Establishment of mouse expanded potential stem cells

Nature

Volumn 550, Issue 7676, 2017, Pages

  Yang, Jian ^a   Ryan, David J ^a   Wang, Wei ^a   Tsang, Jason Cheuk Ho ^a   Lan, Guocheng ^b   Masaki, Hideki ^c   Gao, Xuefei ^a   Antunes, Liliana ^a   Yu, Yong ^a   Zhu, Zhexin ^a   Wang, Juexuan ^a   Kolodziejczyk, Aleksandra A ^a,d   Campos, Lia S ^a   Wang, Cui ^a   Yang, Fengtang ^a   Zhong, Zhen ^e   Fu, Beiyuan ^a   Eckersley Maslin, Melanie A ^f   Woods, Michael ^a   Tanaka, Yosuke ^b,c,g   Chen, Xi ^a   Wilkinson, Adam C ^b,g   Bussell, James ^a   White, Jacqui ^a   Ramirez Solis, Ramiro ^a   Reik, Wolf ^a,f   Göttgens, Berthold ^b,g   Teichmann, Sarah A ^a,d   Tam, Patrick P L ^h,i   Nakauchi, Hiromitsu ^c,j   Zou, Xiangang ^b   Lu, Liming ^a,k   Liu, Pentao ^a   more..

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UNIVERSITY OF TOKYO   (Japan)

^d EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^e MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^f BABRAHAM INSTITUTE   (United Kingdom)

^g UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^h UNIVERSITY OF SYDNEY   (Australia)

ⁱ UNIVERSITY OF SYDNEY   (Australia)

^j STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^k SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

more..

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR CDX2; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; TRANSCRIPTOME;

BIOASSAY; CELLS AND CELL COMPONENTS; DNA; EMBRYO; MOLECULAR ANALYSIS; REINTRODUCTION;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BLASTOCYTE; CELL DIFFERENTIATION; CHIMERA; EMBRYO; GENE ACTIVATION; GENE EXPRESSION; IN VITRO STUDY; INDUCED PLURIPOTENT STEM CELL; JAK-STAT SIGNALING; MOUSE; MOUSE EMBRYONIC STEM CELL; NIDATION; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; TROPHOBLAST; ANIMAL; BLASTOCYST; BLASTOMA; CELL CULTURE; CELL LINEAGE; CYTOLOGY; ENDODERM; EPIGENETICS; FEMALE; GENETIC EPIGENESIS; MALE; MAMMALIAN EMBRYO; METABOLISM; PLACENTA; PLURIPOTENT STEM CELL; PREGNANCY; SINGLE CELL ANALYSIS;

MAMMALIA;

ANIMALS; BLASTOCYST; BLASTOMERES; CELL LINEAGE; CELLS, CULTURED; CHIMERA; EMBRYO, MAMMALIAN; ENDODERM; EPIGENESIS, GENETIC; EPIGENOMICS; FEMALE; MALE; MICE; MOUSE EMBRYONIC STEM CELLS; PLACENTA; PLURIPOTENT STEM CELLS; PREGNANCY; SINGLE-CELL ANALYSIS; TRANSCRIPTOME; TROPHOBLASTS;

EID: 85031943044     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature24052     Document Type: Article

References (54)

