Epigenetic modification of retinoic acid-treated human embryonic stem cells

被引：24

作者：

Cheong, Hyun Sub ^{[2
]}

Lee, Han Chul ^{[1
]}

Park, Byung Lae ^{[2
]}

Kim, Hyemin ^{[3
,4
]}

Jang, Min Jin ^{[3
,4
]}

Han, Yong Mahn ^{[3
,4
]}

Kim, Seun-Young ^{[1
]}

Kim, Yong Sung ^{[1
]}

Shin, Hyoung Doo ^{[2
,5
]}

机构：

[1] Korea Res Inst Biosci & Biotechnol, Med Genom Res Ctr, Taejon 305806, South Korea

[2] SNP Genet Inc, Dept Genet Epidemiol, Seoul 153803, South Korea

[3] Korea Adv Inst Sci & Technol, Ctr Stem Cell Differentiat, Taejon 305701, South Korea

[4] Korea Adv Inst Sci & Technol, Dept Biol Sci, Taejon 305701, South Korea

[5] Sogang Univ, Dept Life Sci, Seoul 121742, South Korea

来源：

BMB REPORTS | 2010年 / 43卷 / 12期

关键词：

DNA methylation; Epigenetic modification; Gene expression; Human embryonic stem cell; Retinoic acid; DNA METHYLATION; GENE-EXPRESSION; PROMOTER HYPERMETHYLATION; PROSTATE-CANCER; CARCINOMA-CELLS; MARKER GENES; DIFFERENTIATION; PROTEIN; LINES; GENOME;

D O I：

10.5483/BMBRep.2010.43.12.830

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Epigenetic modification of the genome through DNA methylation is the key to maintaining the differentiated state of human embryonic stem cells (hESCs), and it must be reset during differentiation by retinoic acid (RA) treatment. A genome-wide methylation/gene expression assay was performed in order to identify epigenetic modifications of RA-treated hESCs. Between undifferentiated and RA-treated hESCs, 166 differentially methylated CpG sites and 2,013 differentially expressed genes were discovered. Combined analysis of methylation and expression data revealed that 19 genes (STAP2, VAMP8, C10orf26, WFIKKN1, ELF3, C1QTNF6, C10orf10, MRGPRF, ARSE, LSAMP, CENTD3, LDB2, POU5F1, GSPT2, THY1, ZNF574, MSX1, SCMH1, and RARB) were highly correlated with each other. The results provided in this study will facilitate future investigations into the interplay between DNA methylation and gene expression through further functional and biological studies. [BMB reports 2010; 43(12): 830-835]

引用

页码：830 / 835

页数：6

共 45 条

[1] Unique gene expression signatures of independently-derived human embryonic stem cell lines [J].

Abeyta, MJ ;

Clark, AT ;

Rodriguez, RT ;

Bodnar, MS ;

Pera, RAR ;

Firpo, MT .

HUMAN MOLECULAR GENETICS, 2004, 13 (06) :601-608

[2] Characterization of human embryonic stem cell lines by the International Stem Cell Initiative [J].

Adewumi, Oluseun ;

Aflatoonian, Behrouz ;

Ahrlund-Richter, Lars ;

Amit, Michal ;

Andrews, Peter W. ;

Beighton, Gemma ;

Bello, Paul A. ;

Benvenisty, Nissim ;

Berry, Lorraine S. ;

Bevan, Simon ;

Blum, Barak ;

Brooking, Justin ;

Chen, Kevin G. ;

Choo, Andre B. H. ;

Churchill, Gary A. ;

Corbel, Marie ;

Damjanov, Ivan ;

Draper, Jon S. ;

Dvorak, Petr ;

Emanuelsson, Katarina ;

Fleck, Roland A. ;

Ford, Angela ;

Gertow, Karin ;

Gertsenstein, Marina ;

Gokhale, Paul J. ;

Hamilton, Rebecca S. ;

Hampl, Ales ;

Healy, Lyn E. ;

Hovatta, Outi ;

Hyllner, Johan ;

Imreh, Marta P. ;

Itskovitz-Eldor, Joseph ;

Jackson, Jamie ;

Johnson, Jacqueline L. ;

Jones, Mark ;

Kee, Kehkooi ;

King, Benjamin L. ;

Knowles, Barbara B. ;

Lako, Majlinda ;

Lebrin, Franck ;

Mallon, Barbara S. ;

Manning, Daisy ;

Mayshar, Yoav ;

Mckay, Ronald D. G. ;

Michalska, Anna E. ;

Mikkola, Milla ;

Mileikovsky, Masha ;

Minger, Stephen L. ;

Moore, Harry D. ;

Mummery, Christine L. .

