Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

Nature Biotechnology

Volumn 27, Issue 4, 2009, Pages 361-368

  Ball, Madeleine P ^a,b   Li, Jin Billy ^a,b   Gao, Yuan ^c   Lee, Je Hyuk ^a,b   Leproust, Emily M ^d   Park, In Hyun ^a,e   Xie, Bin ^c   Daley, George Q ^a,e   Church, George M ^a,b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^d AGILENT TECHNOLOGIES   (United States)

^e BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B-LYMPHOCYTES; CHROMATIN IMMUNOPRECIPITATION; CPG ISLANDS; EPIGENETIC MODIFICATIONS; EXPRESSED GENES; HIGH THROUGHPUTS; HUMAN CELLS; HUMAN GENOMES; IMPROVED METHODS; METHYL SENSITIVES; PILOT PROJECTS; PLURIPOTENT STEM CELLS; PROMOTER METHYLATIONS; PROMOTER REGIONS;

CELL CULTURE; GENES; METHYLATION; NUCLEIC ACIDS; TISSUE;

ALKYLATION;

BISULFITE; CYTOSINE; DNA;

ARTICLE; B LYMPHOCYTE; CHROMATIN IMMUNOPRECIPITATION; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FIBROBLAST; GENE EXPRESSION; GENOME; HUMAN; HUMAN CELL; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS;

BASE SEQUENCE; CELL NUCLEUS; CHROMOSOME MAPPING; DNA; DNA METHYLATION; GENE TARGETING; HUMANS; METABOLOME; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SULFITES;

EID: 64349091471     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.1533     Document Type: Article

References (42)

1. Suzuki, M.M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465-476 (2008).
2. Goll, M.G. & Bestor, T.H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 74, 481-514 (2005).
3. Feinberg, A.P. & Tycko, B. The history of cancer epigenetics. Nat. Rev. Cancer 4, 143-153 (2004).
4. Jiang, Y.H., Bressler, J. & Beaudet, A.L. Epigenetics and human disease. Annu. Rev. Genomics Hum. Genet. 5, 479-510 (2004).
5. Clark, S.J., Harrison, J., Paul, C.L. & Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990-2997 (1994).
6. Bird, A.P. & Southern, E.M. Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis. J. Mot. Biol. 118, 27-47 (1978).
7. Keshet, I. et al. Evidence for an instructive mechanism of ?enovo methylation in cancer cells. Nat. Genet. 38, 149-153 (2006).
8. Cross, S.H., Charlton, J.A., Nan, X. & Bird, A.P Purification of CpG islands using a methylated DNA binding column. Nat. Genet. 6, 236-244 (1994).
9. Rauch,T.A., Wu,X., Zhong, X., Riggs, A.D. & Pfeifer, G.P A human Bcell methylomeat 100-base pair resolution. Proc. Nati. Acad. Sci. USA 106, 671-678 (2009).
10. Hellman, A. & Chess, A. Gene body-specific methylation on the active X chromosome. Science 315, 1141-1143 (2007).
11. Khulan, B. et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 16, 1046-1055 (2006).
12. Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189-1201 (2006).
13. Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T. & Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39, 61-69 (2007).
14. Bibikova, M. et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16, 383-393 (2006).
15. Irizarry, R.A. et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41, 178-186 (2009).
16. Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770 (2008).
17. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
18. Cokus, SJ. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals
19. DNA methylation patterning. Nature 452, 215-219 (2008). 19. Bentley, D.R. et al. Accurate whole human genome sequencing using reversible
20. terminator chemistry. Nature 456, 53-59 (2008). 20.Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial
21. genome. Science 309, 1728-1732 (2005). 21. Birney, E. et al. Identification and analysis of functional elements in 1% of the human
22. genome by the ENCODE pilot project. Nature 447, 799-816 (2007).
23. Shann, YJ. et al. Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines. Genome Res. 18, 791-801 (2008).
24. Nilsson, M. et al. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265, 2085-2088 (1994).
25. Hardenbol, P. et al. Multiplexed genotypingwith sequence-tagged molecular inversion probes. Nat. Biotechnol. 21, 673-678 (2003).
26. Porreca, GJ. et al. Multiplex amplification of large sets of human exons. Nat. Methods 4, 931-936 (2007).
27. Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat. Biotechnol. advance online publication, doi:10/1038/nbt.1530 (29 March 2009).
28. Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378-1385 (2006).
29. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007).
30. Church, G.M. The personal genome project. Mol. Syst. Biol. 1, 0030 (2005.).
31. Appanah, R., Dickerson, D.R., Goyal, P., Groudine, M. & Lorincz, M.C. An unmethy-lated 3' promoter-proximal region is required for efficient transcription initiation. PLoS Genet. 3, e27 (2007).
32. Buratowski, S. Transcription. Gene expression-where to start? Science 322, 1804-1805 (2008).
33. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457-466 (2007).
34. Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135-1145(2008).
35. Schuster, S.C. Next-generation sequencing transforms today's biology. Nat. MethodsS, 16-18 (2008).
36. Mardis, E.R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9, 387-402 (2008).
37. Kahvejian, A., Quackenbush, J. & Thompson, J.F What would you do if you could sequence everything? Nat. Biotechnol. 26, 1125-1133 (2008).
38. Jones, PA. The DNA methylation paradox. Trends Genet. 15, 34-37 (1999).
39. Illingworth, R. et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6, e22 (2008).
40. Park, I.H., Lerou, P.H., Zhao, R., Huo, H. & Daley, G.Q. Generation of human-induced pluripotent stem cells. Nat. Protoc. 3, 1180-1186 (2008).
41. Ge, B. et al. Survey of allelic expression using EST mining. Genome Res. 15, 1584-1591 (2005).
42. Lewin, J.,Schmitt, A.O., Adorjan, P., Hildmann, T. & Piepenbrock, C. Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates. Bioinformatics 20, 3005-3012 (2004).