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Profiling DNA Methylation in Human Naïve Pluripotent Stem Cells

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Human Naïve Pluripotent Stem Cells

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2416))


DNA methylation represents one of the best characterized epigenetic modifications. In particular, global demethylation is a common feature of epigenetic reprogramming to naïve pluripotency in human and mouse pluripotent stem cells. In parallel to the global changes, several locus-specific changes to the DNA methylation landscape occur and also loss of imprinting has been observed in naïve human pluripotent stem cells. The current gold standard to assess and quantitively map DNA methylation is bisulfite sequencing. Various protocols are available for genome-wide bisulfite sequencing and here I describe an optimized method based on Post Bisulfite Adapter Tagging (PBAT) for low amounts of DNA or cells, with as little as 50 cells as minimum requirement, and with the possibility to process a large number of samples in parallel. I outline the basic bioinformatic steps needed to process raw Illumina sequencing data and then describe the inital steps of the analysis of DNA methylation datasets, including an assessment of imprint control regions.

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This protocol is based on method developments and optimizations at the Babraham Institute in Cambridge, UK, and, in particular, on protocols established by Sebastien Smallwood and Stephen Clark.

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Correspondence to Ferdinand von Meyenn .

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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von Meyenn, F. (2022). Profiling DNA Methylation in Human Naïve Pluripotent Stem Cells. In: Rugg-Gunn, P. (eds) Human Naïve Pluripotent Stem Cells. Methods in Molecular Biology, vol 2416. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1907-0

  • Online ISBN: 978-1-0716-1908-7

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