Information
References
Contents
Download
[1]J. B. Stanford, T. A. Parnell and P. C. Boyle: Outcomes from treatment of infertility with natural procreative technology in an Irish general practice. J Am Board Fam Med, 21(5), 375-84 (2008)
[2]H. T. Bjornsson, M. D. Fallin and A. P. Feinberg: An integrated epigenetic and genetic approach to common human disease. Trends Genet, 20(8), 350-8 (2004)
[3]L. Liu, Y. Li and T. O. Tollefsbol: Gene-environment interactions and epigenetic basis of human diseases. Curr Issues Mol Biol, 10(1-2), 25-36 (2008)
[4]N. Bunkar, N. Pathak, N. K. Lohiya and P. K. Mishra: Epigenetics: A key paradigm in reproductive health. Clin Exp Reprod Med, 43(2), 59-81 (2016)
[5]F. S. Collins, E. D. Green, A. E. Guttmacher and M. S. Guyer: A vision for the future of genomics research. Nature, 422(6934), 835-47 (2003)
[6]M. L. Whitfield, G. Sherlock, A. J. Saldanha, J. I. Murray, C. A. Ball, K. E. Alexander, J. C. Matese, C. M. Perou, M. M. Hurt, P. O. Brown and D. Botstein: Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell, 13(6), 1977-2000 (2002)
[7]E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigo, T. R. Gingeras, E. H. Margulies, Z. Weng, M. Snyder, E. T. Dermitzakis, R. E. Thurman, M. S. Kuehn, C. M. Taylor, S. Neph, C. M. Koch, S. Asthana, A. Malhotra, I. Adzhubei, J. A. Greenbaum, R. M. Andrews, P. Flicek, P. J. Boyle, H. Cao, N. P. Carter, G. K. Clelland, S. Davis, N. Day, P. Dhami, S. C. Dillon, M. O. Dorschner, H. Fiegler, P. G. Giresi, J. Goldy, M. Hawrylycz, A. Haydock, R. Humbert, K. D. James, B. E. Johnson, E. M. Johnson, T. T. Frum, E. R. Rosenzweig, N. Karnani, K. Lee, G. C. Lefebvre, P. A. Navas, F. Neri, S. C. Parker, P. J. Sabo, R. Sandstrom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, M. Yu, F. S. Collins, J. Dekker, J. D. Lieb, T. D. Tullius, G. E. Crawford, S. Sunyaev, W. S. Noble, I. Dunham, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D. Zheng, R. Castelo, A. Frankish, J. Harrow, S. Ghosh, A. Sandelin, I. L. Hofacker, R. Baertsch, D. Keefe, S. Dike, J. Cheng, H. A. Hirsch, E. A. Sekinger, J. Lagarde, J. F. Abril, A. Shahab, C. Flamm, C. Fried, J. Hackermuller, J. Hertel, M. Lindemeyer, K. Missal, A. Tanzer, S. Washietl, J. Korbel, O. Emanuelsson, J. S. Pedersen, N. Holroyd, R. Taylor, D. Swarbreck, N. Matthews, M. C. Dickson, D. J. Thomas, M. T. Weirauch, J. Gilbert, J. Drenkow, I. Bell, X. Zhao, K. G. Srinivasan, W. K. Sung, H. S. Ooi, K. P. Chiu, S. Foissac, T. Alioto, M. Brent, L. Pachter, M. L. Tress, A. Valencia, S. W. Choo, C. Y. Choo, C. Ucla, C. Manzano, C. Wyss, E. Cheung, T. G. Clark, J. B. Brown, M. Ganesh, S. Patel, H. Tammana, J. Chrast, C. N. Henrichsen, C. Kai, J. Kawai, U. Nagalakshmi, J. Wu, Z. Lian, J. Lian, P. Newburger, X. Zhang, P. Bickel, J. S. Mattick, P. Carninci, Y. Hayashizaki, S. Weissman, T. Hubbard, R. M. Myers, J. Rogers, P. F. Stadler, T. M. Lowe, C. L. Wei, Y. Ruan, K. Struhl, M. Gerstein, S. E. Antonarakis, Y. Fu, E. D. Green, U. Karaoz, A. Siepel, J. Taylor, L. A. Liefer, K. A. Wetterstrand, P. J. Good, E. A. Feingold, M. S. Guyer, G. M. Cooper, G. Asimenos, C. N. Dewey, M. Hou, S. Nikolaev, J. I. Montoya-Burgos, A. Loytynoja, S. Whelan, F. Pardi, T. Massingham, H. Huang, N. R. Zhang, I. Holmes, J. C. Mullikin, A. Ureta-Vidal, B. Paten, M. Seringhaus, D. Church, K. Rosenbloom, W. J. Kent, E. A. Stone, S. Batzoglou, N. Goldman, R. C. Hardison, D. Haussler, W. Miller, A. Sidow, N. D. Trinklein, Z. D. Zhang, L. Barrera, R. Stuart, D. C. King, A. Ameur, S. Enroth, M. C. Bieda, J. Kim, A. A. Bhinge, N. Jiang, J. Liu, F. Yao, V. B. Vega, C. W. Lee, P. Ng, A. Shahab, A. Yang, Z. Moqtaderi, Z. Zhu, X. Xu, S. Squazzo, M. J. Oberley, D. Inman, M. A. Singer, T. A. Richmond, K. J. Munn, A. Rada-Iglesias, O. Wallerman, J. Komorowski, J. C. Fowler, P. Couttet, A. W. Bruce, O. M. Dovey, P. D. Ellis, C. F. Langford, D. A. Nix, G. Euskirchen, S. Hartman, A. E. Urban, P. Kraus, S. Van Calcar, N. Heintzman, T. H. Kim, K. Wang, C. Qu, G. Hon, R. Luna, C. K. Glass, M. G. Rosenfeld, S. F. Aldred, S. J. Cooper, A. Halees, J. M. Lin, H. P. Shulha, X. Zhang, M. Xu, J. N. Haidar, Y. Yu, Y. Ruan, V. R. Iyer, R. D. Green, C. Wadelius, P. J. Farnham, B. Ren, R. A. Harte, A. S. Hinrichs, H. Trumbower, H. Clawson, J. Hillman-Jackson, A. S. Zweig, K. Smith, A. Thakkapallayil, G. Barber, R. M. Kuhn, D. Karolchik, L. Armengol, C. P. Bird, P. I. de Bakker, A. D. Kern, N. Lopez-Bigas, J. D. Martin, B. E. Stranger, A. Woodroffe, E. Davydov, A. Dimas, E. Eyras, I. B. Hallgrimsdottir, J. Huppert, M. C. Zody, G. R. Abecasis, X. Estivill, G. G. Bouffard, X. Guan, N. F. Hansen, J. R. Idol, V. V. Maduro, B. Maskeri, J. C. McDowell, M. Park, P. J. Thomas, A. C. Young, R. W. Blakesley, D. M. Muzny, E. Sodergren, D. A. Wheeler, K. C. Worley, H. Jiang, G. M. Weinstock, R. A. Gibbs, T. Graves, R. Fulton, E. R. Mardis, R. K. Wilson, M. Clamp, J. Cuff, S. Gnerre, D. B. Jaffe, J. L. Chang, K. Lindblad-Toh, E. S. Lander, M. Koriabine, M. Nefedov, K. Osoegawa, Y. Yoshinaga, B. Zhu and P. J. de Jong: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816 (2007)
[8]J. T. Kung, D. Colognori and J. T. Lee: Long noncoding RNAs: past, present, and future. Genetics, 193(3), 651-69 (2013)
[9]H. B. Fraser: Cell-cycle regulated transcription associates with DNA replication timing in yeast and human. Genome Biol, 14(10), R111 (2013)
[10]S. Minocherhomji, A. S. Athalye, P. F. Madon, D. Kulkarni, S. A. Uttamchandani and F. R. Parikh: A case-control study identifying chromosomal polymorphic variations as forms of epigenetic alterations associated with the infertility phenotype. Fertil Steril, 92(1), 88-95 (2009)
[11]K. Rull, L. Nagirnaja and M. Laan: Genetics of recurrent miscarriage: challenges, current knowledge, future directions. Front Genet, 3, 34 (2012)
[12]G. Egger, G. Liang, A. Aparicio and P. A. Jones: Epigenetics in human disease and prospects for epigenetic therapy. Nature, 429(6990), 457-63 (2004)
[13]K. Stotz: Extended evolutionary psychology: the importance of transgenerational developmental plasticity. Front Psychol, 5, 908 (2014)
[14]S. Sharma, T. K. Kelly and P. A. Jones: Epigenetics in cancer. Carcinogenesis, 31(1), 27-36 (2010)
[15]D. E. Handy, R. Castro and J. Loscalzo: Epigenetic modifications: basic mechanisms and role in cardiovascular disease. Circulation, 123(19), 2145-56 (2011)
[16]A. Portela and M. Esteller: Epigenetic modifications and human disease. Nat Biotechnol, 28(10), 1057-68 (2010)
[17]P. B. Talbert and S. Henikoff: Spreading of silent chromatin: inaction at a distance. Nat Rev Genet, 7(10), 793-803 (2006)
[18]P. R. Kanherkar, N. Bhatia-Dey and A. B. Csoka: Epigenetics across the human lifespan. Front Cell Dev Biol, 2, 49 (2014)
[19]M. Teperek and K. Miyamoto: Nuclear reprogramming of sperm and somatic nuclei in eggs and oocytes. Reprod Med Biol, 12, 133-149 (2013)
[20]E. Li: Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet, 3(9), 662-73 (2002)
[21]R. Jaenisch and A. Bird: Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet, 33 Suppl, 245-54 (2003)
[22]E. R. Gibney and C. M. Nolan: Epigenetics and gene expression. Heredity (Edinb), 105(1), 4-13 (2010)
[23]B. Jin, Y. Li and K. D. Robertson: DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer, 2(6), 607-17 (2011)
[24]P. A. Jones and G. Liang: Rethinking how DNA methylation patterns are maintained. Nat Rev Genet, 10(11), 805-11 (2009)
[25]J. A. Law and S. E. Jacobsen: Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet, 11(3), 204-20 (2010)
[26]J. Barau, A. Teissandier, N. Zamudio, S. Roy, V. Nalesso, Y. Herault, F. Guillou and D. Bourc’his: The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science, 354(6314), 909-912 (2016)
[27]F. Chedin, M. R. Lieber and C. L. Hsieh: The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A, 99(26), 16916-21 (2002)
[28]C. W. Hanna and G. Kelsey: The specification of imprints in mammals. Heredity (Edinb), 113(2), 176-83 (2014)
[29]G. Raddatz, P. M. Guzzardo, N. Olova, M. R. Fantappie, M. Rampp, M. Schaefer, W. Reik, G. J. Hannon and F. Lyko: Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proc Natl Acad Sci U S A, 110(21), 8627-31 (2013)
[30]O. Bogdanovic and G. J. Veenstra: DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma, 118(5), 549-65 (2009)
[31]T. Clouaire and I. Stancheva: Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin? Cell Mol Life Sci, 65(10), 1509-22 (2008)
[32]H. Wu and Y. Zhang: Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev, 25(23), 2436-52 (2011)
[33]N. Bhutani, D. M. Burns and H. M. Blau: DNA demethylation dynamics. Cell, 146(6), 866-72 (2011)
[34]C. C. Chen, K. Y. Wang and C. K. Shen: DNA 5-methylcytosine demethylation activities of the mammalian DNA methyltransferases. J Biol Chem, 288(13), 9084-91 (2013)
[35]H. Wu and Y. Zhang: Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell, 156(1-2), 45-68 (2014)
[36]D. Sengupta, M. Deb, S. K. Rath, S. Kar, S. Parbin, N. Pradhan and S. K. Patra: DNA methylation and not H3K4 trimethylation dictates the expression status of miR-152 gene which inhibits migration of breast cancer cells via DNMT1/CDH1 loop. Exp Cell Res, 346(2), 176-87 (2016)
[37]A. Shilpi, S. Parbin, D. Sengupta, S. Kar, M. Deb, S. K. Rath, N. Pradhan, M. Rakshit and S. K. Patra: Mechanisms of DNA methyltransferase-inhibitor interactions: Procyanidin B2 shows new promise for therapeutic intervention of cancer. Chem Biol Interact, 233, 122-38 (2015)
[38]S. Kar, D. Sengupta, M. Deb, A. Shilpi, S. Parbin, S. K. Rath, N. Pradhan, M. Rakshit and S. K. Patra: Expression profiling of DNA methylation-mediated epigenetic gene-silencing factors in breast cancer. Clin Epigenetics, 6(1), 20 (2014)
[39]M. Deb, S. Kar, D. Sengupta, A. Shilpi, S. Parbin, S. K. Rath, V. A. Londhe and S. K. Patra: Chromatin dynamics: H3K4 methylation and H3 variant replacement during development and in cancer. Cell Mol Life Sci, 71(18), 3439-63 (2014)
[40]S. Kar, M. Deb, D. Sengupta, A. Shilpi, S. Parbin, J. Torrisani, S. Pradhan and S. Patra: An insight into the various regulatory mechanisms modulating human DNA methyltransferase 1 stability and function. Epigenetics, 7(9), 994-1007 (2012)
[41]S. K. Patra, A. Patra, F. Rizzi, T. C. Ghosh and S. Bettuzzi: Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development. Cancer Metastasis Rev, 27(2), 315-34 (2008)
[42]S. K. Patra and M. Szyf: DNA methylation-mediated nucleosome dynamics and oncogenic Ras signaling: insights from FAS, FAS ligand and RASSF1A. FEBS J, 275(21), 5217-35 (2008)
[43]V. Morales and H. Richard-Foy: Role of histone N-terminal tails and their acetylation in nucleosome dynamics. Mol Cell Biol, 20(19), 7230-7 (2000)
[44]S. D. Taverna, H. Li, A. J. Ruthenburg, C. D. Allis and D. J. PaTel: How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol, 14(11), 1025-40 (2007)
[45]L. Marino-Ramirez, M. G. Kann, B. A. Shoemaker and D. Landsman: Histone structure and nucleosome stability. Expert Rev Proteomics, 2(5), 719-29 (2005)
[46]H. J. Szerlong and J. C. Hansen: Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure. Biochem Cell Biol, 89(1), 24-34 (2011)
[47]C. Wood, A. Snijders, J. Williamson, C. Reynolds, J. Baldwin and M. Dickman: Post-translational modifications of the linker histone variants and their association with cell mechanisms. FEBS J, 276(14), 3685-97 (2009)
[48]D. Bonenfant, H. Towbin, M. Coulot, P. Schindler, D. R. Mueller and J. van Oostrum: Analysis of dynamic changes in post-translational modifications of human histones during cell cycle by mass spectrometry. Mol Cell Proteomics, 6(11), 1917-32 (2007)
[49]B. E. Bernstein, A. Meissner and E. S. Lander: The mammalian epigenome. Cell, 128(4), 669-81 (2007)
[50]J. Bannister and T. Kouzarides: Regulation of chromatin by histone modifications. Cell Res, 21(3), 381-95 (2011)
[51]B. D. Price and A. D. D’Andrea: Chromatin remodeling at DNA double-strand breaks. Cell, 152(6), 1344-54 (2013)
[52]M. Papamichos-Chronakis and C. L. Peterson: Chromatin and the genome integrity network. Nat Rev Genet, 14(1), 62-75 (2013)
