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Epigenomes 2018, 2(4), 21; https://doi.org/10.3390/epigenomes2040021

How to Design a Whole-Genome Bisulfite Sequencing Experiment

1
Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von Seckendorff-Platz 1, 06120 Halle (Saale), Germany
2
Institute of Agronomy and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Soil Biogeochemistry, von-Seckendorff-Platz 3, 06120 Halle (Saale), Germany
3
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
4
Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
5
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
*
Author to whom correspondence should be addressed.
Received: 5 November 2018 / Revised: 25 November 2018 / Accepted: 3 December 2018 / Published: 11 December 2018
(This article belongs to the Special Issue Plant Epigenetics)
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Abstract

Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases. DNA methylation can be found in both prokaryotes and eukaryotes. In the latter, dynamic variation is shown across species, along development, and by cell type. DNA methylation usually leads to a lower binding affinity of DNA-interacting proteins and often results in a lower expression rate of the subsequent genome region, a process also referred to as transcriptional gene silencing. We give an overview of the current state of research facilitating the planning and implementation of whole-genome bisulfite-sequencing (WGBS) experiments. We refrain from discussing alternative methods for DNA methylation analysis, such as reduced representation bisulfite sequencing (rrBS) and methylated DNA immunoprecipitation sequencing (MeDIPSeq), which have value in specific experimental contexts but are generally disadvantageous compared to WGBS. View Full-Text
Keywords: WGBS; coverage; library; DNA methylation; 5mC; epigenome; epigenetics WGBS; coverage; library; DNA methylation; 5mC; epigenome; epigenetics
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Grehl, C.; Kuhlmann, M.; Becker, C.; Glaser, B.; Grosse, I. How to Design a Whole-Genome Bisulfite Sequencing Experiment. Epigenomes 2018, 2, 21.

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