Abstract
DNA methylation is a key epigenetic modification controlling the transcriptional activity of mammalian retrotransposable elements. Its oxidation to DNA hydroxymethylation has been linked to DNA demethylation and reactivation of retrotransposons. Here we describe in detail protocols for three methods to measure DNA methylation and hydroxymethylation at specific genomic targets: glucMS-qPCR, and two sequencing approaches (pyrosequencing and high-throughput sequencing) for analyzing bisulfite- and oxidative bisulfite-modified DNA. All three techniques provide absolute measurements of methylation and hydroxymethylation levels at single-base resolution. Differences between the methods are discussed, mainly with respect to throughput and target coverage. These constitute the core techniques that are used in our laboratory for accurately surveying the epigenetics of retrotransposable elements.
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© 2016 Springer Science+Business Media New York
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de la Rica, L., Stanley, J.S., Branco, M.R. (2016). Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements. In: Garcia-Pérez, J. (eds) Transposons and Retrotransposons. Methods in Molecular Biology, vol 1400. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3372-3_24
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DOI: https://doi.org/10.1007/978-1-4939-3372-3_24
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Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3370-9
Online ISBN: 978-1-4939-3372-3
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