[53]C. R. Vakoc, M. M. Sachdeva, H. Wang and G. A. Blobel: Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol, 26(24), 9185-95 (2006)
[54]T. Kouzarides: Chromatin modifications and their function. Cell, 128(4), 693-705 (2007)
[55]A. Sadakierska-Chudy and M. Filip: A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs. Neurotox Res, 27(2), 172-97 (2015)
[56]M. Deb, D. Sengupta, S. Kar, S. K. Rath, S. Roy, G. Das and S. K. Patra: Epigenetic drift towards histone modifications regulates CAV1 gene expression in colon cancer. Gene, 581(1), 75-84 (2016)
[57]M. Deb, D. Sengupta, S. K. Rath, S. Kar, S. Parbin, A. Shilpi, N. Pradhan, S. K. Bhutia, S. Roy and S. K. Patra: Clusterin gene is predominantly regulated by histone modifications in human colon cancer and ectopic expression of the nuclear isoform induces cell death. Biochim Biophys Acta, 1852(8), 1630-45 (2015)
[58]K. C. Wang and H. Y. Chang: Molecular mechanisms of long noncoding RNAs. Mol Cell, 43(6), 904-14 (2011)
[59]J. L. Rinn and H. Y. Chang: Genome regulation by long noncoding RNAs. Annu Rev Biochem, 81, 145-66 (2012)
[60]J. S. Mattick and I. V. Makunin: Non-coding RNA. Hum Mol Genet, 15 Spec No 1, R17-29 (2006)
[61]K. V. Prasanth and D. L. Spector: Eukaryotic regulatory RNAs: an answer to the ’genome complexity’ conundrum. Genes Dev, 21(1), 11-42 (2007)
[62]M. V. Koerner, F. M. Pauler, R. Huang and D. P. Barlow: The function of non-coding RNAs in genomic imprinting. Development, 136(11), 1771-83 (2009)
[63]V. E. Villegas and P. G. Zaphiropoulos: Neighboring gene regulation by antisense long non-coding RNAs. Int J Mol Sci, 16(2), 3251-66 (2015)
[64]V. J. Peschansky and C. Wahlestedt: Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics, 9(1), 3-12 (2014)
[65]R. S. Pillai: MicroRNA function: multiple mechanisms for a tiny RNA? RNA, 11(12), 1753-61 (2005)
[66]K. Prevost, G. Desnoyers, J. F. Jacques, F. Lavoie and E. Masse: Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev, 25(4), 385-96 (2011)
[67]S. Lamouille, J. Xu and R. Derynck: Molecular mechanisms of epithelial-mesenchymal transition. Nat Rev Mol Cell Biol, 15(3), 178-96 (2014)
[68]R. W. Carthew and E. J. Sontheimer: Origins and Mechanisms of miRNAs and siRNAs. Cell, 136(4), 642-55 (2009)
[69]D. Moazed: Small RNAs in transcriptional gene silencing and genome defence. Nature, 457(7228), 413-20 (2009)
[70]M. U. Kaikkonen, M. T. Lam and C. K. Glass: Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res, 90(3), 430-40 (2011)
[71]J. Brennecke, A. A. Aravin, A. Stark, M. Dus, M. Kellis, R. Sachidanandam and G. J. Hannon: Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128(6), 1089-103 (2007)
[72]T. R. Mercer and J. S. Mattick: Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol, 20(3), 300-7 (2013)
[73]P. Han and C. P. Chang: Long non-coding RNA and chromatin remodeling. RNA Biol, 12(10), 1094-8 (2015)
[74]S. Geisler and J. Coller: RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol, 14(11), 699-712 (2013)
[75]A. Saxena and P. Carninci: Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays, 33(11), 830-9 (2011)
[76]L. Bai and A. V. Morozov: Gene regulation by nucleosome positioning. Trends Genet, 26(11), 476-83 (2010)
[77]K. Struhl and E. Segal: Determinants of nucleosome positioning. Nat Struct Mol Biol, 20(3), 267-73 (2013)
[78]T. K. Kelly, T. B. Miranda, G. Liang, B. P. Berman, J. C. Lin, A. Tanay and P. A. Jones: H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell, 39(6), 901-11 (2010)
[79]H. Cedar and Y. Bergman: Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet, 10(5), 295-304 (2009)
[80]S. Kimmins and P. Sassone-Corsi: Chromatin remodelling and epigenetic features of germ cells. Nature, 434(7033), 583-9 (2005)
[81]S. Seisenberger, J. R. Peat, T. A. Hore, F. Santos, W. Dean and W. Reik: Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers. Philos Trans R Soc Lond B Biol Sci, 368(1609), 20110330 (2013)
[82]S. K. Kota and R. Feil: Epigenetic transitions in germ cell development and meiosis. Dev Cell, 19(5), 675-86 (2010)
[83]H. Sasaki and Y. Matsui: Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet, 9(2), 129-40 (2008)
[84]M. Saitou and M. Yamaji: Primordial germ cells in mice. Cold Spring Harb Perspect Biol, 4(11) (2012)
[85]K. Hogg and P. S. Western: Refurbishing the germline epigenome: Out with the old, in with the new. Semin Cell Dev Biol, 45, 104-13 (2015)
[86]A. Nikolic, V. Volarevic, L. Armstrong, M. Lako and M. Stojkovic: Primordial Germ Cells: Current Knowledge and Perspectives. Stem Cells Int, 2016, 1741072 (2016)
[87]Z. Hochberg, R. Feil, M. Constancia, M. Fraga, C. Junien, J. C. Carel, P. Boileau, Y. Le Bouc, C. L. Deal, K. Lillycrop, R. Scharfmann, A. Sheppard, M. Skinner, M. Szyf, R. A. Waterland, D. J. Waxman, E. Whitelaw, K. Ong and K. Albertsson-Wikland: Child health, developmental plasticity, and epigenetic programming. Endocr Rev, 32(2), 159-224 (2011)
[88]M. H. Vickers: Early life nutrition, epigenetics and programming of later life disease. Nutrients, 6(6), 2165-78 (2014)
[89]J. C. Jimenez-Chillaron, M. J. Nijland, A. A. Ascensao, V. A. Sardao, J. Magalhaes, M. J. Hitchler, F. E. Domann and P. J. Oliveira: Back to the future: transgenerational transmission of xenobiotic-induced epigenetic remodeling. Epigenetics, 10(4), 259-73 (2015)
[90]J. S. Godde and K. Ura: Dynamic alterations of linker histone variants during development. Int J Dev Biol, 53(2-3), 215-24 (2009)
[91]J. Bao and W. Yan: Male germline control of transposable elements. Biol Reprod, 86(5), 162, 1-14 (2012)
[92]E. Casas and T. Vavouri: Sperm epigenomics: challenges and opportunities. Front Genet, 5, 330 (2014)
[93]C. Yao, Y. Liu, M. Sun, M. Niu, Q. Yuan, Y. Hai, Y. Guo, Z. Chen, J. Hou, Y. Liu and Z. He: MicroRNAs and DNA methylation as epigenetic regulators of mitosis, meiosis and spermiogenesis. Reproduction, 150(1), R25-34 (2015)
[94]A. S. Paradowska, D. Miller, A. N. Spiess, M. Vieweg, M. Cerna, K. Dvorakova-Hortova, M. Bartkuhn, H. C. Schuppe, W. Weidner and K. Steger: Genome wide identification of promoter binding sites for H4K12ac in human sperm and its relevance for early embryonic development. Epigenetics, 7(9), 1057-70 (2012)
[95]S. Gunes and T. Kulac: The role of epigenetics in spermatogenesis. Turk J Urol, 39(3), 181-7 (2013)
[96]J. Castillo, J. M. Estanyol, J. L. Ballesca and R. Oliva: Human sperm chromatin epigenetic potential: genomics, proteomics, and male infertility. Asian J Androl, 17(4), 601-9 (2015)
[97]L. Stuppia, M. Franzago, P. Ballerini, V. Gatta and I. Antonucci: Epigenetics and male reproduction: the consequences of paternal lifestyle on fertility, embryo development, and children lifetime health. Clin Epigenetics, 7, 120 (2015)
[98]S. Rajender, K. Avery and A. Agarwal: Epigenetics, spermatogenesis and male infertility. Mutat Res, 727(3), 62-71 (2011)
[99]D. J. Finnegan: Eukaryotic transposable elements and genome evolution. Trends Genet, 5(4), 103-7 (1989)
[100]R. Cordaux and M. A. Batzer: The impact of retrotransposons on human genome evolution. Nat Rev Genet, 10(10), 691-703 (2009)
[101]A. J. Sharp, E. Stathaki, E. Migliavacca, M. Brahmachary, S. B. Montgomery, Y. Dupre and S. E. Antonarakis: DNA methylation profiles of human active and inactive X chromosomes. Genome Res, 21(10), 1592-600 (2011)
[102]N. V. Fedoroff: Presidential address. Transposable elements, epigenetics, and genome evolution. Science, 338(6108), 758-67 (2012)
[103]D. P. Barlow and M. S. Bartolomei: Genomic imprinting in mammals. Cold Spring Harb Perspect Biol, 6(2) (2014)
[104]J. M. Turner: Meiotic sex chromosome inactivation. Development, 134(10), 1823-31 (2007)
[105]W. Yan and J. R. McCarrey: Sex chromosome inactivation in the male. Epigenetics, 4(7), 452-6 (2009)
[106]A. M. Khalil and C. Wahlestedt: Epigenetic mechanisms of gene regulation during mammalian spermatogenesis. Epigenetics, 3(1), 21-8 (2008)
[107]M. Becker, A. Becker, F. Miyara, Z. Han, M. Kihara, D. T. Brown, G. L. Hager, K. Latham, E. Y. Adashi and T. Misteli: Differential in vivo binding dynamics of somatic and oocyte-specific linker histones in oocytes and during ES cell nuclear transfer. Mol Biol Cell, 16(8), 3887-95 (2005)
[108]S. Bao, Y. Obata, J. Carroll, I. Domeki and T. Kono: Epigenetic modifications necessary for normal development are established during oocyte growth in mice. Biol Reprod, 62(3), 616-21 (2000)
[109]P. Ma and R. M. Schultz: Histone deacetylase 2 (HDAC2) regulates chromosome segregation and kinetochore function via H4K16 deacetylation during oocyte maturation in mouse. PLoS Genet, 9(3), e1003377 (2013)
[110]L. Gu, Q. Wang and Q. Y. Sun: Histone modifications during mammalian oocyte maturation: dynamics, regulation and functions. Cell Cycle, 9(10), 1942-50 (2010)
[111]M. Tachibana, M. Nozaki, N. Takeda and Y. Shinkai: Functional dynamics of H3K9 methylation during meiotic prophase progression. EMBO J, 26(14), 3346-59 (2007)
[112]W. M. Baarends, E. Wassenaar, R. van der Laan, J. Hoogerbrugge, E. Sleddens-Linkels, J. H. Hoeijmakers, P. de Boer and J. A. Grootegoed: Silencing of unpaired chromatin and histone H2A ubiquitination in mammalian meiosis. Mol Cell Biol, 25(3), 1041-53 (2005)
[113]K. R. Stewart, L. Veselovska and G. Kelsey: Establishment and functions of DNA methylation in the germline. Epigenomics, 8(10), 1399-1413 (2016)
[114]Y. Seki, K. Hayashi, K. Itoh, M. Mizugaki, M. Saitou and Y. Matsui: Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice. Dev Biol, 278(2), 440-58 (2005)
[115]J. Bromfield, W. Messamore and D. F. Albertini: Epigenetic regulation during mammalian oogenesis. Reprod Fertil Dev, 20(1), 74-80 (2008)
[116]G. D. Bowman and M. G. Poirier: Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev, 115(6), 2274-95 (2015)
[117]C. L. Woodcock and R. P. Ghosh: Chromatin higher-order structure and dynamics. Cold Spring Harb Perspect Biol, 2(5), a000596 (2010)
[118]P. W. Tai, S. K. Zaidi, H. Wu, R. A. Grandy, M. Montecino, A. J. van Wijnen, J. B. Lian, G. S. Stein and J. L. Stein: The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. J Cell Physiol, 229(6), 711-27 (2014)
[119]B. J. Venters and B. F. Pugh: How eukaryotic genes are transcribed. Crit Rev Biochem Mol Biol, 44(2-3), 117-41 (2009)
[120]C. Ling and L. Groop: Epigenetics: a molecular link between environmental factors and type 2 diabetes. Diabetes, 58(12), 2718-25 (2009)
[121]L. C. Layman: The genetic basis of female reproductive disorders: etiology and clinical testing. Mol Cell Endocrinol, 370(1-2), 138-48 (2013)
[122]C. Guerrero-Bosagna and M. K. Skinner: Environmentally induced epigenetic transgenerational inheritance of male infertility. Curr Opin Genet Dev, 26, 79-88 (2014)
[123]S. Houshdaran, V. K. Cortessis, K. Siegmund, A. Yang, P. W. Laird and R. Z. Sokol: Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm. PLoS One, 2(12), e1289 (2007)
[124]S. Hartmann, M. Bergmann, R. M. Bohle, W. Weidner and K. Steger: Genetic imprinting during impaired spermatogenesis. Mol Hum Reprod, 12(6), 407-11 (2006)
[125]D. Montjean, C. Ravel, M. Benkhalifa, P. Cohen-Bacrie, I. Berthaut, A. Bashamboo and K. McElreavey: Methylation changes in mature sperm deoxyribonucleic acid from oligozoospermic men: assessment of genetic variants and assisted reproductive technology outcome. Fertil Steril, 100(5), 1241-7 (2013)
[126]S. Manipalviratn, A. DeCherney and J. Segars: Imprinting disorders and assisted reproductive technology. Fertil Steril, 91(2), 305-15 (2009)
[127]A. Botezatu, R. Socolov, D. Socolov, I. V. Iancu and G. Anton: Methylation pattern of methylene tetrahydrofolate reductase and small nuclear ribonucleoprotein polypeptide N promoters in oligoasthenospermia: a case-control study. Reprod Biomed Online, 28(2), 225-31 (2014)
[128]C. J. Marques, P. Costa, B. Vaz, F. Carvalho, S. Fernandes, A. Barros and M. Sousa: Abnormal methylation of imprinted genes in human sperm is associated with oligozoospermia. Mol Hum Reprod, 14(2), 67-74 (2008)
