Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing
Epigenetic modifications of chromatin and DNA are relevant for eukaryotic gene expression. DNA methylation is the paradigm epigenetic modification that is associated with transcriptional repression. Perturbations of DNA methylation patterns are frequently associated with cancer and aging, raising a great interest in understanding the contribution of this mark to human health. High-throughput sequencing allows interrogating the status of methylated DNA at nucleotide resolution and genome-wide, bringing unprecedented views on the distribution and dynamics of this relevant modification in healthy and diseased tissues. Here we discuss commonly used wet-lab methodologies and computational approaches to identify DNA methylation patterns and measure their dynamics during biological processes in a quantitative and unbiased manner.
KeywordsEpigenetic modifications DNA methylation
- Laird PW, Jaenisch R (1994) DNA methylation and cancer. Hum Mol Genet 3 Spec No: 1487–1495Google Scholar
- Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1)Google Scholar
- Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article 3. doi: 10.2202/1544-6115.1027