Erratum: Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification (Developmental Cell (2016) 39(1) (104–115), (S1534580716306372), (10.1016/j.devcel.2016.09.015));Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification

Developmental Cell

Volumn 39, Issue 1, 2016, Pages 104-115

  von Meyenn, Ferdinand ^a   Berrens, Rebecca V ^a   Andrews, Simon ^a   Santos, Fátima ^a   Collier, Amanda J ^a   Krueger, Felix ^a   Osorno, Rodrigo ^a   Dean, Wendy ^a   Rugg Gunn, Peter J ^a   Reik, Wolf ^a,b  

^a BABRAHAM INSTITUTE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

chromatin; DNA methylation; epigenetic reprogramming; epigenetic resetting; PGC; PGC specification; PGC like cell; piRNA; Piwi interacting RNA; primordial germ cell

Indexed keywords

ANIMAL CELL; ARTICLE; CELL SPECIFICITY; CHROMATIN; COMPARATIVE STUDY; DEMETHYLATION; DNA METHYLATION; ECTODERM; EMBRYO; EMBRYONIC STEM CELL; EPIGENETICS; FEMALE; GERM LINE; HUMAN; HUMAN CELL; IN VITRO STUDY; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; PRIMORDIAL GERM CELL; PRIORITY JOURNAL; REGULATORY MECHANISM; SPECIES DIFFERENCE; TRANSPOSON; ANIMAL; CYTOLOGY; GENETIC TRANSCRIPTION; GENETICS; GERM CELL; HUMAN EMBRYONIC STEM CELL; METABOLISM; MORPHOGENESIS; MOUSE EMBRYONIC STEM CELL;

TRANSPOSON;

ANIMALS; BODY PATTERNING; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; GERM CELLS; HUMAN EMBRYONIC STEM CELLS; HUMANS; MICE; MOUSE EMBRYONIC STEM CELLS; TRANSCRIPTION, GENETIC;

EID: 84992653738     PISSN: 15345807     EISSN: 18781551     Source Type: Journal    
DOI: 10.1016/j.devcel.2022.11.009     Document Type: Erratum

References (65)

