Quantitative dynamics of chromatin remodeling during germ cell specification from mouse embryonic stem cells

Cell Stem Cell

Volumn 16, Issue 5, 2015, Pages 517-532

  Kurimoto, Kazuki ^a,b   Yabuta, Yukihiro ^a,b   Hayashi, Katsuhiko ^a,b,c   Ohta, Hiroshi ^a,b   Kiyonari, Hiroshi ^d   Mitani, Tadahiro ^a   Moritoki, Yoshinobu ^a,e   Kohri, Kenjiro ^e   Kimura, Hiroshi ^f   Yamamoto, Takuya ^g,i   Katou, Yuki ^h   Shirahige, Katsuhiko ^h   Saitou, Mitinori ^a,b,g,i  

^a KYOTO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c KYUSHU UNIVERSITY   (Japan)

^d RIKEN   (Japan)

^e NAGOYA CITY UNIVERSITY GRADUATE SCHOOL OF MEDICAL SCIENCES   (Japan)

^f TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^g KYOTO UNIVERSITY   (Japan)

^h UNIVERSITY OF TOKYO   (Japan)

ⁱ KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVIN A; APC PROTEIN; B LYMPHOCYTE INDUCED MATURATION PROTEIN 1; BRCA1 PROTEIN; FIBROBLAST GROWTH FACTOR 2; HISTONE H3; MITOGEN ACTIVATED PROTEIN KINASE; BRACHYURY PROTEIN; FETOPROTEIN; HISTONE; HOMEODOMAIN PROTEIN; HOXA PROTEIN; KLF9 PROTEIN, MOUSE; KRUPPEL LIKE FACTOR; PRDM1 PROTEIN, MOUSE; PROTEIN BINDING; T BOX TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR;

ANIMAL CELL; APOPTOSIS; ARTICLE; CELL DIFFERENTIATION; CELL SPECIFICITY; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA METHYLATION; EMBRYONIC STEM CELL; ENHANCER REGION; GENE EXPRESSION; GENE REPRESSION; GERM CELL; HETEROCHROMATIN; HISTONE MODIFICATION; IN VITRO STUDY; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; QUANTITATIVE ANALYSIS; REGULATOR GENE; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; UPREGULATION; ANIMAL; CELL CULTURE; EMBRYONIC GERM CELL; EPIGENETIC REPRESSION; EPIGENETICS; GENETIC EPIGENESIS; GENETICS; METABOLISM; METHYLATION; PHYSIOLOGY;

ANIMALS; CELL DIFFERENTIATION; CELLS, CULTURED; CHROMATIN ASSEMBLY AND DISASSEMBLY; EMBRYONIC GERM CELLS; EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; EPIGENETIC REPRESSION; EPIGENOMICS; FETAL PROTEINS; HISTONES; HOMEODOMAIN PROTEINS; KRUPPEL-LIKE TRANSCRIPTION FACTORS; METHYLATION; MICE; PROTEIN BINDING; T-BOX DOMAIN PROTEINS; TRANSCRIPTION FACTORS;

EID: 84929281565     PISSN: 19345909     EISSN: 18759777     Source Type: Journal    
DOI: 10.1016/j.stem.2015.03.002     Document Type: Article

References (36)

