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Brief Report

Novel imprinted single CpG sites found by global DNA methylation analysis in human parthenogenetic induced pluripotent stem cells

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Pages 343-351 | Received 15 Dec 2017, Accepted 23 Mar 2018, Published online: 03 May 2018

References

  • Morison IM, Paton CJ, Cleverley SD. The imprinted gene and parent-of-origin effect database. Nucleic Acids Research. 2001;29:275–6. doi:10.1093/nar/29.1.275. PMID:11125110
  • Ishida M, Moore GE. The role of imprinted genes in humans. Molecular Aspects of Medicine. 2013;34:826–40. doi:10.1016/j.mam.2012.06.009. PMID:22771538
  • Morison IM, Ramsay JP, Spencer HG. A census of mammalian imprinting. Trends Genet. 2005;21:457–65. doi:10.1016/j.tig.2005.06.008. PMID:15990197
  • Surani MA, Kothary R, Allen ND, et al. Genome imprinting and development in the mouse. Dev Suppl.1990:89–98.
  • Smith RJ, Dean W, Konfortova G, et al. Identification of novel imprinted genes in a genome-wide screen for maternal methylation. Genome Res. 2003;13:558–69. doi:10.1101/gr.781503. PMID:12670997
  • Paulsen M, Ferguson-Smith AC. DNA methylation in genomic imprinting, development, and disease. J Pathol. 2001;195:97–110. doi:10.1002/path.890. PMID:11568896
  • Moore GE, Ishida M, Demetriou C, et al. The role and interaction of imprinted genes in human fetal growth. Philos Trans R Soc Lond B Biol Sci. 2015;370:20140074. doi:10.1098/rstb.2014.0074. PMID:25602077
  • Szabo P, Mann JR. Expression and methylation of imprinted genes during in vitro differentiation of mouse parthenogenetic and androgenetic embryonic stem cell lines. Development. 1994;120:1651–60. PMID:8050371
  • Glenn CC, Driscoll DJ, Yang TP, et al. Genomic imprinting: potential function and mechanisms revealed by the Prader-Willi and Angelman syndromes. Mol Hum Reprod. 1997;3:321–32. doi:10.1093/molehr/3.4.321. PMID:9237260
  • Bressan FF, De Bem TH, Perecin F, Lopes FL, et al. Unearthing the roles of imprinted genes in the placenta. Placenta. 2009;30:823–34. doi:10.1016/j.placenta.2009.07.007. PMID:19679348
  • Luedi PP, Dietrich FS, Weidman JR, et al. Computational and experimental identification of novel human imprinted genes. Genome Res. 2007;17:1723–30. doi:10.1101/gr.6584707. PMID:18055845
  • Stevens LC, Varnum DS, Eicher EM. Viable chimaeras produced from normal and parthenogenetic mouse embryos. Nature. 1977;269:515–7. doi:10.1038/269515a0. PMID:909600
  • Leeb M, Walker R, Mansfield B, et al. Germline potential of parthenogenetic haploid mouse embryonic stem cells. Development. 2012;139:3301–5. doi:10.1242/dev.083675. PMID:22912412
  • Iles SA, McBurney MW, Bramwell SR, et al. Development of parthenogenetic and fertilized mouse embryos in the uterus and in extra-uterine sites. J Embryol Exp Morphol. 1975;34:387–405. PMID:1194837
  • Oliveira FG, Dozortsev D, Diamond MP, et al. Evidence of parthenogenetic origin of ovarian teratoma: case report. Hum Reprod. 2004;19:1867–70. doi:10.1093/humrep/deh345. PMID:15192066
  • Choufani S, Shapiro JS, Susiarjo M, et al. A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes. Genome Res. 2011;21:465–76. doi:10.1101/gr.111922.110. PMID:21324877
  • Wolff EF, Hughes M, Merino MJ, et al. Expression of benign and malignant thyroid tissue in ovarian teratomas and the importance of multimodal management as illustrated by a BRAF-positive follicular variant of papillary thyroid cancer. Thyroid. 2010;20:981–7. doi:10.1089/thy.2009.0458. PMID:20718682
  • Outwater EK, Siegelman ES, Hunt JL. Ovarian teratomas: tumor types and imaging characteristics. Radiographics. 2001;21:475–90. doi:10.1148/radiographics.21.2.g01mr09475. PMID:11259710
  • Rugg-Gunn PJ, Ferguson-Smith AC, Pedersen RA. Status of genomic imprinting in human embryonic stem cells as revealed by a large cohort of independently derived and maintained lines. Hum Mol Genet. 2007;16 Spec No. 2:R243–51. doi:10.1093/hmg/ddm245. PMID:17911167
  • Kim KP, Thurston A, Mummery C, et al. Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines. Genome Res. 2007;17:1731–42. doi:10.1101/gr.6609207. PMID:17989250
  • Bibikova M, Barnes B, Tsan C, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98:288–95. doi:10.1016/j.ygeno.2011.07.007. PMID:21839163
  • Sandoval J, Heyn H, Moran S, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6:692–702. doi:10.4161/epi.6.6.16196. PMID:21593595
  • Morris TJ, Beck S. Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data. Methods. 2015;72:3–8. doi:10.1016/j.ymeth.2014.08.011. PMID:25233806
