oxBS-Seq
Oxidative Bisulfite Sequencing
oxBS-Seq differentiates between 5mC and 5hmC (Booth et al., 2012). In this method, 5hmC is oxidized to 5fC with a selective chemical agent, while 5mC remains unchanged. Sodium bisulfite treatment of 5fC results in its deamination to uracil which, upon sequencing, is read as a thymidine. Deep sequencing of oxBS-treated DNA and sequence comparison of treated vs untreated libraries can identify 5hmC locations at single-base resolution.
Advantages:
- Covers CpG and non-CpG methylation throughout the genome at single-base resolution
- Covers 5mC in dense and less dense repeat regions
- Clearly differentiates between 5mC and 5hmC
Disadvantages:
- Harsh oxidation conditions lead to a substantial loss of DNA (99.5%)
- Must be combined with BS-Seq in order to distinguish and quantify C, 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
Marx V. Genetics: profiling DNA methylation and beyond. Nat Methods. 2016;13:119-122
Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26
Meldi K. M. and Figueroa M. E. Cytosine modifications in myeloid malignancies. Pharmacol Ther. 2015;152:42-53
Shull A. Y., Noonepalle S. K., Lee E. J., Choi J. H. and Shi H. Sequencing the cancer methylome. Methods Mol Biol. 2015;1238:627-651
References:
Hadad N., Masser D. R., Logan S., et al. Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice. Epigenetics Chromatin. 2016;9:30
Feng J., Shao N., Szulwach K. E., et al. Role of Tet1 and 5-hydroxymethylcytosine in cocaine action. Nat Neurosci. 2015;18:536-544
Aijo T., Huang Y., Mannerstrom H., et al. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol. 2016;17:49
Page A., Paoli P., Moran Salvador E., White S., French J., et al. Hepatic stellate cell transdifferentiation involves genome-wide remodeling of the DNA methylation landscape. J Hepatol. 2016;64:661-673
Wallner S., Schroder C., Leitao E., Berulava T., Haak C., et al. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016;9:33
Related
History: oxBS-Seq
Revision by sbrumpton on 2017-06-21 07:50:20 - Show/Hide
Oxidative Bisulfite Sequencing
oxBS-Seq differentiates between 5mC and 5hmC (Booth et al., 2012). In this method, 5hmC is oxidized to 5fC with a selective chemical agent, while 5mC remains unchanged. Sodium bisulfite treatment of 5fC results in its deamination to uracil which, upon sequencing, is read as a thymidine. Deep sequencing of oxBS-treated DNA and sequence comparison of treated vs untreated libraries can identify 5hmC locations at single-base resolution.
Advantages:- Covers CpG and non-CpG methylation throughout the genome at single-base resolution
- Covers 5mC in dense and less dense repeat regions
- Clearly differentiates between 5mC and 5hmC
Disadvantages:- Harsh oxidation conditions lead to a substantial loss of DNA (99.5%)
- Must be combined with BS-Seq in order to distinguish and quantify C, 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;625:47-55Marx V. Genetics: profiling DNA methylation and beyond. Nat Methods. 2016;13:119-122Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26Meldi K. M. and Figueroa M. E. Cytosine modifications in myeloid malignancies. Pharmacol Ther. 2015;152:42-53Shull A. Y., Noonepalle S. K., Lee E. J., Choi J. H. and Shi H. Sequencing the cancer methylome. Methods Mol Biol. 2015;1238:627-651References:Hadad N., Masser D. R., Logan S., et al. Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice. Epigenetics Chromatin. 2016;9:30Feng J., Shao N., Szulwach K. E., et al. Role of Tet1 and 5-hydroxymethylcytosine in cocaine action. Nat Neurosci. 2015;18:536-544Aijo T., Huang Y., Mannerstrom H., et al. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol. 2016;17:49Page A., Paoli P., Moran Salvador E., White S., French J., et al. Hepatic stellate cell transdifferentiation involves genome-wide remodeling of the DNA methylation landscape. J Hepatol. 2016;64:661-673Wallner S., Schroder C., Leitao E., Berulava T., Haak C., et al. Epigenetic dynamics of monocyte-to-macrophage differentiation. Epigenetics Chromatin. 2016;9:33