1. Evans, M. J. & Kaufman, M. H. Establishment in culture of pluripotential cells from mouse embryos. Nature 292, 154-156 (1981).
2. Tam, P. P. & Rossant, J. Mouse embryonic chimeras: tools for studying mammalian development. Development 130, 6155-6163 (2003).
3. Saba-El-Leil, M. K. et al. An essential function of the mitogen-activated protein kinase Erk2 in mouse trophoblast development. EMBO Rep. 4, 964-968 (2003).
4. Nishioka, N. et al. The Hippo signaling pathway components Lats and Yap pattern Tead4 activity to distinguish mouse trophectoderm from inner cell mass. Dev. Cell 16, 398-410 (2009).
5. Li, X. et al. Calcineurin-NFAT signaling critically regulates early lineage specification in mouse embryonic stem cells and embryos. Cell Stem Cell 8, 46-58 (2011).
6. Hemberger, M. et al. Parp1-deficiency induces differentiation of ES cells into trophoblast derivatives. Dev. Biol. 257, 371-381 (2003).
7. Koh, D. W. et al. Failure to degrade poly(ADP-ribose) causes increased sensitivity to cytotoxicity and early embryonic lethality. Proc. Natl Acad. Sci. USA 101, 17699-17704 (2004).
8. Loh, K. M., van Amerongen, R. & Nusse, R. Generating cellular diversity and spatial form: Wnt signaling and the evolution of multicellular animals. Dev. Cell 38, 643-655 (2016).
9. Kapoor, A. et al. Yap1 activation enables bypass of oncogenic Kras addiction in pancreatic cancer. Cell 158, 185-197 (2014).
10. Shao, D. D. et al. KRAS and YAP1 converge to regulate EMT and tumor survival. Cell 158, 171-184 (2014).
11. Azzolin, L. et al. YAP/TAZ incorporation in the β-catenin destruction complex orchestrates the Wnt response. Cell 158, 157-170 (2014).
12. Wilson, M. B., Schreiner, S. J., Choi, H. J., Kamens, J. & Smithgall, T. E. Selective pyrrolo-pyrimidine inhibitors reveal a necessary role for Src family kinases in Bcr-Abl signal transduction and oncogenesis. Oncogene 21, 8075-8088 (2002).
13. Huang, S. M. et al. Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling. Nature 461, 614-620 (2009).
14. Wang, W. et al. Tankyrase inhibitors target YAP by stabilizing angiomotin family proteins. Cell Reports 13, 524-532 (2015).
15. Martello, G. et al. Esrrb is a pivotal target of the Gsk3/Tcf3 axis regulating embryonic stem cell self-renewal. Cell Stem Cell 11, 491-504 (2012).
16. Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519-523 (2008).
17. Kim, H. et al. Modulation of β-catenin function maintains mouse epiblast stem cell and human embryonic stem cell self-renewal. Nat. Commun. 4, 2403 (2013).
18. Zimmerlin, L. et al. Tankyrase inhibition promotes a stable human naïve pluripotent state with improved functionality. Development 143, 4368-4380 (2016).
19. Morgani, S. M. et al. Totipotent embryonic stem cells arise in ground-state culture conditions. Cell Reports 3, 1945-1957 (2013).
20. Latos, P. A. & Hemberger, M. From the stem of the placental tree: trophoblast stem cells and their progeny. Development 143, 3650-3660 (2016).
21. Kolodziejczyk, A. A. et al. Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 17, 471-485 (2015).
22. Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590-604 (2012).
23. Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193-196 (2014).
24. Wu, J. et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature 534, 652-657 (2016).
25. Macfarlan, T. S. et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57-63 (2012).
26. Abad, M. et al. Reprogramming in vivo produces teratomas and iPS cells with totipotency features. Nature 502, 340-345 (2013).
27. Leitch, H. G. et al. Naive pluripotency is associated with global DNA hypomethylation. Nat. Struct. Mol. Biol. 20, 311-316 (2013).
28. Dahl, J. A. et al. Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature 537, 548-552 (2016).
29. Kubaczka, C. et al. Derivation and maintenance of murine trophoblast stem cells under defined conditions. Stem Cell Reports 2, 232-242 (2014).
30. Niakan, K. K., Schrode, N., Cho, L. T. & Hadjantonakis, A. K. Derivation of extraembryonic endoderm stem (XEN) cells from mouse embryos and embryonic stem cells. Nat. Protoc. 8, 1028-1041 (2013).
31. Ryan, D. J., Yang, J., Lan, G. & Liu, P. Derivation and maintenance of mouse expanded potential stem cells. Protoc. Exch. http://doi.org/10.1038// protex.2017.102 (2017).
32. Nichols, J., Silva, J., Roode, M. & Smith, A. Suppression of Erk signalling promotes ground state pluripotency in the mouse embryo. Development 136, 3215-3222 (2009).
33. Yang, J. et al. Quenching autofluorescence in tissue immunofluorescence. Wellcome Open Res. 2, 79 (2017).
34. Tanaka, S., Kunath, T., Hadjantonakis, A. K., Nagy, A. & Rossant, J. Promotion of trophoblast stem cell proliferation by FGF4. Science 282, 2072-2075 (1998).
35. Schröter, C., Rué, P., Mackenzie, J. P. & Martinez Arias, A. FGF/MAPK signaling sets the switching threshold of a bistable circuit controlling cell fate decisions in embryonic stem cells. Development 142, 4205-4216 (2015).
36. Freyer, L. et al. A loss-of-function and H2B-Venus transcriptional reporter allele for Gata6 in mice. BMC Dev. Biol. 15, 38 (2015).
37. Ng, R. K. et al. Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5. Nat. Cell Biol. 10, 1280-1290 (2008).
38. Wang, L., Jin, Q., Lee, J. E., Su, I. H. & Ge, K. Histone H3K27 methyltransferase Ezh2 represses Wnt genes to facilitate adipogenesis. Proc. Natl Acad. Sci. USA 107, 7317-7322 (2010).
39. Brennecke, P. et al. Accounting for technical noise in single-cell RNA-seq experiments. Nat. Methods 10, 1093-1095 (2013).
40. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
41. Anders, S., Pyl, P. T. & Huber, W. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
42. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
43. Huang, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
44. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
45. Lee, T. I., Johnstone, S. E. & Young, R. A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 1, 729-748 (2006).
46. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
47. Buecker, C. et al. Reorganization of enhancer patterns in transition from naive to primed pluripotency. Cell Stem Cell 14, 838-853 (2014).
48. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
49. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
50. Liu, X. et al. Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 537, 558-562 (2016).
51. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
52. Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014).
53. Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
54. Ficz, G. et al. FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell 13, 351-359 (2013).