  • Lo B, Parham L. Ethical issues in stem cell research. Endocr Rev. 2009;30:204–13. doi:10.1210/er.2008-0031. PMID:19366754
  • de Wert G, Mummery C. Human embryonic stem cells: research, ethics and policy. Hum Reprod. 2003;18:672–82. doi:10.1093/humrep/deg143. PMID:12660256
  • Hyun I. The bioethics of stem cell research and therapy. J Clin Invest. 2010;120:71–5. doi:10.1172/JCI40435. PMID:20051638
  • Baylin S, Bestor TH. Altered methylation patterns in cancer cell genomes: cause or consequence? Cancer Cell. 2002;1:299–305. doi:10.1016/S1535-6108(02)00061-2. PMID:12086841
  • Holm TM, Jackson-Grusby L, Brambrink T, et al. Global loss of imprinting leads to widespread tumorigenesis in adult mice. Cancer Cell. 2005;8:275–85. doi:10.1016/j.ccr.2005.09.007. PMID:16226703
  • Claydon K, Owens L. Attempts at immortalization of crustacean primary cell cultures using human cancer genes. In Vitro Cell Dev Biol Anim. 2008;44:451–7. doi:10.1007/s11626-008-9141-x. PMID:18830775
  • Sritanaudomchai H, Ma H, Clepper L, et al. Discovery of a novel imprinted gene by transcriptional analysis of parthenogenetic embryonic stem cells. Hum Reprod. 2010;25:1927–41. doi:10.1093/humrep/deq144. PMID:20522441
  • Stelzer Y, Yanuka O, Benvenisty N. Global analysis of parental imprinting in human parthenogenetic induced pluripotent stem cells. Nat Struct Mol Biol. 2011;18:735–41. doi:10.1038/nsmb.2050. PMID:21572443
  • Kobayashi H, Yamada K, Morita S, et al. Identification of the mouse paternally expressed imprinted gene Zdbf2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2. Genomics. 2009;93:461–72. doi:10.1016/j.ygeno.2008.12.012. PMID:19200453
  • Kim MJ, Choi HW, Jang HJ, et al. Conversion of genomic imprinting by reprogramming and redifferentiation. J Cell Sci. 2013;126:2516–24. doi:10.1242/jcs.122754. PMID:23525019
  • Lee HJ, Choi NY, Lee SW, et al. Epigenetic alteration of imprinted genes during neural differentiation of germline-derived pluripotent stem cells. Epigenetics. 2016;11:177–83. doi:10.1080/15592294.2016.1146852. PMID:26962997
  • Henckel A, Arnaud P. Genome-wide identification of new imprinted genes. Brief Funct Genomics. 2010;9:304–14. doi:10.1093/bfgp/elq016. PMID:20591836
  • Frost JM, Moore GE. The importance of imprinting in the human placenta. PLoS Genet. 2010;6:e1001015. doi:10.1371/journal.pgen.1001015. PMID:20617174
  • Strichman-Almashanu LZ, Lee RS, Onyango PO, et al. A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res. 2002;12:543–54. doi:10.1101/gr.224102. PMID:11932239
  • Molaro A, Hodges E, Fang F, et al. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell. 2011;146:1029–41. doi:10.1016/j.cell.2011.08.016. PMID:21925323
  • Hammoud SS, Nix DA, Zhang H, et al. Distinctive chromatin in human sperm packages genes for embryo development. Nature. 2009;460:473–8. doi:10.1038/nature08162. PMID:19525931
  • Pogribny IP, Pogribna M, Christman JK, et al. Single-site methylation within the p53 promoter region reduces gene expression in a reporter gene construct: Possible in vivo relevance during tumorigenesis. Cancer Res. 2000;60:588–94. PMID:10676641
  • Medvedeva YA, Khamis AM, Kulakovskiy IV, et al. Effects of cytosine methylation on transcription factor binding sites. BMC Genomics. 2014;15:119. doi:10.1186/1471-2164-15-119. PMID:24669864
  • Sohn BH, Park IY, Lee JJ, et al. Functional switching of TGF-beta1 signaling in liver cancer via epigenetic modulation of a single CpG site in TTP promoter. Gastroenterology. 2010;138:1898–908. doi:10.1053/j.gastro.2009.12.044. PMID:20038433
  • Furst RW, Kliem H, Meyer HH, et al. A differentially methylated single CpG-site is correlated with estrogen receptor alpha transcription. J Steroid Biochem Mol Biol. 2012;130:96–104. doi:10.1016/j.jsbmb.2012.01.009. PMID:22342840
  • Zhang Z, Gao Y, Gordon A, et al. Efficient generation of fully reprogrammed human iPS cells via polycistronic retroviral vector and a new cocktail of chemical compounds. PLoS One. 2011;6:e26592. doi:10.1371/journal.pone.0026592. PMID:22046312
  • Kim JB, Greber B, Arauzo-Bravo MJ, et al. Direct reprogramming of human neural stem cells by OCT4. Nature. 2009;461:649–3. doi:10.1038/nature08436. PMID:19718018
  • Kim K, Ng K, Rugg-Gunn PJ, et al. Recombination signatures distinguish embryonic stem cells derived by parthenogenesis and somatic cell nuclear transfer. Cell Stem Cell. 2007;1:346–52. doi:10.1016/j.stem.2007.07.001. PMID:18371368

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