TAB-Seq
Tet-Assisted Bisulfite Sequencing
TAB-Seq is a novel method that uses bisulfite conversion and Tet proteins to study 5hmC (Yu et al., 2012). In this method, 5hmC is first protected selectively with a glucose moiety, followed by subsequent oxidation of 5mC to 5caC by Tet proteins. Next, the oxidized gDNA is treated with bisulfite; 5hmC remains unchanged and is read as a cytosine, while 5mC and unmethylated cytosines are deaminated to uracil and read as thymidines upon sequencing. Deep sequencing of TAB-treated DNA compared with untreated DNA provides accurate representation of 5hmC localization in the genome.
Advantages:
- Covers CpG and non-CpG hydroxymethylation throughout the genome at single-base resolution
- Covers 5hmC in dense and less dense repeat regions
- Clearly differentiates between 5hmC and 5mC, specifically identifying 5hmC
Disadvantages:
- Harsh oxidation can lead to substantial loss of DNA
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Aijo T., Huang Y., Mannerstrom H., Chavez L., Tsagaratou A., et al. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol. 2016;17:49
Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26
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:
Bogdanovic O., Smits A. H., de la Calle Mustienes E., Tena J. J., Ford E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426
Chen K., Zhang J., Guo Z., et al. Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Res. 2016;26:103-118
Greco C. M., Kunderfranco P., Rubino M., et al. DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy. Nat Commun. 2016;7:12418
Yu P., Ji L., Lee K. J., et al. Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine. PLoS One. 2016;11:e0154949
Mooijman D., Dey S. S., Boisset J. C., Crosetto N. and van Oudenaarden A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat Biotechnol. 2016;34:852-856
Serandour A. A., Avner S., Mahe E. A., et al. Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets. Genome Biol. 2016;17:56
Thienpont B., Steinbacher J., Zhao H., D’Anna F., Kuchnio A., et al. Tumour hypoxia causes DNA hypermethylation by reducing TET activity. Nature. 2016;537:63-68
Guo F., Yan L., Guo H., Li L., Hu B., et al. The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell. 2015;161:1437-1452
Li Q., Suzuki M., Wendt J., et al. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic Acids Res. 2015;43:e81
Xia B., Han D., Lu X., Sun Z., Zhou A., et al. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat Methods. 2015;12:1047-1050
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History: TAB-Seq
Revision by sbrumpton on 2017-06-21 07:50:20 - Show/Hide
Tet-Assisted Bisulfite Sequencing
TAB-Seq is a novel method that uses bisulfite conversion and Tet proteins to study 5hmC (Yu et al., 2012). In this method, 5hmC is first protected selectively with a glucose moiety, followed by subsequent oxidation of 5mC to 5caC by Tet proteins. Next, the oxidized gDNA is treated with bisulfite; 5hmC remains unchanged and is read as a cytosine, while 5mC and unmethylated cytosines are deaminated to uracil and read as thymidines upon sequencing. Deep sequencing of TAB-treated DNA compared with untreated DNA provides accurate representation of 5hmC localization in the genome.
Advantages:- Covers CpG and non-CpG hydroxymethylation throughout the genome at single-base resolution
- Covers 5hmC in dense and less dense repeat regions
- Clearly differentiates between 5hmC and 5mC, specifically identifying 5hmC
Disadvantages:- Harsh oxidation can lead to substantial loss of DNA
Reagents:Illumina Library prep and Array Kit SelectorReviews:Aijo T., Huang Y., Mannerstrom H., Chavez L., Tsagaratou A., et al. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol. 2016;17:49Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26Shull 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:Bogdanovic O., Smits A. H., de la Calle Mustienes E., Tena J. J., Ford E., et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet. 2016;48:417-426Chen K., Zhang J., Guo Z., et al. Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer. Cell Res. 2016;26:103-118Greco C. M., Kunderfranco P., Rubino M., et al. DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy. Nat Commun. 2016;7:12418Yu P., Ji L., Lee K. J., et al. Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine. PLoS One. 2016;11:e0154949Mooijman D., Dey S. S., Boisset J. C., Crosetto N. and van Oudenaarden A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat Biotechnol. 2016;34:852-856Serandour A. A., Avner S., Mahe E. A., et al. Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets. Genome Biol. 2016;17:56Thienpont B., Steinbacher J., Zhao H., D'Anna F., Kuchnio A., et al. Tumour hypoxia causes DNA hypermethylation by reducing TET activity. Nature. 2016;537:63-68Guo F., Yan L., Guo H., Li L., Hu B., et al. The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell. 2015;161:1437-1452Li Q., Suzuki M., Wendt J., et al. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic Acids Res. 2015;43:e81Xia B., Han D., Lu X., Sun Z., Zhou A., et al. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat Methods. 2015;12:1047-1050