NATURE BIOTECHNOLOGY, 2007, 25 (07) :803-816

[3]

Andrews PW, 2005, NAT BIOTECHNOL, V23, P795, DOI 10.1038/nbt0705-798

[4] Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells [J].

Ball, Madeleine P. ;

Li, Jin Billy ;

Gao, Yuan ;

Lee, Je-Hyuk ;

LeProust, Emily M. ;

Park, In-Hyun ;

Xie, Bin ;

Daley, George Q. ;

Church, George M. .

NATURE BIOTECHNOLOGY, 2009, 27 (04) :361-368

[5] High-throughput DNA methylation profiling using universal bead arrays [J].

Bibikova, M ;

Lin, ZW ;

Zhou, LX ;

Chudin, E ;

Garcia, EW ;

Wu, B ;

Doucet, D ;

Thomas, NJ ;

Wang, YH ;

Vollmer, E ;

Goldmann, T ;

Seifart, C ;

Jiang, W ;

Barker, DL ;

Chee, MS ;

Floros, J ;

Fan, JB .

GENOME RESEARCH, 2006, 16 (03) :383-393

[6] Human embryonic stem cells have a unique epigenetic signature [J].

Bibikova, Marina ;

Chudin, Eugene ;

Wu, Bonnie ;

Zhou, Lixin ;

Garcia, Eliza Wickham ;

Liu, Ying ;

Shin, Soojung ;

Plaia, Todd W. ;

Auerbach, Jonathan M. ;

Arking, Dan E. ;

Gonzalez, Rodolfo ;

Crook, Jeremy ;

Davidson, Bruce ;

Schulz, Thomas C. ;

Robins, Allan ;

Khanna, Aparna ;

Sartipy, Peter ;

Hyllner, Johan ;

Vanguri, Padmavathy ;

Savant-Bhonsale, Smita ;

Smith, Alan K. ;

Chakravarti, Aravinda ;

Maitra, Anirban ;

Rao, Mahendra ;

Barker, David L. ;

Loring, Jeanne F. ;

Fan, Jian-Bing .

GENOME RESEARCH, 2006, 16 (09) :1075-1083

[7] Core transcriptional regulatory circuitry in human embryonic stem cells [J].

Boyer, LA ;

Lee, TI ;

Cole, MF ;

Johnstone, SE ;

Levine, SS ;

Zucker, JR ;

Guenther, MG ;

Kumar, RM ;

Murray, HL ;

Jenner, RG ;

Gifford, DK ;

Melton, DA ;

Jaenisch, R ;

Young, RA .

CELL, 2005, 122 (06) :947-956

[8] Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver [J].

Brunner, Alayne L. ;

Johnson, David S. ;

Kim, Si Wan ;

Valouev, Anton ;

Reddy, Timothy E. ;

Neff, Norma F. ;

Anton, Elizabeth ;

Medina, Catherine ;

Nguyen, Loan ;

Chiao, Eric ;

Oyolu, Chuba B. ;

Schroth, Gary P. ;

Absher, Devin M. ;

Baker, Julie C. ;

Myers, Richard M. .

GENOME RESEARCH, 2009, 19 (06) :1044-1056

[9] A decade of molecular biology of retinoic acid receptors [J].

Chambon, P .

FASEB JOURNAL, 1996, 10 (09) :940-954

[10] A model of technical variation of microarray signals [J].

Chudin, E. ;

Kruglyak, S. ;

Baker, S. C. ;

Oeser, S. ;

Barker, D. ;

McDaniel, T. K. .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2006, 13 (04) :996-1003

← 1 2 3 4 5 →