1. S. Aramaki, K. Hayashi, K. Kurimoto, H. Ohta, Y. Yabuta, H. Iwanari, Y. Mochizuki, T. Hamakubo, Y. Kato, K. Shirahige, and M. Saitou A mesodermal factor, T, specifies mouse germ cell fate by directly activating germline determinants Dev. Cell 27 2013 516 529
2. C. Buecker, R. Srinivasan, Z. Wu, E. Calo, D. Acampora, T. Faial, A. Simeone, M. Tan, T. Swigut, and J. Wysocka Reorganization of enhancer patterns in transition from naive to primed pluripotency Cell Stem Cell 14 2014 838 853
3. E. Calo, and J. Wysocka Modification of enhancer chromatin: what, how, and why? Mol. Cell 49 2013 825 837
4. D.C. Factor, O. Corradin, G.E. Zentner, A. Saiakhova, L. Song, J.G. Chenoweth, R.D. McKay, G.E. Crawford, P.C. Scacheri, and P.J. Tesar Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency Cell Stem Cell 14 2014 854 863
5. M. Ginsburg, M.H. Snow, and A. McLaren Primordial germ cells in the mouse embryo during gastrulation Development 110 1990 521 528
6. L. Guelen, L. Pagie, E. Brasset, W. Meuleman, M.B. Faza, W. Talhout, B.H. Eussen, A. de Klein, L. Wessels, W. de Laat, and B. van Steensel Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions Nature 453 2008 948 951
7. J.B. Gurdon Adult frogs derived from the nuclei of single somatic cells Dev. Biol. 4 1962 256 273
8. J.A. Hackett, J.P. Reddington, C.E. Nestor, D.S. Dunican, M.R. Branco, J. Reichmann, W. Reik, M.A. Surani, I.R. Adams, and R.R. Meehan Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline Development 139 2012 3623 3632
9. K. Hayashi, H. Ohta, K. Kurimoto, S. Aramaki, and M. Saitou Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells Cell 146 2011 519 532
10. 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 2012 971 975
11. Y. Hayashi-Takanaka, K. Yamagata, T. Wakayama, T.J. Stasevich, T. Kainuma, T. Tsurimoto, M. Tachibana, Y. Shinkai, H. Kurumizaka, N. Nozaki, and H. Kimura Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling Nucleic Acids Res. 39 2011 6475 6488
12. T. Kafri, M. Ariel, M. Brandeis, R. Shemer, L. Urven, J. McCarrey, H. Cedar, and A. Razin Developmental pattern of gene-specific DNA methylation in the mouse embryo and germ line Genes Dev. 6 1992 705 714
13. S. Kagiwada, K. Kurimoto, T. Hirota, M. Yamaji, and M. Saitou Replication-coupled passive DNA demethylation for the erasure of genome imprints in mice EMBO J. 32 2013 340 353
14. K. Kurimoto, Y. Yabuta, Y. Ohinata, Y. Ono, K.D. Uno, R.G. Yamada, H.R. Ueda, and M. Saitou An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis Nucleic Acids Res. 34 2006 e42
15. K. Kurimoto, Y. Yabuta, Y. Ohinata, M. Shigeta, K. Yamanaka, and M. Saitou Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice Genes Dev. 22 2008 1617 1635
16. H.J. Lee, T.A. Hore, and W. Reik Reprogramming the methylome: erasing memory and creating diversity Cell Stem Cell 14 2014 710 719
17. R.X. Luo, A.A. Postigo, and D.C. Dean Rb interacts with histone deacetylase to repress transcription Cell 92 1998 463 473
18. D.M. Maatouk, L.D. Kellam, M.R. Mann, H. Lei, E. Li, M.S. Bartolomei, and J.L. Resnick DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages Development 133 2006 3411 3418
19. E. Magnúsdóttir, S. Dietmann, K. Murakami, U. Günesdogan, F. Tang, S. Bao, E. Diamanti, K. Lao, B. Gottgens, and M. Azim Surani A tripartite transcription factor network regulates primordial germ cell specification in mice Nat. Cell Biol. 15 2013 905 915
20. R. Margueron, and D. Reinberg The Polycomb complex PRC2 and its mark in life Nature 469 2011 343 349
21. M. Monk, M. Boubelik, and S. Lehnert Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development Development 99 1987 371 382
22. F. Nakaki, K. Hayashi, H. Ohta, K. Kurimoto, Y. Yabuta, and M. Saitou Induction of mouse germ-cell fate by transcription factors in vitro Nature 501 2013 222 226
23. Y. Ohinata, B. Payer, D. O'Carroll, K. Ancelin, Y. Ono, M. Sano, S.C. Barton, T. Obukhanych, M. Nussenzweig, and A. Tarakhovsky Blimp1 is a critical determinant of the germ cell lineage in mice Nature 436 2005 207 213
24. D. Peric-Hupkes, W. Meuleman, L. Pagie, S.W. Bruggeman, I. Solovei, W. Brugman, S. Gräf, P. Flicek, R.M. Kerkhoven, and M. van Lohuizen Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation Mol. Cell 38 2010 603 613
25. C. Runyan, K. Schaible, K. Molyneaux, Z. Wang, L. Levin, and C. Wylie Steel factor controls midline cell death of primordial germ cells and is essential for their normal proliferation and migration Development 133 2006 4861 4869
26. M. Sachs, C. Onodera, K. Blaschke, K.T. Ebata, J.S. Song, and M. Ramalho-Santos Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo Cell Rep. 3 2013 1777 1784
27. M. Saitou, S.C. Barton, and M.A. Surani A molecular programme for the specification of germ cell fate in mice Nature 418 2002 293 300
28. M. Saitou, S. Kagiwada, and K. Kurimoto Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells Development 139 2012 15 31
29. S. Seisenberger, S. Andrews, F. Krueger, J. Arand, J. Walter, F. Santos, C. Popp, B. Thienpont, W. Dean, and W. Reik The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells Mol. Cell 48 2012 849 862
30. 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 2005 440 458
31. Y. Seki, M. Yamaji, Y. Yabuta, M. Sano, M. Shigeta, Y. Matsui, Y. Saga, M. Tachibana, Y. Shinkai, and M. Saitou Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice Development 134 2007 2627 2638
32. M. Tachibana, Y. Matsumura, M. Fukuda, H. Kimura, and Y. Shinkai G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription EMBO J. 27 2008 2681 2690
33. K. Takahashi, and S. Yamanaka Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors Cell 126 2006 663 676
34. P. Voigt, W.W. Tee, and D. Reinberg A double take on bivalent promoters Genes Dev. 27 2013 1318 1338
35. M. Weber, I. Hellmann, M.B. Stadler, L. Ramos, S. Pääbo, M. Rebhan, and D. Schübeler Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome Nat. Genet. 39 2007 457 466
36. S. Yokobayashi, C.Y. Liang, H. Kohler, P. Nestorov, Z. Liu, M. Vidal, M. van Lohuizen, T.C. Roloff, and A.H. Peters PRC1 coordinates timing of sexual differentiation of female primordial germ cells Nature 495 2013 236 240