Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

Nature Protocols

Volumn 6, Issue 4, 2011, Pages 468-481

  Gu, Hongcang ^a   Smith, Zachary D ^a,b,c   Bock, Christoph ^a,b,c,d   Boyle, Patrick ^a   Gnirke, Andreas ^a   Meissner, Alexander ^a,b,c  

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

^b Harvard University   (United States)

^c HARVARD STEM CELL INSTITUTE   (United States)

^d MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; DNA FRAGMENT; FORMALDEHYDE; GENOMIC DNA; PARAFFIN; RESTRICTION ENDONUCLEASE;

ARTICLE; CLINICAL PROTOCOL; CPG ISLAND; DNA FINGERPRINTING; DNA ISOLATION; DNA LIBRARY; DNA METHYLATION; DNA PURIFICATION; DNA REPAIR; DNA SEQUENCE; GENOME ANALYSIS; INTERMETHOD COMPARISON; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

CPG ISLANDS; DNA METHYLATION; GENE LIBRARY; GENOMICS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SULFITES;

EID: 79952788617     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2010.190     Document Type: Article

References (31)

1. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21 (2002). (Pubitemid 34049633)
2. Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770 (2008).
3. Illingworth, R. et al. A novel CpG island set identifes tissue-specifc methylation at developmental gene loci. PLoS Biol. 6, e22 (2008).
4. Mohn, F. et al. Lineage-specifc polycomb targets and de novo DNA methylation defne restriction and potential of neuronal progenitors. Mol. cell. 30, 755-766 (2008).
5. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457-466 (2007). (Pubitemid 46514772)
6. Laurent, L. et al. Dynamic changes in the human methylome during differentiation. Genome Res. 30, 320-331 (2010).
7. Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215-219 (2008). (Pubitemid 351380251)
8. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
9. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 296-297 (2009).
10. Gu, H. et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods 7, 133-136 (2010).
11. Frommer, M. et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89, 1827-1831 (1992).
12. Bibikova, M. et al. Genome-wide DNA methylation profling using Infnium assay. Epigenomics 1, 177-200 (2009).
13. Eckhardt, F. et al. DNA methylation profling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378-1385 (2006). (Pubitemid 44837559)
14. Khulan, B. et al. Comparative isoschizomer profling of cytosine methylation: the HELP assay. Genome Res. 16, 1046-1055 (2006). (Pubitemid 44162264)
15. Brunner, A.L. et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19, 1044-1056 (2009).
16. Irizarry, R.A. et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18, 780-790 (2008). (Pubitemid 351645068)
17. Oda, M. et al. High-resolution genome-wide cytosine methylation profling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 37, 3829-3839 (2009).
18. Down, T.A. et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26, 779-785 (2008). (Pubitemid 351961453)
19. Weber, M. et al. Chromosome-wide and promoter-specifc analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853-862 (2005). (Pubitemid 41077111)
20. Brinkman, A.B. et al. Whole-genome DNA methylation profling using MethylCap-seq. Methods 52, 232-236 (2010).
21. Rauch, T. & Pfeifer, G.P. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab. Invest. 85, 1172-1180 (2005). (Pubitemid 43073989)
22. Serre, D., Lee, B.H. & Ting, A.H. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 38, 391-399 (2009).
23. Bock, C. et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol 28, 1106-1114 (2010).
24. Baranzini, S.E., et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 464, 1351-1356 (2010).
25. Meissner, A. et al. Reduced representation bisulfte sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33, 5868-5877 (2005). (Pubitemid 41742606)
26. Ramsahoye, B.H. et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. USA 97, 5237-5242 (2000). (Pubitemid 30313702)
27. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858 (2008).
28. Chen, P.Y., Cokus, S.J. & Pellegrini, M. BS Seeker: precise mapping for bisulfte sequencing. BMC Bioinformatics 11, 203 (2010).
29. Xi, Y. & Li, W. BSMAP: whole genome bisulfte sequence MAPping program. BMC Bioinformatics 10, 232 (2009).
30. Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51-54 (2003). (Pubitemid 36150331)
31. Beck, S. Taking the measure of the methylome. Nat. Biotechnol. 28, 1016-1028 (2010).