[129]B. Li, J. B. Li, X. F. Xiao, Y. F. Ma, J. Wang, X. X. Liang, H. X. Zhao, F. Jiang, Y. Q. Yao and X. H. Wang: Altered DNA methylation patterns of the H19 differentially methylated region and the DAZL gene promoter are associated with defective human sperm. PLoS One, 8(8), e71215 (2013)
[130]A. Kitamura, N. Miyauchi, H. Hamada, H. Hiura, H. Chiba, H. Okae, A. Sato, R. M. John and T. Arima: Epigenetic alterations in sperm associated with male infertility. Congenit Anom (Kyoto), 55(3), 133-44 (2015)
[131]K. I. Aston, P. J. Uren, T. G. Jenkins, A. Horsager, B. R. Cairns, A. D. Smith and D. T. Carrell: Aberrant sperm DNA methylation predicts male fertility status and embryo quality. Fertil Steril, 104(6), 1388-97 e1-5 (2015)
[132]D. A. Skaar, Y. Li, A. J. Bernal, C. Hoyo, S. K. Murphy and R. L. Jirtle: The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J, 53(3-4), 341-58 (2012)
[133]M. M. Denomme, C. R. White, C. Gillio-Meina, W. A. Macdonald, B. J. Deroo, G. M. Kidder and M. R. Mann: Compromised fertility disrupts Peg1 but not Snrpn and Peg3 imprinted methylation acquisition in mouse oocytes. Front Genet, 3, 129 (2012)
[134]G. Kelsey and R. Feil: New insights into establishment and maintenance of DNA methylation imprints in mammals. Philos Trans R Soc Lond B Biol Sci, 368(1609), 20110336 (2013)
[135]D. M. Messerschmidt, B. B. Knowles and D. Solter: DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev, 28(8), 812-28 (2014)
[136]D. Jia, R. Z. Jurkowska, X. Zhang, A. Jeltsch and X. Cheng: Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature, 449(7159), 248-51 (2007)
[137]D. T. Carrell and S. S. Hammoud: The human sperm epigenome and its potential role in embryonic development. Mol Hum Reprod, 16(1), 37-47 (2010)
[138]L. Li, X. Lu and J. Dean: The maternal to zygotic transition in mammals. Mol Aspects Med, 34(5), 919-38 (2013)
[139]A Paoloni-Giacobino and J. R. Chaillet: Genomic imprinting and assisted reproduction. Reprod Health, 1(1), 6 (2004)
[140]E. Anckaert, M. De Rycke and J. Smitz: Culture of oocytes and risk of imprinting defects. Hum Reprod Update, 19(1), 52-66 (2013)
[141]M. Hazzouri, C. Pivot-Pajot, A. K. Faure, Y. Usson, R. Pelletier, B. Sele, S. Khochbin and S. Rousseaux: Regulated hyperacetylation of core histones during mouse spermatogenesis: involvement of histone deacetylases. Eur J Cell Biol, 79(12), 950-60 (2000)
[142]C. Steilmann, M. C. Cavalcanti, M. Bartkuhn, J. Pons-Kuhnemann, H. C. Schuppe, W. Weidner, K. Steger and A. Paradowska: The interaction of modified histones with the bromodomain testis-specific (BRDT) gene and its mRNA level in sperm of fertile donors and subfertile men. Reproduction, 140(3), 435-43 (2010)
[143]Y. Okada, G. Scott, M. K. Ray, Y. Mishina and Y. Zhang: Histone demethylase JHDM2A is critical for Tnp1 and Prm1 transcription and spermatogenesis. Nature, 450(7166), 119-23 (2007)
[144]V. Sonnack, K. Failing, M. Bergmann and K. Steger: Expression of hyperacetylated histone H4 during normal and impaired human spermatogenesis. Andrologia, 34(6), 384-90 (2002)
[145]I. Fenic, H. M. Hossain, V. Sonnack, S. Tchatalbachev, F. Thierer, J. Trapp, K. Failing, K. S. Edler, M. Bergmann, M. Jung, T. Chakraborty and K. Steger: In vivo application of histone deacetylase inhibitor trichostatin-a impairs murine male meiosis. J Androl, 29(2), 172-85 (2008)
[146]S. Glaser, S. Lubitz, K. L. Loveland, K. Ohbo, L. Robb, F. Schwenk, J. Seibler, D. Roellig, A. Kranz, K. Anastassiadis and A. F. Stewart: The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis. Epigenetics Chromatin, 2(1), 5 (2009)
[147]M. G. Lee, C. Wynder, N. Cooch and R. Shiekhattar: An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature, 437(7057), 432-5 (2005)
[148]J. Bao and M. T. Bedford: Epigenetic regulation of the histone-to-protamine transition during spermiogenesis. Reproduction, 151(5), R55-70 (2016)
[149]Y. Shi, F. Lan, C. Matson, P. Mulligan, J. R. Whetstine, P. A. Cole, R. A. Casero and Y. Shi: Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell, 119(7), 941-53 (2004)
[150]R. A. Waterland and K. B. Michels: Epigenetic epidemiology of the developmental origins hypothesis. Annu Rev Nutr, 27, 363-88 (2007)
[151]Z. Liu, S. Zhou, L. Liao, X. Chen, M. Meistrich and J. Xu: Jmjd1a demethylase-regulated histone modification is essential for cAMP-response element modulator-regulated gene expression and spermatogenesis. J Biol Chem, 285(4), 2758-70 (2010)
[152]C. J. Lin, F. M. Koh, P. Wong, M. Conti and M. Ramalho-Santos: Hira-mediated H3.3. incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote. Dev Cell, 30(3), 268-79 (2014)
[153]B. Nashun, P. W. Hill, S. A. Smallwood, G. Dharmalingam, R. Amouroux, S. J. Clark, V. Sharma, E. Ndjetehe, P. Pelczar, R. J. Festenstein, G. Kelsey and P. Hajkova: Continuous Histone Replacement by Hira Is Essential for Normal Transcriptional Regulation and De Novo DNA Methylation during Mouse Oogenesis. Mol Cell, 60(4), 611-25 (2015)
[154]P. Ma and R. M. Schultz: Histone deacetylase 1 (HDAC1) regulates histone acetylation, development, and gene expression in preimplantation mouse embryos. Dev Biol, 319(1), 110-20 (2008)
[155]O. M. Dovey, C. T. Foster and S. M. Cowley: Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation. Proc Natl Acad Sci U S A, 107(18), 8242-7 (2010)
[156]Z. Liu, X. Chen, S. Zhou, L. Liao, R. Jiang and J. Xu: The histone H3K9 demethylase Kdm3b is required for somatic growth and female reproductive function. Int J Biol Sci, 11(5), 494-507 (2015)
[157]A. Q. Gomes, S. Nolasco and H. Soares: Non-coding RNAs: multi-tasking molecules in the cell. Int J Mol Sci, 14(8), 16010-39 (2013)
[158]J. P. Saxe and H. Lin: Small noncoding RNAs in the germline. Cold Spring Harb Perspect Biol, 3(9), a002717 (2011)
[159]L. T. Gou, P. Dai and M. F. Liu: Small noncoding RNAs and male infertility. Wiley Interdiscip Rev RNA, 5(6), 733-45 (2014)
[160]Y. Khazaie and M. H. Nasr Esfahani: MicroRNA and Male Infertility: A Potential for Diagnosis. Int J Fertil Steril, 8(2), 113-8 (2014)
[161]A. C. Luk, W. Y. Chan, O. M. Rennert and T. L. Lee: Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies. Reproduction, 147(5), R131-41 (2014)
[162]D. Jamsai and M. K. O’Bryan: Mouse models in male fertility research. Asian J Androl, 13(1), 139-51 (2011)
[163]T. Zhou, Z. M. Zhou and X. J. Guo: Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics. Asian J Androl, 15(5), 594-602 (2013)
[164]R. Oliva: Protamines and male infertility. Hum Reprod Update, 12(4), 417-35 (2006)
[165]R. Oliva and J. Castillo: Proteomics and the genetics of sperm chromatin condensation. Asian J Androl, 13(1), 24-30 (2011)
[166]E. Tahmasbpour, D. Balasubramanian and A. Agarwal: A multi-faceted approach to understanding male infertility: gene mutations, molecular defects and assisted reproductive techniques (ART). J Assist Reprod Genet, 31(9), 1115-37 (2014)
[167]R. Sharma, K. R. Biedenharn, J. M. Fedor and A. Agarwal: Lifestyle factors and reproductive health: taking control of your fertility. Reprod Biol Endocrinol, 11, 66 (2013)
[168]J. A. Alegria-Torres, A. Baccarelli and V. Bollati: Epigenetics and lifestyle. Epigenomics, 3(3), 267-77 (2011)
[169]M. M. Matzuk and D. J. Lamb: The biology of infertility: research advances and clinical challenges. Nat Med, 14(11), 1197-213 (2008)
[170]Y. K. Cloonan, V. L. Holt and J. Goldberg: Male factor infertility: a twin study. Paediatr Perinat Epidemiol, 21(3), 229-34 (2007)
[171]V. K. Cortessis, D. C. Thomas, A. J. Levine, C. V. Breton, T. M. Mack, K. D. Siegmund, R. W. Haile and P. W. Laird: Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet, 131(10), 1565-89 (2012)
[172]L. Mirbahai and J. K. Chipman: Epigenetic memory of environmental organisms: a reflection of lifetime stressor exposures. Mutat Res Genet Toxicol Environ Mutagen, 764-765, 10-7 (2014)
[173]Y. Wei, H. Schatten and Q. Y. Sun: Environmental epigenetic inheritance through gametes and implications for human reproduction. Hum Reprod Update, 21(2), 194-208 (2015)
[174]R. H. Dashwood and E. Ho: Dietary histone deacetylase inhibitors: from cells to mice to man. Semin Cancer Biol, 17(5), 363-9 (2007)
[175]A. Izzotti, P. Larghero, M. Longobardi, C. Cartiglia, A. Camoirano, V. E. Steele and S. De Flora: Dose-responsiveness and persistence of microRNA expression alterations induced by cigarette smoke in mouse lung. Mutat Res, 717(1-2), 9-16 (2011)
[176]A Baccarelli and V. Bollati: Epigenetics and environmental chemicals. Curr Opin Pediatr, 21(2), 243-51 (2009)
[177]C. S. Wilhelm-Benartzi, E. A. Houseman, M. A. Maccani, G. M. Poage, D. C. Koestler, S. M. Langevin, L. A. Gagne, C. E. Banister, J. F. Padbury and C. J. Marsit: In utero exposures, infant growth, and DNA methylation of repetitive elements and developmentally related genes in human placenta. Environ Health Perspect, 120(2), 296-302 (2012)
[178]D. B. Martinez-Arguelles, E. Campioli, M. Culty, B. R. Zirkin and V. Papadopoulos: Fetal origin of endocrine dysfunction in the adult: the phthalate model. J Steroid Biochem Mol Biol, 137, 5-17 (2013)
[179]M. K. Skinner, M. Manikkam and C. Guerrero-Bosagna: Epigenetic transgenerational actions of environmental factors in disease etiology. Trends Endocrinol Metab, 21(4), 214-22 (2010)
[180]M. Uzumcu, H. Suzuki and M. K. Skinner: Effect of the anti-androgenic endocrine disruptor vinclozolin on embryonic testis cord formation and postnatal testis development and function. Reprod Toxicol, 18(6), 765-74 (2004)
[181]J. LaRocca, A. Boyajian, C. Brown, S. D. Smith and M. Hixon: Effects of in utero exposure to Bisphenol A or diethylstilbestrol on the adult male reproductive system. Birth Defects Res B Dev Reprod Toxicol, 92(6), 526-33 (2011)
[182]C. J. Park, W. H. Nah, J. E. Lee, Y. S. Oh and M. C. Gye: Butyl paraben-induced changes in DNA methylation in rat epididymal spermatozoa. Andrologia, 44 Suppl 1, 187-93 (2012)
[183]C. Stouder and A. Paoloni-Giacobino: Specific transgenerational imprinting effects of the endocrine disruptor methoxychlor on male gametes. Reproduction, 141(2), 207-16 (2011)
[184]M. D. Anway, A. S. Cupp, M. Uzumcu and M. K. Skinner: Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science, 308(5727), 1466-9 (2005)
[185]T. Doshi, C. D’Souza and G. Vanage: Aberrant DNA methylation at Igf2-H19 imprinting control region in spermatozoa upon neonatal exposure to bisphenol A and its association with post implantation loss. Mol Biol Rep, 40(8), 4747-57 (2013)
[186]T. Doshi, S. S. Mehta, V. Dighe, N. Balasinor and G. Vanage: Hypermethylation of estrogen receptor promoter region in adult testis of rats exposed neonatally to bisphenol A. Toxicology, 289(2-3), 74-82 (2011)
[187]C. Stouder, E. Somm and A. Paoloni-Giacobino: Prenatal exposure to ethanol: a specific effect on the H19 gene in sperm. Reprod Toxicol, 31(4), 507-12 (2011)
[188]N. E. Skakkebaek, E. Rajpert-De Meyts, N. Jorgensen, K. M. Main, H. Leffers, A. M. Andersson, A. Juul, T. K. Jensen and J. Toppari: Testicular cancer trends as ’whistle blowers’ of testicular developmental problems in populations. Int J Androl, 30(4), 198-204; discussion 204-5 (2007)
[189]K. P. Singh, R. Kumari, C. Pevey, D. Jackson and J. W. DuMond: Long duration exposure to cadmium leads to increased cell survival, decreased DNA repair capacity, and genomic instability in mouse testicular Leydig cells. Cancer Lett, 279(1), 84-92 (2009)
[190]Y. E. Dubrova, M. Plumb, B. Gutierrez, E. Boulton and A. J. Jeffreys: Transgenerational mutation by radiation. Nature, 405(6782), 37 (2000)
[191]M. Merrifield and O. Kovalchuk: Epigenetics in radiation biology: a new research frontier. Front Genet, 4, 40 (2013)
[192]B. Kincaid and E. Bossy-Wetzel: Forever young: SIRT3 a shield against mitochondrial meltdown, aging, and neurodegeneration. Front Aging Neurosci, 5, 48 (2013)
[193]N. Braidy, A. Poljak, R. Grant, T. Jayasena, H. Mansour, T. Chan-Ling, G. Smythe, P. Sachdev and G. J. Guillemin: Differential expression of sirtuins in the aging rat brain. Front Cell Neurosci, 9, 167 (2015)