1. Aravin, A.A., Hannon, G.J., Brennecke, J., The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318 (2007), 761–764.
2. Baubec, T., Colombo, D.F., Wirbelauer, C., Schmidt, J., Burger, L., Krebs, A.R., Akalin, A., Schübeler, D., Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 520 (2015), 243–247.
3. Bourc'his, D., Bestor, T.H., Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431 (2004), 96–99.
4. Burns, K.H., Boeke, J.D., Human transposon tectonics. Cell 149 (2012), 740–752.
5. Butler, M.G., Genomic imprinting disorders in humans: a mini-review. J. Assist. Reprod. Genet. 26 (2009), 477–486.
6. Carmell, M.A., Girard, A., van de Kant, H.J.G., Bourc'his, D., Bestor, T.H., de Rooij, D.G., Hannon, G.J., MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12 (2007), 503–514.
7. Cheng, E.-C., Kang, D., Wang, Z., Lin, H., PIWI proteins are dispensable for mouse somatic development and reprogramming of fibroblasts into pluripotent stem cells. PLoS One, 9, 2014, e97821.
8. Citterio, E., Papait, R., Nicassio, F., Vecchi, M., Gomiero, P., Mantovani, R., Di Fiore, P.P., Bonapace, I.M., Np95 is a histone-binding protein endowed with ubiquitin ligase activity. Mol. Cell Biol. 24 (2004), 2526–2535.
9. Clark, A.T., DNA methylation remodeling in vitro and in vivo. Curr. Opin. Genet. Dev. 34 (2015), 82–87.
10. Court, F., Tayama, C., Romanelli, V., Martin-Trujillo, A., Iglesias-Platas, I., Okamura, K., Sugahara, N., Simon, C., Moore, H., Harness, J.V., et al. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res. 24 (2014), 554–569.
11. Daley, G.Q., Gametes from embryonic stem cells: a cup half empty or half full?. Science 316 (2007), 409–410.
12. Ficz, G., Hore, T.A., Santos, F., Lee, H.J., Dean, W., Arand, J., Krueger, F., Oxley, D., Paul, Y.-L., Walter, J., et al. FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell 13 (2013), 351–359.
13. Friedli, M., Trono, D., The developmental control of transposable elements and the evolution of higher species. Annu. Rev. Cell Dev. Biol. 31 (2015), 429–451.
14. Gkountela, S., Li, Z., Vincent, J.J., Zhang, K.X., Chen, A., Pellegrini, M., Clark, A.T., The ontogeny of cKIT+ human primordial germ cells proves to be a resource for human germ line reprogramming, imprint erasure and in vitro differentiation. Nat. Cell Biol. 15 (2013), 113–122.
15. Gkountela, S., Zhang, K.X., Shafiq, T.A., Liao, W.-W., Hargan-Calvopiña, J., Chen, P.-Y., Clark, A.T., DNA demethylation dynamics in the human prenatal germline. Cell 161 (2015), 1425–1436.
16. Guo, H., Zhu, P., Yan, L., Li, R., Hu, B., Lian, Y., Yan, J., Ren, X., Lin, S., Li, J., et al. The DNA methylation landscape of human early embryos. Nature 511 (2014), 606–610.
17. Guo, F., Yan, L., Guo, H., Li, L., Hu, B., Zhao, Y., Yong, J., Hu, Y., Wang, X., Wei, Y., et al. The transcriptome and DNA methylome landscapes of human primordial germ cells. Cell 161 (2015), 1437–1452.
18. Guo, G., von Meyenn, F., Santos, F., Chen, Y., Reik, W., Bertone, P., Smith, A., Nichols, J., Naive pluripotent stem cells derived directly from isolated cells of the human inner cell mass. Stem Cell Rep. 6 (2016), 437–446.
19. Hackett, J.A., Sengupta, R., Zylicz, J.J., Murakami, K., Lee, C., Down, T.A., Surani, M.A., Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339 (2013), 448–452.
20. Han, B.W., Wang, W., Zamore, P.D., Weng, Z., piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. Bioinformatics 31 (2015), 593–595.
21. Hayashi, K., Ohta, H., Kurimoto, K., Aramaki, S., Saitou, M., Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell 146 (2011), 519–532.
22. Hayashi, K., Ogushi, S., Kurimoto, K., Shimamoto, S., Ohta, H., Saitou, M., Offspring from oocytes derived from in vitro primordial germ cell-like cells in mice. Science 338 (2012), 971–975.
23. Irie, N., Tang, W.W.C., Surani, M.A., Germ cell specification and pluripotency in mammals: a perspective from early embryogenesis. Reprod. Med. Biol. 13 (2014), 203–215.
