BS-Seq/Bisulfite-Seq/WGBS

Whole-Genome Bisulfite Sequencing

BS-Seq/Bisulfite-seq or WGBS is a well-established protocol to detect methylated cytosines in gDNA (Feil et al., 1994). In this method, gDNA 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.

Advantages:

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

Disadvantages:

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


Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

Devall M., Roubroeks J., Mill J., Weedon M. and Lunnon K. Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies. Neurosci Lett. 2016;625:47-55

Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26



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Rehan S. M., Glastad K. M., Lawson S. P. and Hunt B. G. The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata. Genome Biol Evol. 2016;8:1401-1410

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Zhang X., Su J., Jeong M., et al. DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells. Nat Genet. 2016;48:1014-1023