[194]D. Nettersheim, L. C. Heukamp, F. Fronhoffs, M. J. Grewe, N. Haas, A. Waha, F. Honecker, A. Waha, G. Kristiansen and H. Schorle: Analysis of TET expression/activity and 5mC oxidation during normal and malignant germ cell development. PLoS One, 8(12), e82881 (2013)
[195]K. Ni, T. Dansranjavin, N. Rogenhofer, N. Oeztuerk, J. Deuker, M. Bergmann, H. C. Schuppe, F. Wagenlehner, W. Weidner, K. Steger and U. Schagdarsurengin: TET enzymes are successively expressed during human spermatogenesis and their expression level is pivotal for male fertility. Hum Reprod, 31(7), 1411-24 (2016)
[196]B. R. Carone, L. Fauquier, N. Habib, J. M. Shea, C. E. Hart, R. Li, C. Bock, C. Li, H. Gu, P. D. Zamore, A. Meissner, Z. Weng, H. A. Hofmann, N. Friedman and O. J. Rando: Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell, 143(7), 1084-96 (2010)
[197]E. J. Radford, M. Ito, H. Shi, J. A. Corish, K. Yamazawa, E. Isganaitis, S. Seisenberger, T. A. Hore, W. Reik, S. Erkek, A. H. Peters, M. E. Patti and A. C. Ferguson-Smith: In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. Science, 345(6198), 1255903 (2014)
[198]R. C. Painter, T. J. Roseboom and O. P. Bleker: Prenatal exposure to the Dutch famine and disease in later life: an overview. Reprod Toxicol, 20(3), 345-52 (2005)
[199]T. J. Roseboom, J. H. van der Meulen, A. C. Ravelli, C. Osmond, D. J. Barker and O. P. Bleker: Effects of prenatal exposure to the Dutch famine on adult disease in later life: an overview. Mol Cell Endocrinol, 185(1-2), 93-8 (2001)
[200]B. T. Heijmans, E. W. Tobi, A. D. Stein, H. Putter, G. J. Blauw, E. S. Susser, P. E. Slagboom and L. H. Lumey: Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A, 105(44), 17046-9 (2008)
[201]E. W. Tobi, J. J. Goeman, R. Monajemi, H. Gu, H. Putter, Y. Zhang, R. C. Slieker, A. P. Stok, P. E. Thijssen, F. Muller, E. W. van Zwet, C. Bock, A. Meissner, L. H. Lumey, P. Eline Slagboom and B. T. Heijmans: DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun, 5, 5592 (2014)
[202]G. Kaati, L. O. Bygren and S. Edvinsson: Cardiovascular and diabetes mortality determined by nutrition during parents’ and grandparents’ slow growth period. Eur J Hum Genet, 10(11), 682-8 (2002)
[203]G. Kaati, L. O. Bygren, M. Pembrey and M. Sjostrom: Transgenerational response to nutrition, early life circumstances and longevity. Eur J Hum Genet, 15(7), 784-90 (2007)
[204]N. K. MacLennan, S. J. James, S. Melnyk, A. Piroozi, S. Jernigan, J. L. Hsu, S. M. Janke, T. D. Pham and R. H. Lane: Uteroplacental insufficiency alters DNA methylation, one-carbon metabolism, and histone acetylation in IUGR rats. Physiol Genomics, 18(1), 43-50 (2004)
[205]K. A. Lillycrop, J. L. Slater-Jefferies, M. A. Hanson, K. M. Godfrey, A. A. Jackson and G. C. Burdge: Induction of altered epigenetic regulation of the hepatic glucocorticoid receptor in the offspring of rats fed a protein-restricted diet during pregnancy suggests that reduced DNA methyltransferase-1 expression is involved in impaired DNA methylation and changes in histone modifications. Br J Nutr, 97(6), 1064-73 (2007)
[206]K. A. Lillycrop, E. S. Phillips, A. A. Jackson, M. A. Hanson and G. C. Burdge: Dietary protein restriction of pregnant rats induces and folic acid supplementation prevents epigenetic modification of hepatic gene expression in the offspring. J Nutr, 135(6), 1382-6 (2005)
[207]I. C. Weaver, N. Cervoni, F. A. Champagne, A. C. D’Alessio, S. Sharma, J. R. Seckl, S. Dymov, M. Szyf and M. J. Meaney: Epigenetic programming by maternal behavior. Nat Neurosci, 7(8), 847-54 (2004)
[208]M. J. Meaney, M. Szyf and J. R. Seckl: Epigenetic mechanisms of perinatal programming of hypothalamic-pituitary-adrenal function and health. Trends Mol Med, 13(7), 269-77 (2007)
[209]C. J. Ashworth, L. M. Toma and M. G. Hunter: Nutritional effects on oocyte and embryo development in mammals: implications for reproductive efficiency and environmental sustainability. Philos Trans R Soc Lond B Biol Sci, 364(1534), 3351-61 (2009)
[210]A. Petronis: Human morbid genetics revisited: relevance of epigenetics. Trends Genet, 17(3), 142-6 (2001)
[211]L. Daxinger and E. Whitelaw: Transgenerational epigenetic inheritance: more questions than answers. Genome Res, 20(12), 1623-8 (2010)
[212]P. Hajkova, S. Erhardt, N. Lane, T. Haaf, O. El-Maarri, W. Reik, J. Walter and M. A. Surani: Epigenetic reprogramming in mouse primordial germ cells. Mech Dev, 117(1-2), 15-23 (2002)
[213]Y. Obata and T. Kono: Maternal primary imprinting is established at a specific time for each gene throughout oocyte growth. J Biol Chem, 277(7), 5285-9 (2002)
[214]T. L. Davis, G. J. Yang, J. R. McCarrey and M. S. Bartolomei: The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet, 9(19), 2885-94 (2000)
[215]E. Jablonka and M. J. Lamb: The inheritance of acquired epigenetic variations. Int J Epidemiol, 44(4), 1094-103 (2015)
[216]M. Loi, L. Del Savio and E. Stupka: Social Epigenetics and Equality of Opportunity. Public Health Ethics, 6(2), 142-153 (2013)
[217]W. G. Kelly: Transgenerational epigenetics in the germline cycle of Caenorhabditis elegans. Epigenetics Chromatin, 7(1), 6 (2014)
[218]J. M. Flanagan, V. Popendikyte, N. Pozdniakovaite, M. Sobolev, A. Assadzadeh, A. Schumacher, M. Zangeneh, L. Lau, C. Virtanen, S. C. Wang and A. Petronis: Intra- and interindividual epigenetic variation in human germ cells. Am J Hum Genet, 79(1), 67-84 (2006)
[219]S. Jacob and K. H. Moley: Gametes and embryo epigenetic reprogramming affect developmental outcome: implication for assisted reproductive technologies. Pediatr Res, 58(3), 437-46 (2005)
[220]L. Nanassy, L. Liu, J. Griffin and D. T. Carrell: The clinical utility of the protamine 1/protamine 2 ratio in sperm. Protein Pept Lett, 18(8), 772-7 (2011)
[221]D. Lucifero, J. R. Chaillet and J. M. Trasler: Potential significance of genomic imprinting defects for reproduction and assisted reproductive technology. Hum Reprod Update, 10(1), 3-18 (2004)
[222]T. Goto and M. Monk: Regulation of X-chromosome inactivation in development in mice and humans. Microbiol Mol Biol Rev, 62(2), 362-78 (1998)
[223]K. Plath, S. Mlynarczyk-Evans, D. A. Nusinow and B. Panning: Xist RNA and the mechanism of X chromosome inactivation. Annu Rev Genet, 36, 233-78 (2002)
[224]F. Pacchierotti and M. Spano: Environmental Impact on DNA Methylation in the Germline: State of the Art and Gaps of Knowledge. Biomed Res Int, 2015, 123484 (2015)
[225]V. S. Knopik, M. A. Maccani, S. Francazio and J. E. McGeary: The epigenetics of maternal cigarette smoking during pregnancy and effects on child development. Dev Psychopathol, 24(4), 1377-90 (2012)
[226]K. M. Radtke, M. Ruf, H. M. Gunter, K. Dohrmann, M. Schauer, A. Meyer and T. Elbert: Transgenerational impact of intimate partner violence on methylation in the promoter of the glucocorticoid receptor. Transl Psychiatry, 1, e21 (2011)
[227]M. A. Surani: Reprogramming of genome function through epigenetic inheritance. Nature, 414(6859), 122-8 (2001)
[228]Z. D. Smith, M. M. Chan, T. S. Mikkelsen, H. Gu, A. Gnirke, A. Regev and A. Meissner: A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature, 484(7394), 339-44 (2012)
[229]H. Kobayashi, T. Sakurai, F. Miura, M. Imai, K. Mochiduki, E. Yanagisawa, A. Sakashita, T. Wakai, Y. Suzuki, T. Ito, Y. Matsui and T. Kono: High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res, 23(4), 616-27 (2013)
[230]Z. D. Smith, C. Sindhu and A. Meissner: Molecular features of cellular reprogramming and development. Nat Rev Mol Cell Biol, 17(3), 139-54 (2016)
[231]C. L. Stewart, I. Gadi and H. Bhatt: Stem cells from primordial germ cells can reenter the germ line. Dev Biol, 161(2), 626-8 (1994)
[232]E. Pelosi, A. Forabosco and D. Schlessinger: Germ cell formation from embryonic stem cells and the use of somatic cell nuclei in oocytes. Ann N Y Acad Sci, 1221, 18-26 (2011)
[233]K. Hayashi, S. Ogushi, K. Kurimoto, S. Shimamoto, H. Ohta and M. Saitou: Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice. Science, 338(6109), 971-5 (2012)
[234]I. Cantone and A. G. Fisher: Epigenetic programming and reprogramming during development. Nat Struct Mol Biol, 20(3), 282-9 (2013)
[235]A. B. Stergachis, S. Neph, A. Reynolds, R. Humbert, B. Miller, S. L. Paige, B. Vernot, J. B. Cheng, R. E. Thurman, R. Sandstrom, E. Haugen, S. Heimfeld, C. E. Murry, J. M. Akey and J. A. Stamatoyannopoulos: Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell, 154(4), 888-903 (2013)
[236]K. Shah, G. Sivapalan, N. Gibbons, H. Tempest and D. K. Griffin: The genetic basis of infertility. Reproduction, 126(1), 13-25 (2003)
[237]L. C. Smith, J. Therrien, F. Filion, F. Bressan and F. V. Meirelles: Epigenetic consequences of artificial reproductive technologies to the bovine imprinted genes SNRPN, H19/IGF2, and IGF2R. Front Genet, 6, 58 (2015)
[238]C. Choux, V. Carmignac, C. Bruno, P. Sagot, D. Vaiman and P. Fauque: The placenta: phenotypic and epigenetic modifications induced by Assisted Reproductive Technologies throughout pregnancy. Clin Epigenetics, 7, 87 (2015)
[239]M. G. Butler: Genomic imprinting disorders in humans: a mini-review. J Assist Reprod Genet, 26(9-10), 477-86 (2009)
[240]J. A. Piedrahita: The role of imprinted genes in fetal growth abnormalities. Birth Defects Res A Clin Mol Teratol, 91(8), 682-92 (2011)
[241]F. L. Lopes, A. L. Fortier, N. Darricarrere, D. Chan, D. R. Arnold and J. M. Trasler: Reproductive and epigenetic outcomes associated with aging mouse oocytes. Hum Mol Genet, 18(11), 2032-44 (2009)
[242]A. Soubry, J. M. Schildkraut, A. Murtha, F. Wang, Z. Huang, A. Bernal, J. Kurtzberg, R. L. Jirtle, S. K. Murphy and C. Hoyo: Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort. BMC Med, 11, 29 (2013)
[243]A. Soubry, L. Guo, Z. Huang, C. Hoyo, S. Romanus, T. Price and S. K. Murphy: Obesity-related DNA methylation at imprinted genes in human sperm: Results from the TIEGER study. Clin Epigenetics, 8, 51 (2016)
[244]E. R. Maher: Imprinting and assisted reproductive technology. Hum Mol Genet, 14 Spec No 1, R133-8 (2005)
[245]H. A. Lawson, J. M. Cheverud and J. B. Wolf: Genomic imprinting and parent-of-origin effects on complex traits. Nat Rev Genet, 14(9), 609-17 (2013)
Article Metrics
Download
- Contents
Information
Download
Contents
Frontiers in Bioscience-Scholar (FBS) is published by IMR Press from Volume 13 Issue 1 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on imrpress.com as a courtesy and upon agreement with Frontiers in Bioscience.
Epigenetics of reproductive infertility
1 Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
*Author to whom correspondence should be addressed.
Abstract
Infertility is a complex pathophysiological condition. It may caused by specific or multiple physical and physiological factors, including abnormalities in homeostasis, hormonal imbalances and genetic alterations. In recent times various studies implicated that, aberrant epigenetic mechanisms are associated with reproductive infertility. There might be transgenerational effects associated with epigenetic modifications of gametes and studies suggest the importance of alterations in epigenetic modification at early and late stages of gametogenesis. To determine the causes of infertility it is necessary to understand the altered epigenetic modifications of associated gene and mechanisms involved therein. This review is devoted to elucidate the recent mechanistic advances in regulation of genes by epigenetic modification and emphasizes their possible role related to reproductive infertility. It includes environmental, nutritional, hormonal and physiological factors and influence of internal structural architecture of chromatin nucleosomes affecting DNA and histone modifications in both male and female gametes, early embryogenesis and offspring. Finally, we would like to emphasize that research on human infertility by gene knock out of epigenetic modifiers genes must be relied upon animal models.