24. Irie, N., Weinberger, L., Tang, W.W.C., Kobayashi, T., Viukov, S., Manor, Y.S., Dietmann, S., Hanna, J.H., Surani, M.A., SOX17 is a critical specifier of human primordial germ cell fate. Cell 160 (2015), 253–268.
25. Iwasaki, Y.W., Siomi, M.C., Siomi, H., PIWI-interacting RNA: its biogenesis and functions. Annu. Rev. Biochem. 84 (2015), 405–433.
26. Karagianni, P., Amazit, L., Qin, J., Wong, J., ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation. Mol. Cell Biol. 28 (2008), 705–717.
27. Kobayashi, H., Sakurai, T., Miura, F., Imai, M., Mochiduki, K., Yanagisawa, E., Sakashita, A., Wakai, T., Suzuki, Y., Ito, T., et al. High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res. 23 (2013), 616–627.
28. Krueger, F., Andrews, S.R., Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27 (2011), 1571–1572.
29. Kuramochi-Miyagawa, S., Kimura, T., Ijiri, T.W., Isobe, T., Asada, N., Fujita, Y., Ikawa, M., Iwai, N., Okabe, M., Deng, W., et al. Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development 131 (2004), 839–849.
30. Kurimoto, K., Yabuta, Y., Hayashi, K., Ohta, H., Kiyonari, H., Mitani, T., Moritoki, Y., Kohri, K., Kimura, H., Yamamoto, T., et al. Quantitative dynamics of chromatin remodeling during germ cell specification from mouse embryonic stem cells. Cell Stem Cell 16 (2015), 517–532.
31. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001), 860–921.
32. Li, X.Z., Roy, C.K., Dong, X., Bolcun-Filas, E., Wang, J., Han, B.W., Xu, J., Moore, M.J., Schimenti, J.C., Weng, Z., et al. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol. Cell 50 (2013), 67–81.
33. Liu, S., Brind'Amour, J., Karimi, M.M., Shirane, K., Bogutz, A., Lefebvre, L., Sasaki, H., Shinkai, Y., Lorincz, M.C., Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells. Genes Dev. 28 (2014), 2041–2055.
34. Miura, F., Enomoto, Y., Dairiki, R., Ito, T., Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res., 40, 2012, e136.
35. Molaro, A., Falciatori, I., Hodges, E., Aravin, A.A., Marran, K., Rafii, S., McCombie, W.R., Smith, A.D., Hannon, G.J., Two waves of de novo methylation during mouse germ cell development. Genes Dev. 28 (2014), 1544–1549.
36. Mouse Genome Sequencing Consortium, Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002), 520–562.
37. Nakaki, F., Saitou, M., PRDM14: a unique regulator for pluripotency and epigenetic reprogramming. Trends Biochem. Sci. 39 (2014), 289–298.
38. Nichols, J., Smith, A., Pluripotency in the embryo and in culture. Cold Spring Harb. Perspect. Biol., 4, 2012, a008128.
39. Okae, H., Chiba, H., Hiura, H., Hamada, H., Sato, A., Utsunomiya, T., Kikuchi, H., Yoshida, H., Tanaka, A., Suyama, M., et al. Genome-wide analysis of DNA methylation dynamics during early human development. PLoS Genet., 10, 2014, e1004868.
40. Pastor, W.A., Chen, D., Liu, W., Kim, R., Sahakyan, A., Lukianchikov, A., Plath, K., Jacobsen, S.E., Clark, A.T., Naive human pluripotent cells feature a methylation landscape devoid of blastocyst or germline memory. Cell Stem Cell 18 (2016), 323–329.
41. Picelli, S., Faridani, O.R., Björklund, Å.K., Winberg, G., Sagasser, S., Sandberg, R., Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9 (2014), 171–181.
42. Reik, W., Surani, M.A., Germline and pluripotent stem cells. Cold Spring Harb. Perspect. Biol., 7, 2015, 10.1101/cshperspect.a019422.
43. Rothbart, S.B., Krajewski, K., Nady, N., Tempel, W., Xue, S., Badeaux, A.I., Barsyte-Lovejoy, D., Martinez, J.Y., Bedford, M.T., Fuchs, S.M., et al. Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation. Nat. Struct. Mol. Biol. 19 (2012), 1155–1160.
44. Saitou, M., Miyauchi, H., Gametogenesis from pluripotent stem cells. Cell Stem Cell 18 (2016), 721–735.
45. Saitou, M., Yamaji, M., Germ cell specification in mice: signaling, transcription regulation, and epigenetic consequences. Reproduction 139 (2010), 931–942.
