EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq

De Los Angeles, A. et al. Hallmarks of pluripotency. Nature 525, 469–478 (2015).

Article  Google Scholar 

Shahbazi, M. N., Siggia, E. D. & Zernicka-Goetz, M. Self-organization of stem cells into embryos: a window on early mammalian development. Science 364, 948–951 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Avior, Y., Sagi, I. & Benvenisty, N. Pluripotent stem cells in disease modelling and drug discovery. Nat. Rev. Mol. Cell Biol. 17, 170–182 (2016).

Article  CAS  PubMed  Google Scholar 

Trounson, A. & DeWitt, N. D. Pluripotent stem cells progressing to the clinic. Nat. Rev. Mol. Cell Biol. 17, 194–200 (2016).

Article  CAS  PubMed  Google Scholar 

Halliwell, J., Barbaric, I. & Andrews, P. W. Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat. Rev. Mol. Cell Biol. 21, 715–728 (2020).

Article  CAS  PubMed  Google Scholar 

Avior, Y., Lezmi, E., Eggan, K. & Benvenisty, N. Cancer-related mutations identified in primed human pluripotent stem cells. Cell Stem Cell 28, 10–11 (2021).

Article  CAS  PubMed  Google Scholar 

Lezmi, E. & Benvenisty, N. Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis. Nat. Protoc. 16, 4522–4537 (2021).

Article  CAS  PubMed  Google Scholar 

Ben-David, U., Mayshar, Y. & Benvenisty, N. Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles. Nat. Protoc. 8, 989–997 (2013).

Article  PubMed  Google Scholar 

Bar, S. & Benvenisty, N. Epigenetic aberrations in human pluripotent stem cells. EMBO J. 38, e101033 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Weinberger, L., Ayyash, M., Novershtern, N. & Hanna, J. H. Dynamic stem cell states: naive to primed pluripotency in rodents and humans. Nat. Rev. Mol. Cell Biol. 17, 155–169 (2016).

Article  CAS  PubMed  Google Scholar 

Yilmaz, A. & Benvenisty, N. Defining human pluripotency. Cell Stem Cell 25, 9–22 (2019).

Article  CAS  PubMed  Google Scholar 

Reik, W. & Walter, J. Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2, 21–32 (2001).

Article  CAS  PubMed  Google Scholar 

Tucci, V. et al. Genomic imprinting and physiological processes in mammals. Cell 176, 952–965 (2019).

Article  CAS  PubMed  Google Scholar 

Bar, S., Schachter, M., Eldar-Geva, T. & Benvenisty, N. Large-scale analysis of loss of imprinting in human pluripotent stem cells. Cell Rep. 19, 957–968 (2017).

Article  CAS  PubMed  Google Scholar 

Keshet, G. & Benvenisty, N. Large-scale analysis of imprinting in naive human pluripotent stem cells reveals recurrent aberrations and a potential link to FGF signaling. Stem Cell Rep. 16, 2520–2533 (2021).

Article  CAS  Google Scholar 

Nora, E. P. & Heard, E. X chromosome inactivation: when dosage counts. Cell 139, 865–867 (2009).

Article  CAS  PubMed  Google Scholar 

Brown, C. J. et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71, 527–542 (1992).

Article  CAS  PubMed  Google Scholar 

Heard, E. & Disteche, C. M. Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev. 20, 1848–1867 (2006).

Article  CAS  PubMed  Google Scholar 

Shen, Y. et al. X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations. Proc. Natl Acad. Sci. USA 105, 4709–4714 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bruck, T. & Benvenisty, N. Meta-analysis of the heterogeneity of X chromosome inactivation in human pluripotent stem cells. Stem Cell Res. 6, 187–193 (2011).

Article  CAS  PubMed  Google Scholar 

Patel, S. et al. Human embryonic stem cells do not change their X inactivation status during differentiation. Cell Rep. 18, 54–67 (2017).

Article  CAS  PubMed  Google Scholar 

Yokobayashi, S. et al. Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells. Cell Rep. 37, 109909 (2021).

Article  CAS  PubMed  Google Scholar 

Bar, S., Seaton, L. R., Weissbein, U., Eldar-Geva, T. & Benvenisty, N. Global characterization of X chromosome inactivation in human pluripotent stem cells. Cell Rep. 27, e3 (2019).

Article  Google Scholar 

Werner, J. M., Ballouz, S., Hover, J. & Gillis, J. Variability of cross-tissue X-chromosome inactivation characterizes timing of human embryonic lineage specification events. Dev. Cell 57, 1995–2008.e5 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Theunissen, T. W. et al. Molecular criteria for defining the naive human pluripotent state. Cell Stem Cell 19, 502–515 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sagi, I. & Benvenisty, N. Aspiring to naivety. Nature 540, 211–212 (2016).

Article  CAS  PubMed  Google Scholar 

Sarel-Gallily, R. & Benvenisty, N. Large-scale analysis of X inactivation variations between primed and naïve human embryonic stem cells. Cells 11, 1729 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Morison, I. M., Ramsay, J. P. & Spencer, H. G. A census of mammalian imprinting. Trends Genet. 21, 457–465 (2005).

Article  CAS  PubMed  Google Scholar 

Carrel, L. & Willard, H. F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400–404 (2005).

Article  CAS  PubMed  Google Scholar 

Tukiainen, T. et al. Landscape of X chromosome inactivation across human tissues. Nature 550, 244–248 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Surani, M. A. H., Barton, S. C. & Norris, M. L. Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308, 548–550 (1984).

Article  CAS  PubMed  Google Scholar 

McGrath, J. & Solter, D. Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 37, 179–183 (1984).

Article  CAS  PubMed  Google Scholar 

Sagi, I. et al. Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells. Cell Stem Cell 25, 419–432.e9 (2019).

Article  CAS  PubMed  Google Scholar 

Cassidy, S. B., Schwartz, S., Miller, J. L. & Driscoll, D. J. Prader–Willi syndrome. Genet. Med. 14, 10–26 (2012).

Article  CAS  PubMed  Google Scholar 

Margolis, S. S., Sell, G. L., Zbinden, M. A. & Bird, L. M. Angelman syndrome. Neurotherapeutics 12, 641–650 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Weksberg, R., Shuman, C. & Beckwith, J. B. Beckwith–Wiedemann syndrome. Eur. J. Hum. Genet. 18, 8–14 (2010).

Article  PubMed  Google Scholar 

Ishida, M. New developments in Silver–Russell syndrome and implications for clinical practice. Epigenomics 8, 563–580 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Foong, Y. H., Thorvaldsen, J. L. & Bartolomei, M. S. Two sides of the Dlk1-Dio3

Comments (0)

No login
gif