Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

被引：349

作者：

Deng, Jie ^{[1
]}

Shoemaker, Robert ^{[2
]}

Xie, Bin ^{[3
]}

Gore, Athurva ^{[1
]}

LeProust, Emily M. ^{[5
]}

Antosiewicz-Bourget, Jessica ^{[6
]}

Egli, Dieter ^{[7
,8
]}

Maherali, Nimet ^{[9
,10
]}

Park, In-Hyun ^{[11
,12
]}

Yu, Junying ^{[6
]}

Daley, George Q. ^{[11
,12
]}

Eggan, Kevin ^{[7
,8
]}

Hochedlinger, Konrad ^{[9
,10
]}

Thomson, James ^{[6
]}

Wang, Wei ^{[2
]}

Gao, Yuan ^{[3
,4
]}

Zhang, Kun ^{[1
]}

机构：

[1] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA

[3] Virginia Commonwealth Univ, Ctr Study Biol Complex, Richmond, VA USA

[4] Virginia Commonwealth Univ, Dept Comp Sci, Richmond, VA USA

[5] Agilent Technol, Genom Solut Unit, Santa Clara, CA USA

[6] Univ Wisconsin, Dept Anat, Madison, WI 53706 USA

[7] Harvard Univ, Stowers Med Inst, Harvard Stem Cell Inst, Cambridge, MA 02138 USA

[8] Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA

[9] Massachusetts Gen Hosp, Ctr Canc, Boston, MA USA

[10] Ctr Regenerat Med, Harvard Stem Cell Inst, Boston, MA USA

[11] Childrens Hosp, Div Pediat Hematol Oncol, Boston, MA 02115 USA

[12] Dana Farber Canc Inst, Boston, MA 02115 USA

来源：

NATURE BIOTECHNOLOGY | 2009年 / 27卷 / 04期

关键词：

SOMATIC-CELLS; PLURIPOTENT; EPIGENOME; MAPS;

D O I：

10.1038/nbt.1530

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets. We report a method to specifically capture an arbitrary subset of genomic targets for single-molecule bisulfite sequencing for digital quantification of DNA methylation at single-nucleotide resolution. A set of similar to 30,000 padlock probes was designed to assess methylation of similar to 66,000 CpG sites within 2,020 CpG islands on human chromosome 12, chromosome 20, and 34 selected regions. To investigate epigenetic differences associated with dedifferentiation, we compared methylation in three human fibroblast lines and eight human pluripotent stem cell lines. Chromosome-wide methylation patterns were similar among all lines studied, but cytosine methylation was slightly more prevalent in the pluripotent cells than in the fibroblasts. Induced pluripotent stem (iPS) cells appeared to display more methylation than embryonic stem cells. We found 288 regions methylated differently in fibroblasts and pluripotent cells. This targeted approach should be particularly useful for analyzing DNA methylation in large genomes.

引用

页码：353 / 360

页数：8

共 31 条

[1] 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

[2] 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

[3] 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

[4] Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning [J].

Cokus, Shawn J. ;

Feng, Suhua ;

Zhang, Xiaoyu ;

Chen, Zugen ;

Merriman, Barry ;

Haudenschild, Christian D. ;

Pradhan, Sriharsa ;

Nelson, Stanley F. ;

Pellegrini, Matteo ;

Jacobsen, Steven E. .

NATURE, 2008, 452 (7184) :215-219

[5] Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells [J].

Cowan, CA ;

Atienza, J ;

Melton, DA ;

Eggan, K .

SCIENCE, 2005, 309 (5739) :1369-1373

[6] DAVID: Database for annotation, visualization, and integrated discovery [J].

Dennis, G ;

Sherman, BT ;

Hosack, DA ;

Yang, J ;

Gao, W ;

Lane, HC ;

Lempicki, RA .

GENOME BIOLOGY, 2003, 4 (09)

[7] DNA methylation profiling of human chromosomes 6, 20 and 22 [J].

Eckhardt, Florian ;

Lewin, Joern ;

Cortese, Rene ;

Rakyan, Vardhman K. ;

Attwood, John ;

Burger, Matthias ;

Burton, John ;

Cox, Tony V. ;

Davies, Rob ;

Down, Thomas A. ;

Haefliger, Carolina ;

Horton, Roger ;

Howe, Kevin ;

Jackson, David K. ;

Kunde, Jan ;

Koenig, Christoph ;

Liddle, Jennifer ;

Niblett, David ;

Otto, Thomas ;

Pettett, Roger ;

Seemann, Stefanie ;

Thompson, Christian ;

West, Tony ;

Rogers, Jane ;

Olek, Alex ;

Berlin, Kurt ;

Beck, Stephan .

NATURE GENETICS, 2006, 38 (12) :1378-1385

[8] CPG ISLANDS IN VERTEBRATE GENOMES [J].

GARDINERGARDEN, M ;

FROMMER, M .

JOURNAL OF MOLECULAR BIOLOGY, 1987, 196 (02) :261-282

[9] Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing [J].

Gnirke, Andreas ;

Melnikov, Alexandre ;

Maguire, Jared ;

Rogov, Peter ;

LeProust, Emily M. ;

Brockman, William ;

Fennell, Timothy ;

Giannoukos, Georgia ;

Fisher, Sheila ;

Russ, Carsten ;

Gabriel, Stacey ;

Jaffe, David B. ;

Lander, Eric S. ;

Nusbaum, Chad .

NATURE BIOTECHNOLOGY, 2009, 27 (02) :182-189

[10] Multiplexed genotyping with sequence-tagged molecular inversion probes [J].

Hardenbol, P ;

Banér, J ;

Jain, M ;

Nilsson, M ;

Namsaraev, EA ;

Karlin-Neumann, GA ;

Fakhrai-Rad, H ;

Ronaghi, M ;

Willis, TD ;

Landegren, U ;

Davis, RW .

NATURE BIOTECHNOLOGY, 2003, 21 (06) :673-678

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