Keywords
- Epigenetics
- DNA methylation
- histone modification
- non-coding RNAs
- DNMTs
- Germ Cell
- Spermatogenesis
- Oogenesis
- Reproductive Disorder
- Infertility
- Nutrition
- Environment
- Offspring
- Review
References
- [1] J. B. Stanford, T. A. Parnell and P. C. Boyle: Outcomes from treatment of infertility with natural procreative technology in an Irish general practice. J Am Board Fam Med, 21(5), 375-84 (2008)
- [2] H. T. Bjornsson, M. D. Fallin and A. P. Feinberg: An integrated epigenetic and genetic approach to common human disease. Trends Genet, 20(8), 350-8 (2004)
- [3] L. Liu, Y. Li and T. O. Tollefsbol: Gene-environment interactions and epigenetic basis of human diseases. Curr Issues Mol Biol, 10(1-2), 25-36 (2008)
- [4] N. Bunkar, N. Pathak, N. K. Lohiya and P. K. Mishra: Epigenetics: A key paradigm in reproductive health. Clin Exp Reprod Med, 43(2), 59-81 (2016)
- [5] F. S. Collins, E. D. Green, A. E. Guttmacher and M. S. Guyer: A vision for the future of genomics research. Nature, 422(6934), 835-47 (2003)
- [6] M. L. Whitfield, G. Sherlock, A. J. Saldanha, J. I. Murray, C. A. Ball, K. E. Alexander, J. C. Matese, C. M. Perou, M. M. Hurt, P. O. Brown and D. Botstein: Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell, 13(6), 1977-2000 (2002)
- [7] E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigo, T. R. Gingeras, E. H. Margulies, Z. Weng, M. Snyder, E. T. Dermitzakis, R. E. Thurman, M. S. Kuehn, C. M. Taylor, S. Neph, C. M. Koch, S. Asthana, A. Malhotra, I. Adzhubei, J. A. Greenbaum, R. M. Andrews, P. Flicek, P. J. Boyle, H. Cao, N. P. Carter, G. K. Clelland, S. Davis, N. Day, P. Dhami, S. C. Dillon, M. O. Dorschner, H. Fiegler, P. G. Giresi, J. Goldy, M. Hawrylycz, A. Haydock, R. Humbert, K. D. James, B. E. Johnson, E. M. Johnson, T. T. Frum, E. R. Rosenzweig, N. Karnani, K. Lee, G. C. Lefebvre, P. A. Navas, F. Neri, S. C. Parker, P. J. Sabo, R. Sandstrom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, M. Yu, F. S. Collins, J. Dekker, J. D. Lieb, T. D. Tullius, G. E. Crawford, S. Sunyaev, W. S. Noble, I. Dunham, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D. Zheng, R. Castelo, A. Frankish, J. Harrow, S. Ghosh, A. Sandelin, I. L. Hofacker, R. Baertsch, D. Keefe, S. Dike, J. Cheng, H. A. Hirsch, E. A. Sekinger, J. Lagarde, J. F. Abril, A. Shahab, C. Flamm, C. Fried, J. Hackermuller, J. Hertel, M. Lindemeyer, K. Missal, A. Tanzer, S. Washietl, J. Korbel, O. Emanuelsson, J. S. Pedersen, N. Holroyd, R. Taylor, D. Swarbreck, N. Matthews, M. C. Dickson, D. J. Thomas, M. T. Weirauch, J. Gilbert, J. Drenkow, I. Bell, X. Zhao, K. G. Srinivasan, W. K. Sung, H. S. Ooi, K. P. Chiu, S. Foissac, T. Alioto, M. Brent, L. Pachter, M. L. Tress, A. Valencia, S. W. Choo, C. Y. Choo, C. Ucla, C. Manzano, C. Wyss, E. Cheung, T. G. Clark, J. B. Brown, M. Ganesh, S. Patel, H. Tammana, J. Chrast, C. N. Henrichsen, C. Kai, J. Kawai, U. Nagalakshmi, J. Wu, Z. Lian, J. Lian, P. Newburger, X. Zhang, P. Bickel, J. S. Mattick, P. Carninci, Y. Hayashizaki, S. Weissman, T. Hubbard, R. M. Myers, J. Rogers, P. F. Stadler, T. M. Lowe, C. L. Wei, Y. Ruan, K. Struhl, M. Gerstein, S. E. Antonarakis, Y. Fu, E. D. Green, U. Karaoz, A. Siepel, J. Taylor, L. A. Liefer, K. A. Wetterstrand, P. J. Good, E. A. Feingold, M. S. Guyer, G. M. Cooper, G. Asimenos, C. N. Dewey, M. Hou, S. Nikolaev, J. I. Montoya-Burgos, A. Loytynoja, S. Whelan, F. Pardi, T. Massingham, H. Huang, N. R. Zhang, I. Holmes, J. C. Mullikin, A. Ureta-Vidal, B. Paten, M. Seringhaus, D. Church, K. Rosenbloom, W. J. Kent, E. A. Stone, S. Batzoglou, N. Goldman, R. C. Hardison, D. Haussler, W. Miller, A. Sidow, N. D. Trinklein, Z. D. Zhang, L. Barrera, R. Stuart, D. C. King, A. Ameur, S. Enroth, M. C. Bieda, J. Kim, A. A. Bhinge, N. Jiang, J. Liu, F. Yao, V. B. Vega, C. W. Lee, P. Ng, A. Shahab, A. Yang, Z. Moqtaderi, Z. Zhu, X. Xu, S. Squazzo, M. J. Oberley, D. Inman, M. A. Singer, T. A. Richmond, K. J. Munn, A. Rada-Iglesias, O. Wallerman, J. Komorowski, J. C. Fowler, P. Couttet, A. W. Bruce, O. M. Dovey, P. D. Ellis, C. F. Langford, D. A. Nix, G. Euskirchen, S. Hartman, A. E. Urban, P. Kraus, S. Van Calcar, N. Heintzman, T. H. Kim, K. Wang, C. Qu, G. Hon, R. Luna, C. K. Glass, M. G. Rosenfeld, S. F. Aldred, S. J. Cooper, A. Halees, J. M. Lin, H. P. Shulha, X. Zhang, M. Xu, J. N. Haidar, Y. Yu, Y. Ruan, V. R. Iyer, R. D. Green, C. Wadelius, P. J. Farnham, B. Ren, R. A. Harte, A. S. Hinrichs, H. Trumbower, H. Clawson, J. Hillman-Jackson, A. S. Zweig, K. Smith, A. Thakkapallayil, G. Barber, R. M. Kuhn, D. Karolchik, L. Armengol, C. P. Bird, P. I. de Bakker, A. D. Kern, N. Lopez-Bigas, J. D. Martin, B. E. Stranger, A. Woodroffe, E. Davydov, A. Dimas, E. Eyras, I. B. Hallgrimsdottir, J. Huppert, M. C. Zody, G. R. Abecasis, X. Estivill, G. G. Bouffard, X. Guan, N. F. Hansen, J. R. Idol, V. V. Maduro, B. Maskeri, J. C. McDowell, M. Park, P. J. Thomas, A. C. Young, R. W. Blakesley, D. M. Muzny, E. Sodergren, D. A. Wheeler, K. C. Worley, H. Jiang, G. M. Weinstock, R. A. Gibbs, T. Graves, R. Fulton, E. R. Mardis, R. K. Wilson, M. Clamp, J. Cuff, S. Gnerre, D. B. Jaffe, J. L. Chang, K. Lindblad-Toh, E. S. Lander, M. Koriabine, M. Nefedov, K. Osoegawa, Y. Yoshinaga, B. Zhu and P. J. de Jong: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146), 799-816 (2007)
- [8] J. T. Kung, D. Colognori and J. T. Lee: Long noncoding RNAs: past, present, and future. Genetics, 193(3), 651-69 (2013)
- [9] H. B. Fraser: Cell-cycle regulated transcription associates with DNA replication timing in yeast and human. Genome Biol, 14(10), R111 (2013)
- [10] S. Minocherhomji, A. S. Athalye, P. F. Madon, D. Kulkarni, S. A. Uttamchandani and F. R. Parikh: A case-control study identifying chromosomal polymorphic variations as forms of epigenetic alterations associated with the infertility phenotype. Fertil Steril, 92(1), 88-95 (2009)
- [11] K. Rull, L. Nagirnaja and M. Laan: Genetics of recurrent miscarriage: challenges, current knowledge, future directions. Front Genet, 3, 34 (2012)
- [12] G. Egger, G. Liang, A. Aparicio and P. A. Jones: Epigenetics in human disease and prospects for epigenetic therapy. Nature, 429(6990), 457-63 (2004)
- [13] K. Stotz: Extended evolutionary psychology: the importance of transgenerational developmental plasticity. Front Psychol, 5, 908 (2014)
- [14] S. Sharma, T. K. Kelly and P. A. Jones: Epigenetics in cancer. Carcinogenesis, 31(1), 27-36 (2010)
- [15] D. E. Handy, R. Castro and J. Loscalzo: Epigenetic modifications: basic mechanisms and role in cardiovascular disease. Circulation, 123(19), 2145-56 (2011)
- [16] A. Portela and M. Esteller: Epigenetic modifications and human disease. Nat Biotechnol, 28(10), 1057-68 (2010)
- [17] P. B. Talbert and S. Henikoff: Spreading of silent chromatin: inaction at a distance. Nat Rev Genet, 7(10), 793-803 (2006)
- [18] P. R. Kanherkar, N. Bhatia-Dey and A. B. Csoka: Epigenetics across the human lifespan. Front Cell Dev Biol, 2, 49 (2014)
- [19] M. Teperek and K. Miyamoto: Nuclear reprogramming of sperm and somatic nuclei in eggs and oocytes. Reprod Med Biol, 12, 133-149 (2013)
- [20] E. Li: Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet, 3(9), 662-73 (2002)
- [21] R. Jaenisch and A. Bird: Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet, 33 Suppl, 245-54 (2003)
- [22] E. R. Gibney and C. M. Nolan: Epigenetics and gene expression. Heredity (Edinb), 105(1), 4-13 (2010)
- [23] B. Jin, Y. Li and K. D. Robertson: DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer, 2(6), 607-17 (2011)
- [24] P. A. Jones and G. Liang: Rethinking how DNA methylation patterns are maintained. Nat Rev Genet, 10(11), 805-11 (2009)
- [25] J. A. Law and S. E. Jacobsen: Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet, 11(3), 204-20 (2010)
- [26] J. Barau, A. Teissandier, N. Zamudio, S. Roy, V. Nalesso, Y. Herault, F. Guillou and D. Bourc’his: The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science, 354(6314), 909-912 (2016)
- [27] F. Chedin, M. R. Lieber and C. L. Hsieh: The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A, 99(26), 16916-21 (2002)
- [28] C. W. Hanna and G. Kelsey: The specification of imprints in mammals. Heredity (Edinb), 113(2), 176-83 (2014)
- [29] G. Raddatz, P. M. Guzzardo, N. Olova, M. R. Fantappie, M. Rampp, M. Schaefer, W. Reik, G. J. Hannon and F. Lyko: Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proc Natl Acad Sci U S A, 110(21), 8627-31 (2013)
- [30] O. Bogdanovic and G. J. Veenstra: DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma, 118(5), 549-65 (2009)
- [31] T. Clouaire and I. Stancheva: Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin? Cell Mol Life Sci, 65(10), 1509-22 (2008)
- [32] H. Wu and Y. Zhang: Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev, 25(23), 2436-52 (2011)
- [33] N. Bhutani, D. M. Burns and H. M. Blau: DNA demethylation dynamics. Cell, 146(6), 866-72 (2011)
- [34] C. C. Chen, K. Y. Wang and C. K. Shen: DNA 5-methylcytosine demethylation activities of the mammalian DNA methyltransferases. J Biol Chem, 288(13), 9084-91 (2013)
- [35] H. Wu and Y. Zhang: Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell, 156(1-2), 45-68 (2014)
- [36] D. Sengupta, M. Deb, S. K. Rath, S. Kar, S. Parbin, N. Pradhan and S. K. Patra: DNA methylation and not H3K4 trimethylation dictates the expression status of miR-152 gene which inhibits migration of breast cancer cells via DNMT1/CDH1 loop. Exp Cell Res, 346(2), 176-87 (2016)
- [37] A. Shilpi, S. Parbin, D. Sengupta, S. Kar, M. Deb, S. K. Rath, N. Pradhan, M. Rakshit and S. K. Patra: Mechanisms of DNA methyltransferase-inhibitor interactions: Procyanidin B2 shows new promise for therapeutic intervention of cancer. Chem Biol Interact, 233, 122-38 (2015)
- [38] S. Kar, D. Sengupta, M. Deb, A. Shilpi, S. Parbin, S. K. Rath, N. Pradhan, M. Rakshit and S. K. Patra: Expression profiling of DNA methylation-mediated epigenetic gene-silencing factors in breast cancer. Clin Epigenetics, 6(1), 20 (2014)
- [39] M. Deb, S. Kar, D. Sengupta, A. Shilpi, S. Parbin, S. K. Rath, V. A. Londhe and S. K. Patra: Chromatin dynamics: H3K4 methylation and H3 variant replacement during development and in cancer. Cell Mol Life Sci, 71(18), 3439-63 (2014)
- [40] S. Kar, M. Deb, D. Sengupta, A. Shilpi, S. Parbin, J. Torrisani, S. Pradhan and S. Patra: An insight into the various regulatory mechanisms modulating human DNA methyltransferase 1 stability and function. Epigenetics, 7(9), 994-1007 (2012)
- [41] S. K. Patra, A. Patra, F. Rizzi, T. C. Ghosh and S. Bettuzzi: Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development. Cancer Metastasis Rev, 27(2), 315-34 (2008)
- [42] S. K. Patra and M. Szyf: DNA methylation-mediated nucleosome dynamics and oncogenic Ras signaling: insights from FAS, FAS ligand and RASSF1A. FEBS J, 275(21), 5217-35 (2008)
- [43] V. Morales and H. Richard-Foy: Role of histone N-terminal tails and their acetylation in nucleosome dynamics. Mol Cell Biol, 20(19), 7230-7 (2000)
- [44] S. D. Taverna, H. Li, A. J. Ruthenburg, C. D. Allis and D. J. PaTel: How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol, 14(11), 1025-40 (2007)
- [45] L. Marino-Ramirez, M. G. Kann, B. A. Shoemaker and D. Landsman: Histone structure and nucleosome stability. Expert Rev Proteomics, 2(5), 719-29 (2005)
- [46] H. J. Szerlong and J. C. Hansen: Nucleosome distribution and linker DNA: connecting nuclear function to dynamic chromatin structure. Biochem Cell Biol, 89(1), 24-34 (2011)
- [47] C. Wood, A. Snijders, J. Williamson, C. Reynolds, J. Baldwin and M. Dickman: Post-translational modifications of the linker histone variants and their association with cell mechanisms. FEBS J, 276(14), 3685-97 (2009)
- [48] D. Bonenfant, H. Towbin, M. Coulot, P. Schindler, D. R. Mueller and J. van Oostrum: Analysis of dynamic changes in post-translational modifications of human histones during cell cycle by mass spectrometry. Mol Cell Proteomics, 6(11), 1917-32 (2007)
