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Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions

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TET Proteins and DNA Demethylation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2272))

Abstract

Simultaneous measurement of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level can be obtained by combining data from DNA processing methods including traditional bisulfite (BS), oxidative bisulfite (oxBS), or Tet-assisted (TAB) bisulfite conversion. Array-based technologies have been widely used in this task, due to their time and cost efficiency. For methylation studies using BS data, many protocols and related packages have been suggested in the literature to deal with limitations and confounders that arise from array data. In this chapter, we illustrate how the reader can make small adjustments to these protocols to obtain estimates of methylation and hydroxymethylation proportions.

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Author information

Authors and Affiliations

  1. Department of Statistics, State University of Campinas, Campinas, SP, Brazil

    Samara Flamini Kiihl

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  1. Samara Flamini Kiihl
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Correspondence to Samara Flamini Kiihl .

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Editors and Affiliations

  1. Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia

    Ozren Bogdanovic

  2. Radboud University, Nijmegen, The Netherlands

    Michiel Vermeulen

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Kiihl, S.F. (2021). Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions. In: Bogdanovic, O., Vermeulen, M. (eds) TET Proteins and DNA Demethylation. Methods in Molecular Biology, vol 2272. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1294-1_8

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  • DOI: https://doi.org/10.1007/978-1-0716-1294-1_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1293-4

  • Online ISBN: 978-1-0716-1294-1

  • eBook Packages: Springer Protocols

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