The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives
Open accessAbstract
SUMMARY Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting, and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.
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Cites
GREAT improves functional interpretation of cis-regulatory regions
McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502
Somatic coding mutations in human induced pluripotent stem cells
Gore, A., Li, Z., Fung, H.-L., Young, J. E., Agarwal, S., Antosiewicz-Bourget, J., Canto, I., Giorgetti, A., Israel, M. A., Kiskinis, E., et al. (2011) · Nature · doi:10.1038/nature09805 · Cited by 1,273
The bHLH Transcription Factors OLIG2 and OLIG1 Couple Neuronal and Glial Subtype Specification
Zhou, Q., & Anderson, D. J. (2002) · Cell · doi:10.1016/s0092-8674(02)00677-3 · Cited by 1,059 · cited 2×
“…of several genes known to regulate oligodendrocyte differentiation including SKI, QKI, and OLIG2 (Aberg et al., 2006; Atanasoski et al., 2004; Zhou and Anderson, 2002) and the myelin proteins PLP1 and PMP22 (Figure 3D) was observed and reflected in the GREAT enrichments for myelination and…”
Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome
Sandoval, J., Heyn, H., Moran, S., Serra-Musach, J., Pujana, M. A., Bibikova, M., & Esteller, M. (2011) · Epigenetics · doi:10.4161/epi.6.6.16196 · Cited by 990 · cited 2×
“…DNA methylation at 27,578 CpG sites associated with 14,500 well-annotated genes (27K DNA Methylation array), >450,000 CpG sites associated with both coding and noncoding genes (450K DNA Methylation array) (Sandoval et al., 2011), and the expression of more than 30,000 mRNA transcripts (HT12v3).”
Laurent, L. C., Ulitsky, I., Slavin, I., Tran, H., Schork, A., Morey, R., Lynch, C., Harness, J. V., Lee, S., Barrero, M. J., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2010.12.003 · Cited by 890
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Cited by
DNA methylation age of human tissues and cell types
Horvath, S. (2013) · Genome Biology · doi:10.1186/gb-2013-14-10-r115 · Cited by 7,075
Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
Malta, T. M., Sokolov, A., Gentles, A. J., Burzykowski, T., Poisson, L., Weinstein, J. N., Kamińska, B., Huelsken, J., Omberg, L., Gevaert, O., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.034 · Cited by 2,180
Self-citationCharting a dynamic DNA methylation landscape of the human genome
Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T.-Y., Kohlbacher, O., De Jager, P. L., Rosen, E. D., Bennett, D. A., Bernstein, B. E., et al. (2013) · Nature · doi:10.1038/nature12433 · Cited by 1,357
Self-citationCommon genetic variation drives molecular heterogeneity in human iPSCs
Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., et al. (2017) · Nature · doi:10.1038/nature22403 · Cited by 586
Teschendorff, A. E., Breeze, C. E., Zheng, S. C., & Beck, S. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1511-5 · Cited by 544
Metadata
- Authors
- Nazor, K. L., Altun, G., Lynch, C., Tran, H., Harness, J. V., Slavin, I., Garitaonandia, I., Müller, F.-J., Wang, Y.-C., Boscolo, F. S., Fakunle, E., Dumevska, B., Lee, S., Park, H. S., Olee, T., D'Lima, D. D., Semechkin, R., Parast, M. M., Galat, V., Laslett, A. L., Schmidt, U., Keirstead, H. S., Loring, J. F., & Laurent, L. C.
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2012-05
- Volume
- 10
- Issue
- 5
- Pages
- 620-634
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- OpenAlex
- W2152627215
- Cited by
- 407
- References
- 5
- FWCI
- 16.15
- Type
- journal article
- Language
- en
- Open access
- bronze
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- The paper
- Nazor, K. L., Altun, G., Lynch, C., Tran, H., Harness, J. V., Slavin, I., Garitaonandia, I., Müller, F.-J., Wang, Y.-C., Boscolo, F. S., Fakunle, E., Dumevska, B., Lee, S., Park, H. S., Olee, T., D'Lima, D. D., Semechkin, R., Parast, M. M., Galat, V., . . . Laurent, L. C. (2012). Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives. Cell Stem Cell. https://doi.org/10.1016/j.stem.2012.02.013
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