- [49] B. E. Bernstein, A. Meissner and E. S. Lander: The mammalian epigenome. Cell, 128(4), 669-81 (2007)
- [50] J. Bannister and T. Kouzarides: Regulation of chromatin by histone modifications. Cell Res, 21(3), 381-95 (2011)
- [51] B. D. Price and A. D. D’Andrea: Chromatin remodeling at DNA double-strand breaks. Cell, 152(6), 1344-54 (2013)
- [52] M. Papamichos-Chronakis and C. L. Peterson: Chromatin and the genome integrity network. Nat Rev Genet, 14(1), 62-75 (2013)
- [53] C. R. Vakoc, M. M. Sachdeva, H. Wang and G. A. Blobel: Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol, 26(24), 9185-95 (2006)
- [54] T. Kouzarides: Chromatin modifications and their function. Cell, 128(4), 693-705 (2007)
- [55] A. Sadakierska-Chudy and M. Filip: A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs. Neurotox Res, 27(2), 172-97 (2015)
- [56] M. Deb, D. Sengupta, S. Kar, S. K. Rath, S. Roy, G. Das and S. K. Patra: Epigenetic drift towards histone modifications regulates CAV1 gene expression in colon cancer. Gene, 581(1), 75-84 (2016)
- [57] M. Deb, D. Sengupta, S. K. Rath, S. Kar, S. Parbin, A. Shilpi, N. Pradhan, S. K. Bhutia, S. Roy and S. K. Patra: Clusterin gene is predominantly regulated by histone modifications in human colon cancer and ectopic expression of the nuclear isoform induces cell death. Biochim Biophys Acta, 1852(8), 1630-45 (2015)
- [58] K. C. Wang and H. Y. Chang: Molecular mechanisms of long noncoding RNAs. Mol Cell, 43(6), 904-14 (2011)
- [59] J. L. Rinn and H. Y. Chang: Genome regulation by long noncoding RNAs. Annu Rev Biochem, 81, 145-66 (2012)
- [60] J. S. Mattick and I. V. Makunin: Non-coding RNA. Hum Mol Genet, 15 Spec No 1, R17-29 (2006)
- [61] K. V. Prasanth and D. L. Spector: Eukaryotic regulatory RNAs: an answer to the ’genome complexity’ conundrum. Genes Dev, 21(1), 11-42 (2007)
- [62] M. V. Koerner, F. M. Pauler, R. Huang and D. P. Barlow: The function of non-coding RNAs in genomic imprinting. Development, 136(11), 1771-83 (2009)
- [63] V. E. Villegas and P. G. Zaphiropoulos: Neighboring gene regulation by antisense long non-coding RNAs. Int J Mol Sci, 16(2), 3251-66 (2015)
- [64] V. J. Peschansky and C. Wahlestedt: Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics, 9(1), 3-12 (2014)
- [65] R. S. Pillai: MicroRNA function: multiple mechanisms for a tiny RNA? RNA, 11(12), 1753-61 (2005)
- [66] K. Prevost, G. Desnoyers, J. F. Jacques, F. Lavoie and E. Masse: Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev, 25(4), 385-96 (2011)
- [67] S. Lamouille, J. Xu and R. Derynck: Molecular mechanisms of epithelial-mesenchymal transition. Nat Rev Mol Cell Biol, 15(3), 178-96 (2014)
- [68] R. W. Carthew and E. J. Sontheimer: Origins and Mechanisms of miRNAs and siRNAs. Cell, 136(4), 642-55 (2009)
- [69] D. Moazed: Small RNAs in transcriptional gene silencing and genome defence. Nature, 457(7228), 413-20 (2009)
- [70] M. U. Kaikkonen, M. T. Lam and C. K. Glass: Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res, 90(3), 430-40 (2011)
- [71] J. Brennecke, A. A. Aravin, A. Stark, M. Dus, M. Kellis, R. Sachidanandam and G. J. Hannon: Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128(6), 1089-103 (2007)
- [72] T. R. Mercer and J. S. Mattick: Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol, 20(3), 300-7 (2013)
- [73] P. Han and C. P. Chang: Long non-coding RNA and chromatin remodeling. RNA Biol, 12(10), 1094-8 (2015)
- [74] S. Geisler and J. Coller: RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol, 14(11), 699-712 (2013)
- [75] A. Saxena and P. Carninci: Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays, 33(11), 830-9 (2011)
- [76] L. Bai and A. V. Morozov: Gene regulation by nucleosome positioning. Trends Genet, 26(11), 476-83 (2010)
- [77] K. Struhl and E. Segal: Determinants of nucleosome positioning. Nat Struct Mol Biol, 20(3), 267-73 (2013)
- [78] T. K. Kelly, T. B. Miranda, G. Liang, B. P. Berman, J. C. Lin, A. Tanay and P. A. Jones: H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell, 39(6), 901-11 (2010)
- [79] H. Cedar and Y. Bergman: Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet, 10(5), 295-304 (2009)
- [80] S. Kimmins and P. Sassone-Corsi: Chromatin remodelling and epigenetic features of germ cells. Nature, 434(7033), 583-9 (2005)
- [81] S. Seisenberger, J. R. Peat, T. A. Hore, F. Santos, W. Dean and W. Reik: Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers. Philos Trans R Soc Lond B Biol Sci, 368(1609), 20110330 (2013)
- [82] S. K. Kota and R. Feil: Epigenetic transitions in germ cell development and meiosis. Dev Cell, 19(5), 675-86 (2010)
- [83] H. Sasaki and Y. Matsui: Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet, 9(2), 129-40 (2008)
- [84] M. Saitou and M. Yamaji: Primordial germ cells in mice. Cold Spring Harb Perspect Biol, 4(11) (2012)
- [85] K. Hogg and P. S. Western: Refurbishing the germline epigenome: Out with the old, in with the new. Semin Cell Dev Biol, 45, 104-13 (2015)
- [86] A. Nikolic, V. Volarevic, L. Armstrong, M. Lako and M. Stojkovic: Primordial Germ Cells: Current Knowledge and Perspectives. Stem Cells Int, 2016, 1741072 (2016)
- [87] Z. Hochberg, R. Feil, M. Constancia, M. Fraga, C. Junien, J. C. Carel, P. Boileau, Y. Le Bouc, C. L. Deal, K. Lillycrop, R. Scharfmann, A. Sheppard, M. Skinner, M. Szyf, R. A. Waterland, D. J. Waxman, E. Whitelaw, K. Ong and K. Albertsson-Wikland: Child health, developmental plasticity, and epigenetic programming. Endocr Rev, 32(2), 159-224 (2011)
- [88] M. H. Vickers: Early life nutrition, epigenetics and programming of later life disease. Nutrients, 6(6), 2165-78 (2014)
- [89] J. C. Jimenez-Chillaron, M. J. Nijland, A. A. Ascensao, V. A. Sardao, J. Magalhaes, M. J. Hitchler, F. E. Domann and P. J. Oliveira: Back to the future: transgenerational transmission of xenobiotic-induced epigenetic remodeling. Epigenetics, 10(4), 259-73 (2015)
- [90] J. S. Godde and K. Ura: Dynamic alterations of linker histone variants during development. Int J Dev Biol, 53(2-3), 215-24 (2009)
- [91] J. Bao and W. Yan: Male germline control of transposable elements. Biol Reprod, 86(5), 162, 1-14 (2012)
- [92] E. Casas and T. Vavouri: Sperm epigenomics: challenges and opportunities. Front Genet, 5, 330 (2014)
- [93] C. Yao, Y. Liu, M. Sun, M. Niu, Q. Yuan, Y. Hai, Y. Guo, Z. Chen, J. Hou, Y. Liu and Z. He: MicroRNAs and DNA methylation as epigenetic regulators of mitosis, meiosis and spermiogenesis. Reproduction, 150(1), R25-34 (2015)
- [94] A. S. Paradowska, D. Miller, A. N. Spiess, M. Vieweg, M. Cerna, K. Dvorakova-Hortova, M. Bartkuhn, H. C. Schuppe, W. Weidner and K. Steger: Genome wide identification of promoter binding sites for H4K12ac in human sperm and its relevance for early embryonic development. Epigenetics, 7(9), 1057-70 (2012)
- [95] S. Gunes and T. Kulac: The role of epigenetics in spermatogenesis. Turk J Urol, 39(3), 181-7 (2013)
- [96] J. Castillo, J. M. Estanyol, J. L. Ballesca and R. Oliva: Human sperm chromatin epigenetic potential: genomics, proteomics, and male infertility. Asian J Androl, 17(4), 601-9 (2015)
- [97] L. Stuppia, M. Franzago, P. Ballerini, V. Gatta and I. Antonucci: Epigenetics and male reproduction: the consequences of paternal lifestyle on fertility, embryo development, and children lifetime health. Clin Epigenetics, 7, 120 (2015)
- [98] S. Rajender, K. Avery and A. Agarwal: Epigenetics, spermatogenesis and male infertility. Mutat Res, 727(3), 62-71 (2011)
- [99] D. J. Finnegan: Eukaryotic transposable elements and genome evolution. Trends Genet, 5(4), 103-7 (1989)
- [100] R. Cordaux and M. A. Batzer: The impact of retrotransposons on human genome evolution. Nat Rev Genet, 10(10), 691-703 (2009)
- [101] A. J. Sharp, E. Stathaki, E. Migliavacca, M. Brahmachary, S. B. Montgomery, Y. Dupre and S. E. Antonarakis: DNA methylation profiles of human active and inactive X chromosomes. Genome Res, 21(10), 1592-600 (2011)
- [102] N. V. Fedoroff: Presidential address. Transposable elements, epigenetics, and genome evolution. Science, 338(6108), 758-67 (2012)
- [103] D. P. Barlow and M. S. Bartolomei: Genomic imprinting in mammals. Cold Spring Harb Perspect Biol, 6(2) (2014)
- [104] J. M. Turner: Meiotic sex chromosome inactivation. Development, 134(10), 1823-31 (2007)
- [105] W. Yan and J. R. McCarrey: Sex chromosome inactivation in the male. Epigenetics, 4(7), 452-6 (2009)
- [106] A. M. Khalil and C. Wahlestedt: Epigenetic mechanisms of gene regulation during mammalian spermatogenesis. Epigenetics, 3(1), 21-8 (2008)
- [107] M. Becker, A. Becker, F. Miyara, Z. Han, M. Kihara, D. T. Brown, G. L. Hager, K. Latham, E. Y. Adashi and T. Misteli: Differential in vivo binding dynamics of somatic and oocyte-specific linker histones in oocytes and during ES cell nuclear transfer. Mol Biol Cell, 16(8), 3887-95 (2005)
- [108] S. Bao, Y. Obata, J. Carroll, I. Domeki and T. Kono: Epigenetic modifications necessary for normal development are established during oocyte growth in mice. Biol Reprod, 62(3), 616-21 (2000)
- [109] P. Ma and R. M. Schultz: Histone deacetylase 2 (HDAC2) regulates chromosome segregation and kinetochore function via H4K16 deacetylation during oocyte maturation in mouse. PLoS Genet, 9(3), e1003377 (2013)
- [110] L. Gu, Q. Wang and Q. Y. Sun: Histone modifications during mammalian oocyte maturation: dynamics, regulation and functions. Cell Cycle, 9(10), 1942-50 (2010)
- [111] M. Tachibana, M. Nozaki, N. Takeda and Y. Shinkai: Functional dynamics of H3K9 methylation during meiotic prophase progression. EMBO J, 26(14), 3346-59 (2007)
- [112] W. M. Baarends, E. Wassenaar, R. van der Laan, J. Hoogerbrugge, E. Sleddens-Linkels, J. H. Hoeijmakers, P. de Boer and J. A. Grootegoed: Silencing of unpaired chromatin and histone H2A ubiquitination in mammalian meiosis. Mol Cell Biol, 25(3), 1041-53 (2005)
- [113] K. R. Stewart, L. Veselovska and G. Kelsey: Establishment and functions of DNA methylation in the germline. Epigenomics, 8(10), 1399-1413 (2016)
- [114] Y. Seki, K. Hayashi, K. Itoh, M. Mizugaki, M. Saitou and Y. Matsui: Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice. Dev Biol, 278(2), 440-58 (2005)
- [115] J. Bromfield, W. Messamore and D. F. Albertini: Epigenetic regulation during mammalian oogenesis. Reprod Fertil Dev, 20(1), 74-80 (2008)
- [116] G. D. Bowman and M. G. Poirier: Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev, 115(6), 2274-95 (2015)
- [117] C. L. Woodcock and R. P. Ghosh: Chromatin higher-order structure and dynamics. Cold Spring Harb Perspect Biol, 2(5), a000596 (2010)
- [118] P. W. Tai, S. K. Zaidi, H. Wu, R. A. Grandy, M. Montecino, A. J. van Wijnen, J. B. Lian, G. S. Stein and J. L. Stein: The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. J Cell Physiol, 229(6), 711-27 (2014)
- [119] B. J. Venters and B. F. Pugh: How eukaryotic genes are transcribed. Crit Rev Biochem Mol Biol, 44(2-3), 117-41 (2009)
- [120] C. Ling and L. Groop: Epigenetics: a molecular link between environmental factors and type 2 diabetes. Diabetes, 58(12), 2718-25 (2009)
- [121] L. C. Layman: The genetic basis of female reproductive disorders: etiology and clinical testing. Mol Cell Endocrinol, 370(1-2), 138-48 (2013)
- [122] C. Guerrero-Bosagna and M. K. Skinner: Environmentally induced epigenetic transgenerational inheritance of male infertility. Curr Opin Genet Dev, 26, 79-88 (2014)
- [123] S. Houshdaran, V. K. Cortessis, K. Siegmund, A. Yang, P. W. Laird and R. Z. Sokol: Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm. PLoS One, 2(12), e1289 (2007)
- [124] S. Hartmann, M. Bergmann, R. M. Bohle, W. Weidner and K. Steger: Genetic imprinting during impaired spermatogenesis. Mol Hum Reprod, 12(6), 407-11 (2006)
