeletal muscle. Epigenetics 2012, 7:239-252.
  • Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE: methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 2012, 13:R87.