An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

被引：280

作者：

Rakyan, Vardhman K. ^{[1
]}

Down, Thomas A. ^{[2
]}

Thorne, Natalie P. ^{[3
]}

Flicek, Paul ^{[4
]}

Kulesha, Eugene ^{[4
]}

Graf, Stefan ^{[4
]}

Tomazou, Eleni M. ^{[5
]}

Backdahl, Liselotte ^{[6
]}

Johnson, Nathan ^{[4
]}

Herberth, Marlis ^{[7
]}

Howe, Kevin L. ^{[3
]}

Jackson, David K. ^{[5
]}

Miretti, Marcos M. ^{[5
]}

Fiegler, Heike ^{[5
]}

Marioni, John C. ^{[3
]}

Birney, Ewan ^{[4
]}

Hubbard, Tim J. P. ^{[5
]}

Carter, Nigel P. ^{[5
]}

Tavare, Simon ^{[3
]}

Beck, Stephan ^{[6
]}

机构：

[1] Inst Cell & Mol Sci, London E1 2AT, England

[2] Univ Cambridge, Wellcome Trust Canc Res UK Gurdon Inst, Cambridge CB2 1QR, England

[3] Univ Cambridge, Canc Res UK Cambridge Res Inst, Dept Oncol, Cambridge CB2 0RE, England

[4] EMBL EBI, Hinxton CB10 1SA, Cambs, England

[5] Wellcome Trust Sanger Inst, Hinxton CB10 1SA, Cambs, England

[6] UCL, Inst Canc, London WC1E 6DD, England

[7] Univ Cambridge, Inst Biotechnol, Cambridge CB2 1QT, England

来源：

GENOME RESEARCH | 2008年 / 18卷 / 09期

基金：

英国惠康基金; 英国医学研究理事会;

关键词：

D O I：

10.1101/gr.077479.108

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：

We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists of three fully integrated parts, genome-wide DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, a visualization tool that has been integrated with the Ensembl genome browser and a new algorithm for the analysis of immunoprecipitation-based DNA methylation profiles. We demonstrate the utility of our resource by identifying the first comprehensive genome-wide set of tissue-specific differentially methylated regions (tDMRs) that may play a role in cellular identity and the regulation of tissue-specific genome function. We also discuss the implications of our findings with respect to the regulatory potential of regions with varied CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications.

引用

页码：1518 / 1529

页数：12

共 41 条

[1] High-resolution profiling of histone methylations in the human genome [J].

Barski, Artern ;

Cuddapah, Suresh ;

Cui, Kairong ;

Roh, Tae-Young ;

Schones, Dustin E. ;

Wang, Zhibin ;

Wei, Gang ;

Chepelev, Iouri ;

Zhao, Keji .

CELL, 2007, 129 (04) :823-837

[2] DNA methylation patterns and epigenetic memory [J].

Bird, A .

GENES & DEVELOPMENT, 2002, 16 (01) :6-21

[3]

BIRD A, 1985, CELL, V40, P91, DOI 10.1016/0092-8674(85)90312-5

[4] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[5] A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis [J].

Down, Thomas A. ;

Rakyan, Vardhman K. ;

Turner, Daniel J. ;

Flicek, Paul ;

Li, Heng ;

Kulesha, Eugene ;

Graf, Stefan ;

Johnson, Nathan ;

Herrero, Javier ;

Tomazou, Eleni M. ;

Thorne, Natalie P. ;

Backdahl, Liselotte ;

Herberth, Marlis ;

Howe, Kevin L. ;

Jackson, David K. ;

Miretti, Marcos M. ;

Marioni, John C. ;

Birney, Ewan ;

Hubbard, Tim J. P. ;

Durbin, Richard ;

Tavare, Simon ;

Beck, Stephan .

NATURE BIOTECHNOLOGY, 2008, 26 (07) :779-785

[6] 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

[7] High-throughput methylation profiling by MCA coupled to CpG island microarray [J].

Estecio, Marcos R. H. ;

Yan, Pearlly S. ;

Ibrahim, Ashraf E. K. ;

Tellez, Carmen S. ;

Shen, Lanlan ;

Huang, Tim H-M ;

Issa, Jean-Pierre J. .

GENOME RESEARCH, 2007, 17 (10) :1529-1536

[8] Ensembl 2008 [J].

Flicek, P. ;

Aken, B. L. ;

Beal, K. ;

Ballester, B. ;

Caccamo, M. ;

Chen, Y. ;

Clarke, L. ;

Coates, G. ;

Cunningham, F. ;

Cutts, T. ;

Down, T. ;

Dyer, S. C. ;

Eyre, T. ;

Fitzgerald, S. ;

Fernandez-Banet, J. ;

Graf, S. ;

Haider, S. ;

Hammond, M. ;

Holland, R. ;

Howe, K. L. ;

Howe, K. ;

Johnson, N. ;

Jenkinson, A. ;

Kahari, A. ;

Keefe, D. ;

Kokocinski, F. ;

Kulesha, E. ;

Lawson, D. ;

Longden, I. ;

Megy, K. ;

Meidl, P. ;

Overduin, B. ;

Parker, A. ;

Pritchard, B. ;

Prlic, A. ;

Rice, S. ;

Rios, D. ;

Schuster, M. ;

Sealy, I. ;

Slater, G. ;

Smedley, D. ;

Spudich, G. ;

Trevanion, S. ;

Vilella, A. J. ;

Vogel, J. ;

White, S. ;

Wood, M. ;

Birney, E. ;

Cox, T. ;

Curwen, V. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D707-D714

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

GARDINERGARDEN, M ;

FROMMER, M .

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

[10] CG dinucleotide clustering is a species-specific property of the genome [J].

Glass, Jacob L. ;

Thompson, Reid F. ;

Khulan, Batbayar ;

Figueroa, Maria E. ;

Olivier, Emmanuel N. ;

Oakley, Erin J. ;

Van Zant, Gary ;

Bouhassira, Eric E. ;

Melnick, Ari ;

Golden, Aaron ;

Fazzari, Melissa J. ;

Greally, John M. .

NUCLEIC ACIDS RESEARCH, 2007, 35 (20) :6798-6807

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