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Tet-Assisted Bisulfite Sequencing (TAB-seq)

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DNA Methylation Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1708))

Abstract

5-Hydroxymethylcytosine (5hmC) is a modified form of cytosine, which has recently been found in mammalian cells and tissues. 5hmC is derived from 5-methylcytosine (5mC) by Ten-eleven translocation (TET) family protein-mediated oxidation and may regulate gene expression. Numerous affinity-based profiling methods have been developed to help understand the exact function of 5hmC in the genome. However, these methods have a relatively low resolution (~100 bp) without quantitative information of the modification percentage on each site. Here we demonstrated the detailed procedure of Tet-Assistant Bisulfite Sequencing (TAB-Seq), which can detect 5hmC at single-base resolution and quantify its abundance at each site. In this protocol, the genomic DNA is first treated with βGT and recombinant mTet1 consecutively to convert 5hmC to 5gmC and 5mC to 5caC, respectively. The treated genomic DNA can be directly applied to bisulfite treatment to detect 5hmC on specific loci or applied to whole-genome bisulfite sequencing as needed.

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Acknowledgments

This work is supported by National Institutes of Health 1R01 HG006827 to C.H.

Author information

Authors and Affiliations

  1. Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA

    Miao Yu & Chuan He

  2. Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA

    Dali Han

  3. Howard Hughes Medical Institute, The University of Chicago, 929 E. 57th Street, Chicago, IL, 60637, USA

    Dali Han & Chuan He

  4. University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA

    Gary C. Hon

Authors
  1. Miao Yu
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  2. Dali Han
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  3. Gary C. Hon
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  4. Chuan He
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Corresponding author

Correspondence to Chuan He .

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Editors and Affiliations

  1. Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA—Institut de Biologie Francois Jacob, Evry, France

    Jörg Tost

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Yu, M., Han, D., Hon, G.C., He, C. (2018). Tet-Assisted Bisulfite Sequencing (TAB-seq). In: Tost, J. (eds) DNA Methylation Protocols. Methods in Molecular Biology, vol 1708. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7481-8_33

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  • DOI: https://doi.org/10.1007/978-1-4939-7481-8_33

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7479-5

  • Online ISBN: 978-1-4939-7481-8

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