BS-Seq/Bisulfite-seq/WGBS

BS-Seq/Bisulfite-seq/WGBS

Method Category: Epigenome > Methylation

Description: Bisulfite sequencing (BS-Seq) or whole-genome bisulfite sequencing (WGBS) is a well-established protocol to detect methylated cytosines in genomic DNA . In this method, genomic DNA is treated with sodium bisulfite and then sequenced, providing single-base resolution of methylated cytosines in the genome. Upon bisulfite treatment, unmethylated cytosines are deaminated to uracils which, upon sequencing, are converted to thymidines. Simultaneously, methylated cytosines resist deamination and are read as cytosines. The location of the methylated cytosines can then be determined by comparing treated and untreated sequences. Bisulfite treatment of DNA converts unmethylated cytosines to thymidines, leading to reduced sequence complexity. Very accurate deep sequencing serves to mitigate this loss of complexity.

Pros:

• CpG and non-CpG methylation throughout the genome is covered at single-base resolution
• 5mC in dense, less dense, and repeat regions are covered

Cons:

• Bisulfite converts unmethylated cytosines to thymidines, reducing sequence complexity, which can make it difficult to create alignments
• NPs where a cytosine is converted to thymidine will be missed upon bisulfite conversion
• Bisulfite conversion does not distinguish between 5mC and 5hmC

Related Publications

• BS-Seq: Feil R., Charlton J., Bird A. P., Walter J. and Reik W. (1994) Methylation analysis on individual chromosomes: improved protocol for bisulphite genomic sequencing. Nucleic Acids Res 22: 695-696
• Bisulfite-seq: Berman B. P., Weisenberger D. J., Aman J. F., Hinoue T., Ramjan Z., et al. (2012) Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 44: 40-46
• WGBS: Lister R., Pelizzola M., Dowen R. H., Hawkins R. D., Hon G., et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322

Citations:

1. Seki M., Nishimura R., Yoshida K., Shimamura T., Shiraishi Y., et al. (2015) Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma. Nat Commun 6: 7557
2. Nugent B. M., Wright C. L., Shetty A. C., Hodes G. E., Lenz K. M., et al. (2015) Brain feminization requires active repression of masculinization via DNA methylation. Nat Neurosci 18: 690-697
3. Lee H. Y., An J. H., Jung S. E., Oh Y. N., Lee E. Y., et al. (2015) Genome-wide methylation profiling and a multiplex construction for the identification of body fluids using epigenetic markers. Forensic Sci Int Genet 17: 17-24
4. Lin, I. H., Chen D. T., Chang Y. F., Lee Y. L., Su C. H., et al. (2015) Hierarchical clustering of breast cancer methylomes revealed differentially methylated and expressed breast cancer genes. PLoS One 10: e0118453
5. Elliott G., Hong C., Xing X., Zhou X., Li D., et al. (2015) Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun 6: 6363
6. Coit P., Yalavarthi S., Ognenovski M., Zhao W., Hasni S., et al. (2015) Epigenome profiling reveals significant DNA demethylation of interferon signature genes in lupus neutrophils. J Autoimmun 58: 59-66