46. Sasaki, K., Yokobayashi, S., Nakamura, T., Okamoto, I., Yabuta, Y., Kurimoto, K., Ohta, H., Moritoki, Y., Iwatani, C., Tsuchiya, H., et al. Robust in vitro induction of human germ cell fate from pluripotent stem cells. Cell Stem Cell 17 (2015), 178–194.
47. Seisenberger, S., Andrews, S., Krueger, F., Arand, J., Walter, J., Santos, F., Popp, C., Thienpont, B., Dean, W., Reik, W., The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 48 (2012), 849–862.
48. Smallwood, S.A., Lee, H.J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., Andrews, S.R., Stegle, O., Reik, W., Kelsey, G., Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11 (2014), 817–820.
49. Sugawa, F., Araúzo-Bravo, M.J., Yoon, J., Kim, K.-P., Aramaki, S., Wu, G., Stehling, M., Psathaki, O.E., Hübner, K., Schöler, H.R., Human primordial germ cell commitment in vitro associates with a unique PRDM14 expression profile. EMBO J. 34 (2015), 1009–1024.
50. Surani, M.A., Human germline: a new research frontier. Stem Cell Rep. 4 (2015), 1–6.
51. Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al. Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell 158 (2014), 1254–1269.
52. Tang, W.W.C., Dietmann, S., Irie, N., Leitch, H.G., Floros, V.I., Bradshaw, C.R., Hackett, J.A., Chinnery, P.F., Surani, M.A., A unique gene regulatory network resets the human germline epigenome for development. Cell 161 (2015), 1453–1467.
53. Theunissen, T.W., Powell, B.E., Wang, H., Mitalipova, M., Faddah, D.A., Reddy, J., Fan, Z.P., Maetzel, D., Ganz, K., Shi, L., et al. Systematic identification of culture conditions for induction and maintenance of naive human pluripotency. Cell Stem Cell 15 (2014), 471–487.
54. Theunissen, T.W., Friedli, M., He, Y., Planet, E., O'Neil, R.C., Markoulaki, S., Pontis, J., Wang, H., Iouranova, A., Imbeault, M., et al. Molecular criteria for defining the naive human pluripotent state. Cell Stem Cell, 2016, 10.1016/j.stem.2016.06.011.
55. Tomizawa, S.-I., Kobayashi, H., Watanabe, T., Andrews, S., Hata, K., Kelsey, G., Sasaki, H., Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development 138 (2011), 811–820.
56. Vincent, J.J., Huang, Y., Chen, P.-Y., Feng, S., Calvopiña, J.H., Nee, K., Lee, S.A., Le, T., Yoon, A.J., Faull, K., et al. Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell Stem Cell 12 (2013), 470–478.
57. von Meyenn, F., Reik, W., Forget the parents: epigenetic reprogramming in human germ cells. Cell 161 (2015), 1248–1251.
58. von Meyenn, F., Iurlaro, M., Habibi, E., Liu, N.Q., Salehzadeh-Yazdi, A., Santos, F., Petrini, E., Milagre, I., Yu, M., Xie, Z., et al. Impairment of DNA Methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol. Cell 62 (2016), 848–861.
59. Walsh, C.P., Chaillet, J.R., Bestor, T.H., Nat. Genet. 20 (1998), 116–117.
60. Wang, L., Zhang, J., Duan, J., Gao, X., Zhu, W., Lu, X., Yang, L., Zhang, J., Li, G., Ci, W., et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 157 (2014), 979–991.
61. Yamaji, M., Seki, Y., Kurimoto, K., Yabuta, Y., Yuasa, M., Shigeta, M., Yamanaka, K., Ohinata, Y., Saitou, M., Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat. Genet. 40 (2008), 1016–1022.
62. Yeom, Y.I., Fuhrmann, G., Ovitt, C.E., Brehm, A., Ohbo, K., Gross, M., Hubner, K., Schöler, H.R., Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells. Development 122 (1996), 881–894.
63. Ying, Q.-L., Wray, J., Nichols, J., Batlle-Morera, L., Doble, B., Woodgett, J., Cohen, P., Smith, A., The ground state of embryonic stem cell self-renewal. Nature 453 (2008), 519–523.
64. Yoshimizu, T., Sugiyama, N., De Felice, M., Yeom, Y.I., Ohbo, K., Masuko, K., Obinata, M., Abe, K., Schöler, H.R., Matsui, Y., Germline-specific expression of the Oct-4/green fluorescent protein (GFP) transgene in mice. Dev. Growth Differ. 41 (1999), 675–684.
65. Zhou, Q., Wang, M., Yuan, Y., Wang, X., Fu, R., Wan, H., Xie, M., Liu, M., Guo, X., Zheng, Y., et al. Complete meiosis from embryonic stem cell-derived germ cells in vitro. Cell Stem Cell 18 (2016), 330–340.