Human embryonic stem cells have a unique epigenetic signature

Marina Bibikova; Eugene Chudin; Bonnie Wu; Lixin Zhou; Eliza Wickham Garcia; Ying Liu; Soojung Shin; Todd W. Plaia; Jonathan M. Auerbach; Dan E. Arking; Rodolfo Gonzalez; Jeremy Crook; Bruce Davidson; Thomas C. Schulz; Allan Robins; Aparna Khanna; Peter Sartipy; Johan Hyllner; Padmavathy Vanguri; Smita Savant-Bhonsale; Alan K. Smith; Aravinda Chakravarti; Anirban Maitra; Mahendra Rao; David L. Barker; Jeanne F. Loring; Jian Bing Fan

doi:10.1101/gr.5319906

Human embryonic stem cells have a unique epigenetic signature

Marina Bibikova, Eugene Chudin, Bonnie Wu, Lixin Zhou, Eliza Wickham Garcia, Ying Liu, Soojung Shin, Todd W. Plaia, Jonathan M. Auerbach, Dan E. Arking, Rodolfo Gonzalez, Jeremy Crook, Bruce Davidson, Thomas C. Schulz, Allan Robins, Aparna Khanna, Peter Sartipy, Johan Hyllner, Padmavathy Vanguri, Smita Savant-BhonsaleAlan K. Smith, Aravinda Chakravarti, Anirban Maitra, Mahendra Rao, David L. Barker, Jeanne F. Loring, Jian Bing Fan

School of Medicine

Research output: Contribution to journal › Article › peer-review

224 Scopus citations

Abstract

Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We compared the DNA methylation status of 1536 CpG sites (from 371 genes) in 14 independently isolated hES cell lines with five other cell types: 24 cancer cell lines, four adult stem cell populations, four lymphoblastoid cell lines, five normal human tissues, and an embryonal carcinoma cell line. We found that the DNA methylation profile clearly distinguished the hES cells from all of the other cell types. A subset of 49 CpG sites from 40 genes contributed most to the differences among cell types. Another set of 25 sites from 23 genes distinguished hES cells from normal differentiated cells and can be used as biomarkers to monitor differentiation. Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential.

Original language	English (US)
Pages (from-to)	1075-1083
Number of pages	9
Journal	Genome research
Volume	16
Issue number	9
DOIs	https://doi.org/10.1101/gr.5319906
State	Published - 2006

ASJC Scopus subject areas

Genetics
Genetics(clinical)

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Bibikova, M., Chudin, E., Wu, B., Zhou, L., Garcia, E. W., Liu, Y., Shin, S., Plaia, T. W., Auerbach, J. M., Arking, D. E., Gonzalez, R., Crook, J., Davidson, B., Schulz, T. C., Robins, A., Khanna, A., Sartipy, P., Hyllner, J., Vanguri, P., ... Fan, J. B. (2006). Human embryonic stem cells have a unique epigenetic signature. Genome research, 16(9), 1075-1083. https://doi.org/10.1101/gr.5319906

Bibikova, M, Chudin, E, Wu, B, Zhou, L, Garcia, EW, Liu, Y, Shin, S, Plaia, TW, Auerbach, JM, Arking, DE, Gonzalez, R, Crook, J, Davidson, B, Schulz, TC, Robins, A, Khanna, A, Sartipy, P, Hyllner, J, Vanguri, P, Savant-Bhonsale, S, Smith, AK, Chakravarti, A, Maitra, A, Rao, M, Barker, DL, Loring, JF & Fan, JB 2006, 'Human embryonic stem cells have a unique epigenetic signature', Genome research, vol. 16, no. 9, pp. 1075-1083. https://doi.org/10.1101/gr.5319906

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title = "Human embryonic stem cells have a unique epigenetic signature",

abstract = "Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We compared the DNA methylation status of 1536 CpG sites (from 371 genes) in 14 independently isolated hES cell lines with five other cell types: 24 cancer cell lines, four adult stem cell populations, four lymphoblastoid cell lines, five normal human tissues, and an embryonal carcinoma cell line. We found that the DNA methylation profile clearly distinguished the hES cells from all of the other cell types. A subset of 49 CpG sites from 40 genes contributed most to the differences among cell types. Another set of 25 sites from 23 genes distinguished hES cells from normal differentiated cells and can be used as biomarkers to monitor differentiation. Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential.",

author = "Marina Bibikova and Eugene Chudin and Bonnie Wu and Lixin Zhou and Garcia, {Eliza Wickham} and Ying Liu and Soojung Shin and Plaia, {Todd W.} and Auerbach, {Jonathan M.} and Arking, {Dan E.} and Rodolfo Gonzalez and Jeremy Crook and Bruce Davidson and Schulz, {Thomas C.} and Allan Robins and Aparna Khanna and Peter Sartipy and Johan Hyllner and Padmavathy Vanguri and Smita Savant-Bhonsale and Smith, {Alan K.} and Aravinda Chakravarti and Anirban Maitra and Mahendra Rao and Barker, {David L.} and Loring, {Jeanne F.} and Fan, {Jian Bing}",

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AU - Bibikova, Marina

AU - Chudin, Eugene

AU - Wu, Bonnie

AU - Zhou, Lixin

AU - Garcia, Eliza Wickham

AU - Liu, Ying

AU - Shin, Soojung

AU - Plaia, Todd W.

AU - Auerbach, Jonathan M.

AU - Arking, Dan E.

AU - Gonzalez, Rodolfo

AU - Crook, Jeremy

AU - Davidson, Bruce

AU - Schulz, Thomas C.

AU - Robins, Allan

AU - Khanna, Aparna

AU - Sartipy, Peter

AU - Hyllner, Johan

AU - Vanguri, Padmavathy

AU - Savant-Bhonsale, Smita

AU - Smith, Alan K.

AU - Chakravarti, Aravinda

AU - Maitra, Anirban

AU - Rao, Mahendra

AU - Barker, David L.

AU - Loring, Jeanne F.

AU - Fan, Jian Bing

PY - 2006

Y1 - 2006

N2 - Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We compared the DNA methylation status of 1536 CpG sites (from 371 genes) in 14 independently isolated hES cell lines with five other cell types: 24 cancer cell lines, four adult stem cell populations, four lymphoblastoid cell lines, five normal human tissues, and an embryonal carcinoma cell line. We found that the DNA methylation profile clearly distinguished the hES cells from all of the other cell types. A subset of 49 CpG sites from 40 genes contributed most to the differences among cell types. Another set of 25 sites from 23 genes distinguished hES cells from normal differentiated cells and can be used as biomarkers to monitor differentiation. Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential.

AB - Human embryonic stem (hES) cells originate during an embryonic period of active epigenetic remodeling. DNA methylation patterns are likely to be critical for their self-renewal and pluripotence. We compared the DNA methylation status of 1536 CpG sites (from 371 genes) in 14 independently isolated hES cell lines with five other cell types: 24 cancer cell lines, four adult stem cell populations, four lymphoblastoid cell lines, five normal human tissues, and an embryonal carcinoma cell line. We found that the DNA methylation profile clearly distinguished the hES cells from all of the other cell types. A subset of 49 CpG sites from 40 genes contributed most to the differences among cell types. Another set of 25 sites from 23 genes distinguished hES cells from normal differentiated cells and can be used as biomarkers to monitor differentiation. Our results indicate that hES cells have a unique epigenetic signature that may contribute to their developmental potential.

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Human embryonic stem cells have a unique epigenetic signature

Abstract

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