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
References:
Derks M. F., Schachtschneider K. M., Madsen O., Schijlen E., Verhoeven K. J. and van Oers K. Gene and transposable element methylation in great tit (Parus major) brain and blood. BMC Genomics. 2016;17:332
Lu Y. C., Feng S. J., Zhang J. J., Luo F., Zhang S. and Yang H. Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine. Sci Rep. 2016;6:18985
Wang X., Werren J. H. and Clark A. G. Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia. PLoS Biol. 2016;14:e1002500
Zhang Y., Zhang D., Li Q., et al. Nucleation of DNA repair factors by FOXA1 links DNA demethylation to transcriptional pioneering. Nat Genet. 2016;48:1003-1013
Bogdanovic O., Smits A. H., de la Calle Mustienes E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426
Groth M., Moissiard G., Wirtz M., et al. MTHFD1 controls DNA methylation in Arabidopsis. Nat Commun. 2016;7:11640
Jeong Y. H., Lu H., Park C. H., et al. Stochastic anomaly of methylome but persistent SRY hypermethylation in disorder of sex development in canine somatic cell nuclear transfer. Sci Rep. 2016;6:31088
Kaaij L. J., Mokry M., Zhou M., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146
Qu W., Tsukahara T., Nakamura R., et al. Assessing Cell-to-Cell DNA Methylation Variability on Individual Long Reads. Sci Rep. 2016;6:21317
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
Thienpont B., Steinbacher J., Zhao H., et al. Tumour hypoxia causes DNA hypermethylation by reducing TET activity. Nature. 2016;537:63-68
Wallner S., Schroder C., Leitao E., et al. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016;9:33
Yang Y., Zhou R., Mu Y., Hou X., Tang Z. and Li K. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep. 2016;6:30160
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
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History: BS-Seq/Bisulfite-Seq/WGBS
Revision by sbrumpton on 2017-06-21 07:50:20 - Show/Hide
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 SelectorReviews: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;625:47-55Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26References:Derks M. F., Schachtschneider K. M., Madsen O., Schijlen E., Verhoeven K. J. and van Oers K. Gene and transposable element methylation in great tit (Parus major) brain and blood. BMC Genomics. 2016;17:332Lu Y. C., Feng S. J., Zhang J. J., Luo F., Zhang S. and Yang H. Genome-wide identification of DNA methylation provides insights into the association of gene expression in rice exposed to pesticide atrazine. Sci Rep. 2016;6:18985Wang X., Werren J. H. and Clark A. G. Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia. PLoS Biol. 2016;14:e1002500Zhang Y., Zhang D., Li Q., et al. Nucleation of DNA repair factors by FOXA1 links DNA demethylation to transcriptional pioneering. Nat Genet. 2016;48:1003-1013Bogdanovic O., Smits A. H., de la Calle Mustienes E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426Groth M., Moissiard G., Wirtz M., et al. MTHFD1 controls DNA methylation in Arabidopsis. Nat Commun. 2016;7:11640Jeong Y. H., Lu H., Park C. H., et al. Stochastic anomaly of methylome but persistent SRY hypermethylation in disorder of sex development in canine somatic cell nuclear transfer. Sci Rep. 2016;6:31088Kaaij L. J., Mokry M., Zhou M., et al. Enhancers reside in a unique epigenetic environment during early zebrafish development. Genome Biol. 2016;17:146Qu W., Tsukahara T., Nakamura R., et al. Assessing Cell-to-Cell DNA Methylation Variability on Individual Long Reads. Sci Rep. 2016;6:21317Rehan 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;8:1401-1410Thienpont B., Steinbacher J., Zhao H., et al. Tumour hypoxia causes DNA hypermethylation by reducing TET activity. Nature. 2016;537:63-68Wallner S., Schroder C., Leitao E., et al. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016;9:33Yang Y., Zhou R., Mu Y., Hou X., Tang Z. and Li K. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep. 2016;6:30160Zhang 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