- [125] D. Montjean, C. Ravel, M. Benkhalifa, P. Cohen-Bacrie, I. Berthaut, A. Bashamboo and K. McElreavey: Methylation changes in mature sperm deoxyribonucleic acid from oligozoospermic men: assessment of genetic variants and assisted reproductive technology outcome. Fertil Steril, 100(5), 1241-7 (2013)
- [126] S. Manipalviratn, A. DeCherney and J. Segars: Imprinting disorders and assisted reproductive technology. Fertil Steril, 91(2), 305-15 (2009)
- [127] A. Botezatu, R. Socolov, D. Socolov, I. V. Iancu and G. Anton: Methylation pattern of methylene tetrahydrofolate reductase and small nuclear ribonucleoprotein polypeptide N promoters in oligoasthenospermia: a case-control study. Reprod Biomed Online, 28(2), 225-31 (2014)
- [128] C. J. Marques, P. Costa, B. Vaz, F. Carvalho, S. Fernandes, A. Barros and M. Sousa: Abnormal methylation of imprinted genes in human sperm is associated with oligozoospermia. Mol Hum Reprod, 14(2), 67-74 (2008)
- [129] B. Li, J. B. Li, X. F. Xiao, Y. F. Ma, J. Wang, X. X. Liang, H. X. Zhao, F. Jiang, Y. Q. Yao and X. H. Wang: Altered DNA methylation patterns of the H19 differentially methylated region and the DAZL gene promoter are associated with defective human sperm. PLoS One, 8(8), e71215 (2013)
- [130] A. Kitamura, N. Miyauchi, H. Hamada, H. Hiura, H. Chiba, H. Okae, A. Sato, R. M. John and T. Arima: Epigenetic alterations in sperm associated with male infertility. Congenit Anom (Kyoto), 55(3), 133-44 (2015)
- [131] K. I. Aston, P. J. Uren, T. G. Jenkins, A. Horsager, B. R. Cairns, A. D. Smith and D. T. Carrell: Aberrant sperm DNA methylation predicts male fertility status and embryo quality. Fertil Steril, 104(6), 1388-97 e1-5 (2015)
- [132] D. A. Skaar, Y. Li, A. J. Bernal, C. Hoyo, S. K. Murphy and R. L. Jirtle: The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J, 53(3-4), 341-58 (2012)
- [133] M. M. Denomme, C. R. White, C. Gillio-Meina, W. A. Macdonald, B. J. Deroo, G. M. Kidder and M. R. Mann: Compromised fertility disrupts Peg1 but not Snrpn and Peg3 imprinted methylation acquisition in mouse oocytes. Front Genet, 3, 129 (2012)
- [134] G. Kelsey and R. Feil: New insights into establishment and maintenance of DNA methylation imprints in mammals. Philos Trans R Soc Lond B Biol Sci, 368(1609), 20110336 (2013)
- [135] D. M. Messerschmidt, B. B. Knowles and D. Solter: DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev, 28(8), 812-28 (2014)
- [136] D. Jia, R. Z. Jurkowska, X. Zhang, A. Jeltsch and X. Cheng: Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature, 449(7159), 248-51 (2007)
- [137] D. T. Carrell and S. S. Hammoud: The human sperm epigenome and its potential role in embryonic development. Mol Hum Reprod, 16(1), 37-47 (2010)
- [138] L. Li, X. Lu and J. Dean: The maternal to zygotic transition in mammals. Mol Aspects Med, 34(5), 919-38 (2013)
- [139] A Paoloni-Giacobino and J. R. Chaillet: Genomic imprinting and assisted reproduction. Reprod Health, 1(1), 6 (2004)
- [140] E. Anckaert, M. De Rycke and J. Smitz: Culture of oocytes and risk of imprinting defects. Hum Reprod Update, 19(1), 52-66 (2013)
- [141] M. Hazzouri, C. Pivot-Pajot, A. K. Faure, Y. Usson, R. Pelletier, B. Sele, S. Khochbin and S. Rousseaux: Regulated hyperacetylation of core histones during mouse spermatogenesis: involvement of histone deacetylases. Eur J Cell Biol, 79(12), 950-60 (2000)
- [142] C. Steilmann, M. C. Cavalcanti, M. Bartkuhn, J. Pons-Kuhnemann, H. C. Schuppe, W. Weidner, K. Steger and A. Paradowska: The interaction of modified histones with the bromodomain testis-specific (BRDT) gene and its mRNA level in sperm of fertile donors and subfertile men. Reproduction, 140(3), 435-43 (2010)
- [143] Y. Okada, G. Scott, M. K. Ray, Y. Mishina and Y. Zhang: Histone demethylase JHDM2A is critical for Tnp1 and Prm1 transcription and spermatogenesis. Nature, 450(7166), 119-23 (2007)
- [144] V. Sonnack, K. Failing, M. Bergmann and K. Steger: Expression of hyperacetylated histone H4 during normal and impaired human spermatogenesis. Andrologia, 34(6), 384-90 (2002)
- [145] I. Fenic, H. M. Hossain, V. Sonnack, S. Tchatalbachev, F. Thierer, J. Trapp, K. Failing, K. S. Edler, M. Bergmann, M. Jung, T. Chakraborty and K. Steger: In vivo application of histone deacetylase inhibitor trichostatin-a impairs murine male meiosis. J Androl, 29(2), 172-85 (2008)
- [146] S. Glaser, S. Lubitz, K. L. Loveland, K. Ohbo, L. Robb, F. Schwenk, J. Seibler, D. Roellig, A. Kranz, K. Anastassiadis and A. F. Stewart: The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis. Epigenetics Chromatin, 2(1), 5 (2009)
- [147] M. G. Lee, C. Wynder, N. Cooch and R. Shiekhattar: An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature, 437(7057), 432-5 (2005)
- [148] J. Bao and M. T. Bedford: Epigenetic regulation of the histone-to-protamine transition during spermiogenesis. Reproduction, 151(5), R55-70 (2016)
- [149] Y. Shi, F. Lan, C. Matson, P. Mulligan, J. R. Whetstine, P. A. Cole, R. A. Casero and Y. Shi: Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell, 119(7), 941-53 (2004)
- [150] R. A. Waterland and K. B. Michels: Epigenetic epidemiology of the developmental origins hypothesis. Annu Rev Nutr, 27, 363-88 (2007)
- [151] Z. Liu, S. Zhou, L. Liao, X. Chen, M. Meistrich and J. Xu: Jmjd1a demethylase-regulated histone modification is essential for cAMP-response element modulator-regulated gene expression and spermatogenesis. J Biol Chem, 285(4), 2758-70 (2010)
- [152] C. J. Lin, F. M. Koh, P. Wong, M. Conti and M. Ramalho-Santos: Hira-mediated H3.3. incorporation is required for DNA replication and ribosomal RNA transcription in the mouse zygote. Dev Cell, 30(3), 268-79 (2014)
- [153] B. Nashun, P. W. Hill, S. A. Smallwood, G. Dharmalingam, R. Amouroux, S. J. Clark, V. Sharma, E. Ndjetehe, P. Pelczar, R. J. Festenstein, G. Kelsey and P. Hajkova: Continuous Histone Replacement by Hira Is Essential for Normal Transcriptional Regulation and De Novo DNA Methylation during Mouse Oogenesis. Mol Cell, 60(4), 611-25 (2015)
- [154] P. Ma and R. M. Schultz: Histone deacetylase 1 (HDAC1) regulates histone acetylation, development, and gene expression in preimplantation mouse embryos. Dev Biol, 319(1), 110-20 (2008)
- [155] O. M. Dovey, C. T. Foster and S. M. Cowley: Histone deacetylase 1 (HDAC1), but not HDAC2, controls embryonic stem cell differentiation. Proc Natl Acad Sci U S A, 107(18), 8242-7 (2010)
- [156] Z. Liu, X. Chen, S. Zhou, L. Liao, R. Jiang and J. Xu: The histone H3K9 demethylase Kdm3b is required for somatic growth and female reproductive function. Int J Biol Sci, 11(5), 494-507 (2015)
- [157] A. Q. Gomes, S. Nolasco and H. Soares: Non-coding RNAs: multi-tasking molecules in the cell. Int J Mol Sci, 14(8), 16010-39 (2013)
- [158] J. P. Saxe and H. Lin: Small noncoding RNAs in the germline. Cold Spring Harb Perspect Biol, 3(9), a002717 (2011)
- [159] L. T. Gou, P. Dai and M. F. Liu: Small noncoding RNAs and male infertility. Wiley Interdiscip Rev RNA, 5(6), 733-45 (2014)
- [160] Y. Khazaie and M. H. Nasr Esfahani: MicroRNA and Male Infertility: A Potential for Diagnosis. Int J Fertil Steril, 8(2), 113-8 (2014)
- [161] A. C. Luk, W. Y. Chan, O. M. Rennert and T. L. Lee: Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies. Reproduction, 147(5), R131-41 (2014)
- [162] D. Jamsai and M. K. O’Bryan: Mouse models in male fertility research. Asian J Androl, 13(1), 139-51 (2011)
- [163] T. Zhou, Z. M. Zhou and X. J. Guo: Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics. Asian J Androl, 15(5), 594-602 (2013)
- [164] R. Oliva: Protamines and male infertility. Hum Reprod Update, 12(4), 417-35 (2006)
- [165] R. Oliva and J. Castillo: Proteomics and the genetics of sperm chromatin condensation. Asian J Androl, 13(1), 24-30 (2011)
- [166] E. Tahmasbpour, D. Balasubramanian and A. Agarwal: A multi-faceted approach to understanding male infertility: gene mutations, molecular defects and assisted reproductive techniques (ART). J Assist Reprod Genet, 31(9), 1115-37 (2014)
- [167] R. Sharma, K. R. Biedenharn, J. M. Fedor and A. Agarwal: Lifestyle factors and reproductive health: taking control of your fertility. Reprod Biol Endocrinol, 11, 66 (2013)
- [168] J. A. Alegria-Torres, A. Baccarelli and V. Bollati: Epigenetics and lifestyle. Epigenomics, 3(3), 267-77 (2011)
- [169] M. M. Matzuk and D. J. Lamb: The biology of infertility: research advances and clinical challenges. Nat Med, 14(11), 1197-213 (2008)
- [170] Y. K. Cloonan, V. L. Holt and J. Goldberg: Male factor infertility: a twin study. Paediatr Perinat Epidemiol, 21(3), 229-34 (2007)
- [171] V. K. Cortessis, D. C. Thomas, A. J. Levine, C. V. Breton, T. M. Mack, K. D. Siegmund, R. W. Haile and P. W. Laird: Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet, 131(10), 1565-89 (2012)
- [172] L. Mirbahai and J. K. Chipman: Epigenetic memory of environmental organisms: a reflection of lifetime stressor exposures. Mutat Res Genet Toxicol Environ Mutagen, 764-765, 10-7 (2014)
- [173] Y. Wei, H. Schatten and Q. Y. Sun: Environmental epigenetic inheritance through gametes and implications for human reproduction. Hum Reprod Update, 21(2), 194-208 (2015)
- [174] R. H. Dashwood and E. Ho: Dietary histone deacetylase inhibitors: from cells to mice to man. Semin Cancer Biol, 17(5), 363-9 (2007)
- [175] A. Izzotti, P. Larghero, M. Longobardi, C. Cartiglia, A. Camoirano, V. E. Steele and S. De Flora: Dose-responsiveness and persistence of microRNA expression alterations induced by cigarette smoke in mouse lung. Mutat Res, 717(1-2), 9-16 (2011)
- [176] A Baccarelli and V. Bollati: Epigenetics and environmental chemicals. Curr Opin Pediatr, 21(2), 243-51 (2009)
- [177] C. S. Wilhelm-Benartzi, E. A. Houseman, M. A. Maccani, G. M. Poage, D. C. Koestler, S. M. Langevin, L. A. Gagne, C. E. Banister, J. F. Padbury and C. J. Marsit: In utero exposures, infant growth, and DNA methylation of repetitive elements and developmentally related genes in human placenta. Environ Health Perspect, 120(2), 296-302 (2012)
- [178] D. B. Martinez-Arguelles, E. Campioli, M. Culty, B. R. Zirkin and V. Papadopoulos: Fetal origin of endocrine dysfunction in the adult: the phthalate model. J Steroid Biochem Mol Biol, 137, 5-17 (2013)
- [179] M. K. Skinner, M. Manikkam and C. Guerrero-Bosagna: Epigenetic transgenerational actions of environmental factors in disease etiology. Trends Endocrinol Metab, 21(4), 214-22 (2010)
- [180] M. Uzumcu, H. Suzuki and M. K. Skinner: Effect of the anti-androgenic endocrine disruptor vinclozolin on embryonic testis cord formation and postnatal testis development and function. Reprod Toxicol, 18(6), 765-74 (2004)
- [181] J. LaRocca, A. Boyajian, C. Brown, S. D. Smith and M. Hixon: Effects of in utero exposure to Bisphenol A or diethylstilbestrol on the adult male reproductive system. Birth Defects Res B Dev Reprod Toxicol, 92(6), 526-33 (2011)
- [182] C. J. Park, W. H. Nah, J. E. Lee, Y. S. Oh and M. C. Gye: Butyl paraben-induced changes in DNA methylation in rat epididymal spermatozoa. Andrologia, 44 Suppl 1, 187-93 (2012)
- [183] C. Stouder and A. Paoloni-Giacobino: Specific transgenerational imprinting effects of the endocrine disruptor methoxychlor on male gametes. Reproduction, 141(2), 207-16 (2011)
- [184] M. D. Anway, A. S. Cupp, M. Uzumcu and M. K. Skinner: Epigenetic transgenerational actions of endocrine disruptors and male fertility. Science, 308(5727), 1466-9 (2005)
- [185] T. Doshi, C. D’Souza and G. Vanage: Aberrant DNA methylation at Igf2-H19 imprinting control region in spermatozoa upon neonatal exposure to bisphenol A and its association with post implantation loss. Mol Biol Rep, 40(8), 4747-57 (2013)
- [186] T. Doshi, S. S. Mehta, V. Dighe, N. Balasinor and G. Vanage: Hypermethylation of estrogen receptor promoter region in adult testis of rats exposed neonatally to bisphenol A. Toxicology, 289(2-3), 74-82 (2011)
- [187] C. Stouder, E. Somm and A. Paoloni-Giacobino: Prenatal exposure to ethanol: a specific effect on the H19 gene in sperm. Reprod Toxicol, 31(4), 507-12 (2011)
- [188] N. E. Skakkebaek, E. Rajpert-De Meyts, N. Jorgensen, K. M. Main, H. Leffers, A. M. Andersson, A. Juul, T. K. Jensen and J. Toppari: Testicular cancer trends as ’whistle blowers’ of testicular developmental problems in populations. Int J Androl, 30(4), 198-204; discussion 204-5 (2007)
- [189] K. P. Singh, R. Kumari, C. Pevey, D. Jackson and J. W. DuMond: Long duration exposure to cadmium leads to increased cell survival, decreased DNA repair capacity, and genomic instability in mouse testicular Leydig cells. Cancer Lett, 279(1), 84-92 (2009)
- [190] Y. E. Dubrova, M. Plumb, B. Gutierrez, E. Boulton and A. J. Jeffreys: Transgenerational mutation by radiation. Nature, 405(6782), 37 (2000)
- [191] M. Merrifield and O. Kovalchuk: Epigenetics in radiation biology: a new research frontier. Front Genet, 4, 40 (2013)
- [192] B. Kincaid and E. Bossy-Wetzel: Forever young: SIRT3 a shield against mitochondrial meltdown, aging, and neurodegeneration. Front Aging Neurosci, 5, 48 (2013)
- [193] N. Braidy, A. Poljak, R. Grant, T. Jayasena, H. Mansour, T. Chan-Ling, G. Smythe, P. Sachdev and G. J. Guillemin: Differential expression of sirtuins in the aging rat brain. Front Cell Neurosci, 9, 167 (2015)
- [194] D. Nettersheim, L. C. Heukamp, F. Fronhoffs, M. J. Grewe, N. Haas, A. Waha, F. Honecker, A. Waha, G. Kristiansen and H. Schorle: Analysis of TET expression/activity and 5mC oxidation during normal and malignant germ cell development. PLoS One, 8(12), e82881 (2013)
- [195] K. Ni, T. Dansranjavin, N. Rogenhofer, N. Oeztuerk, J. Deuker, M. Bergmann, H. C. Schuppe, F. Wagenlehner, W. Weidner, K. Steger and U. Schagdarsurengin: TET enzymes are successively expressed during human spermatogenesis and their expression level is pivotal for male fertility. Hum Reprod, 31(7), 1411-24 (2016)
- [196] B. R. Carone, L. Fauquier, N. Habib, J. M. Shea, C. E. Hart, R. Li, C. Bock, C. Li, H. Gu, P. D. Zamore, A. Meissner, Z. Weng, H. A. Hofmann, N. Friedman and O. J. Rando: Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell, 143(7), 1084-96 (2010)
- [197] E. J. Radford, M. Ito, H. Shi, J. A. Corish, K. Yamazawa, E. Isganaitis, S. Seisenberger, T. A. Hore, W. Reik, S. Erkek, A. H. Peters, M. E. Patti and A. C. Ferguson-Smith: In utero effects. In utero undernourishment perturbs the adult sperm methylome and intergenerational metabolism. Science, 345(6198), 1255903 (2014)
- [198] R. C. Painter, T. J. Roseboom and O. P. Bleker: Prenatal exposure to the Dutch famine and disease in later life: an overview. Reprod Toxicol, 20(3), 345-52 (2005)
- [199] T. J. Roseboom, J. H. van der Meulen, A. C. Ravelli, C. Osmond, D. J. Barker and O. P. Bleker: Effects of prenatal exposure to the Dutch famine on adult disease in later life: an overview. Mol Cell Endocrinol, 185(1-2), 93-8 (2001)
- [200] B. T. Heijmans, E. W. Tobi, A. D. Stein, H. Putter, G. J. Blauw, E. S. Susser, P. E. Slagboom and L. H. Lumey: Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A, 105(44), 17046-9 (2008)
- [201] E. W. Tobi, J. J. Goeman, R. Monajemi, H. Gu, H. Putter, Y. Zhang, R. C. Slieker, A. P. Stok, P. E. Thijssen, F. Muller, E. W. van Zwet, C. Bock, A. Meissner, L. H. Lumey, P. Eline Slagboom and B. T. Heijmans: DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun, 5, 5592 (2014)
- [202] G. Kaati, L. O. Bygren and S. Edvinsson: Cardiovascular and diabetes mortality determined by nutrition during parents’ and grandparents’ slow growth period. Eur J Hum Genet, 10(11), 682-8 (2002)
- [203] G. Kaati, L. O. Bygren, M. Pembrey and M. Sjostrom: Transgenerational response to nutrition, early life circumstances and longevity. Eur J Hum Genet, 15(7), 784-90 (2007)
- [204] N. K. MacLennan, S. J. James, S. Melnyk, A. Piroozi, S. Jernigan, J. L. Hsu, S. M. Janke, T. D. Pham and R. H. Lane: Uteroplacental insufficiency alters DNA methylation, one-carbon metabolism, and histone acetylation in IUGR rats. Physiol Genomics, 18(1), 43-50 (2004)
- [205] K. A. Lillycrop, J. L. Slater-Jefferies, M. A. Hanson, K. M. Godfrey, A. A. Jackson and G. C. Burdge: Induction of altered epigenetic regulation of the hepatic glucocorticoid receptor in the offspring of rats fed a protein-restricted diet during pregnancy suggests that reduced DNA methyltransferase-1 expression is involved in impaired DNA methylation and changes in histone modifications. Br J Nutr, 97(6), 1064-73 (2007)
- [206] K. A. Lillycrop, E. S. Phillips, A. A. Jackson, M. A. Hanson and G. C. Burdge: Dietary protein restriction of pregnant rats induces and folic acid supplementation prevents epigenetic modification of hepatic gene expression in the offspring. J Nutr, 135(6), 1382-6 (2005)
- [207] I. C. Weaver, N. Cervoni, F. A. Champagne, A. C. D’Alessio, S. Sharma, J. R. Seckl, S. Dymov, M. Szyf and M. J. Meaney: Epigenetic programming by maternal behavior. Nat Neurosci, 7(8), 847-54 (2004)
- [208] M. J. Meaney, M. Szyf and J. R. Seckl: Epigenetic mechanisms of perinatal programming of hypothalamic-pituitary-adrenal function and health. Trends Mol Med, 13(7), 269-77 (2007)
- [209] C. J. Ashworth, L. M. Toma and M. G. Hunter: Nutritional effects on oocyte and embryo development in mammals: implications for reproductive efficiency and environmental sustainability. Philos Trans R Soc Lond B Biol Sci, 364(1534), 3351-61 (2009)
- [210] A. Petronis: Human morbid genetics revisited: relevance of epigenetics. Trends Genet, 17(3), 142-6 (2001)
- [211] L. Daxinger and E. Whitelaw: Transgenerational epigenetic inheritance: more questions than answers. Genome Res, 20(12), 1623-8 (2010)
- [212] P. Hajkova, S. Erhardt, N. Lane, T. Haaf, O. El-Maarri, W. Reik, J. Walter and M. A. Surani: Epigenetic reprogramming in mouse primordial germ cells. Mech Dev, 117(1-2), 15-23 (2002)
- [213] Y. Obata and T. Kono: Maternal primary imprinting is established at a specific time for each gene throughout oocyte growth. J Biol Chem, 277(7), 5285-9 (2002)
- [214] T. L. Davis, G. J. Yang, J. R. McCarrey and M. S. Bartolomei: The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet, 9(19), 2885-94 (2000)
- [215] E. Jablonka and M. J. Lamb: The inheritance of acquired epigenetic variations. Int J Epidemiol, 44(4), 1094-103 (2015)
- [216] M. Loi, L. Del Savio and E. Stupka: Social Epigenetics and Equality of Opportunity. Public Health Ethics, 6(2), 142-153 (2013)
- [217] W. G. Kelly: Transgenerational epigenetics in the germline cycle of Caenorhabditis elegans. Epigenetics Chromatin, 7(1), 6 (2014)
- [218] J. M. Flanagan, V. Popendikyte, N. Pozdniakovaite, M. Sobolev, A. Assadzadeh, A. Schumacher, M. Zangeneh, L. Lau, C. Virtanen, S. C. Wang and A. Petronis: Intra- and interindividual epigenetic variation in human germ cells. Am J Hum Genet, 79(1), 67-84 (2006)
- [219] S. Jacob and K. H. Moley: Gametes and embryo epigenetic reprogramming affect developmental outcome: implication for assisted reproductive technologies. Pediatr Res, 58(3), 437-46 (2005)
- [220] L. Nanassy, L. Liu, J. Griffin and D. T. Carrell: The clinical utility of the protamine 1/protamine 2 ratio in sperm. Protein Pept Lett, 18(8), 772-7 (2011)
- [221] D. Lucifero, J. R. Chaillet and J. M. Trasler: Potential significance of genomic imprinting defects for reproduction and assisted reproductive technology. Hum Reprod Update, 10(1), 3-18 (2004)
- [222] T. Goto and M. Monk: Regulation of X-chromosome inactivation in development in mice and humans. Microbiol Mol Biol Rev, 62(2), 362-78 (1998)
- [223] K. Plath, S. Mlynarczyk-Evans, D. A. Nusinow and B. Panning: Xist RNA and the mechanism of X chromosome inactivation. Annu Rev Genet, 36, 233-78 (2002)
- [224] F. Pacchierotti and M. Spano: Environmental Impact on DNA Methylation in the Germline: State of the Art and Gaps of Knowledge. Biomed Res Int, 2015, 123484 (2015)
- [225] V. S. Knopik, M. A. Maccani, S. Francazio and J. E. McGeary: The epigenetics of maternal cigarette smoking during pregnancy and effects on child development. Dev Psychopathol, 24(4), 1377-90 (2012)
- [226] K. M. Radtke, M. Ruf, H. M. Gunter, K. Dohrmann, M. Schauer, A. Meyer and T. Elbert: Transgenerational impact of intimate partner violence on methylation in the promoter of the glucocorticoid receptor. Transl Psychiatry, 1, e21 (2011)
- [227] M. A. Surani: Reprogramming of genome function through epigenetic inheritance. Nature, 414(6859), 122-8 (2001)
- [228] Z. D. Smith, M. M. Chan, T. S. Mikkelsen, H. Gu, A. Gnirke, A. Regev and A. Meissner: A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature, 484(7394), 339-44 (2012)
- [229] H. Kobayashi, T. Sakurai, F. Miura, M. Imai, K. Mochiduki, E. Yanagisawa, A. Sakashita, T. Wakai, Y. Suzuki, T. Ito, Y. Matsui and T. Kono: High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res, 23(4), 616-27 (2013)
- [230] Z. D. Smith, C. Sindhu and A. Meissner: Molecular features of cellular reprogramming and development. Nat Rev Mol Cell Biol, 17(3), 139-54 (2016)
- [231] C. L. Stewart, I. Gadi and H. Bhatt: Stem cells from primordial germ cells can reenter the germ line. Dev Biol, 161(2), 626-8 (1994)
- [232] E. Pelosi, A. Forabosco and D. Schlessinger: Germ cell formation from embryonic stem cells and the use of somatic cell nuclei in oocytes. Ann N Y Acad Sci, 1221, 18-26 (2011)
- [233] K. Hayashi, S. Ogushi, K. Kurimoto, S. Shimamoto, H. Ohta and M. Saitou: Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice. Science, 338(6109), 971-5 (2012)
- [234] I. Cantone and A. G. Fisher: Epigenetic programming and reprogramming during development. Nat Struct Mol Biol, 20(3), 282-9 (2013)
- [235] A. B. Stergachis, S. Neph, A. Reynolds, R. Humbert, B. Miller, S. L. Paige, B. Vernot, J. B. Cheng, R. E. Thurman, R. Sandstrom, E. Haugen, S. Heimfeld, C. E. Murry, J. M. Akey and J. A. Stamatoyannopoulos: Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell, 154(4), 888-903 (2013)
- [236] K. Shah, G. Sivapalan, N. Gibbons, H. Tempest and D. K. Griffin: The genetic basis of infertility. Reproduction, 126(1), 13-25 (2003)
- [237] L. C. Smith, J. Therrien, F. Filion, F. Bressan and F. V. Meirelles: Epigenetic consequences of artificial reproductive technologies to the bovine imprinted genes SNRPN, H19/IGF2, and IGF2R. Front Genet, 6, 58 (2015)
- [238] C. Choux, V. Carmignac, C. Bruno, P. Sagot, D. Vaiman and P. Fauque: The placenta: phenotypic and epigenetic modifications induced by Assisted Reproductive Technologies throughout pregnancy. Clin Epigenetics, 7, 87 (2015)
- [239] M. G. Butler: Genomic imprinting disorders in humans: a mini-review. J Assist Reprod Genet, 26(9-10), 477-86 (2009)
- [240] J. A. Piedrahita: The role of imprinted genes in fetal growth abnormalities. Birth Defects Res A Clin Mol Teratol, 91(8), 682-92 (2011)
- [241] F. L. Lopes, A. L. Fortier, N. Darricarrere, D. Chan, D. R. Arnold and J. M. Trasler: Reproductive and epigenetic outcomes associated with aging mouse oocytes. Hum Mol Genet, 18(11), 2032-44 (2009)
- [242] A. Soubry, J. M. Schildkraut, A. Murtha, F. Wang, Z. Huang, A. Bernal, J. Kurtzberg, R. L. Jirtle, S. K. Murphy and C. Hoyo: Paternal obesity is associated with IGF2 hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort. BMC Med, 11, 29 (2013)
- [243] A. Soubry, L. Guo, Z. Huang, C. Hoyo, S. Romanus, T. Price and S. K. Murphy: Obesity-related DNA methylation at imprinted genes in human sperm: Results from the TIEGER study. Clin Epigenetics, 8, 51 (2016)
- [244] E. R. Maher: Imprinting and assisted reproductive technology. Hum Mol Genet, 14 Spec No 1, R133-8 (2005)
- [245] H. A. Lawson, J. M. Cheverud and J. B. Wolf: Genomic imprinting and parent-of-origin effects on complex traits. Nat Rev Genet, 14(9), 609-17 (2013)
