Protocol matters: which methylome are you actually studying?
- Author(s)
- Robinson, MD; Statham, AL; Speed, TP; Clark, SJ;
- Details
- Publication Year 2010-08,Volume 2,Issue #4,Page 587-598
- Journal Title
- EPIGENOMICS
- Publication Type
- Journal Article
- Abstract
- The field of epigenetics is now capitalizing on the vast number of emerging technologies, largely based on second-generation sequencing, which interrogate DNA methylation status and histone modifications genome-wide. However, getting an exhaustive and unbiased view of a methylome at a reasonable cost is proving to be a significant challenge. In this article, we take a closer look at the impact of the DNA sequence and bias effects introduced to datasets by genome-wide DNA methylation technologies and where possible, explore the bioinformatics tools that deconvolve them. There remains much to be learned about the performance of genome-wide technologies, the data we mine from these assays and how it reflects the actual biology. While there are several methods to interrogate the DNA methylation status genome-wide, our opinion is that no single technique suitably covers the minimum criteria of high coverage and, high resolution at a reasonable cost. In fact, the fraction of the methylome that is studied currently depends entirely on the inherent biases of the protocol employed. There is promise for this to change, as the third generation of sequencing technologies is expected to again 'revolutionize' the way that we study genomes and epigenomes.
- Publisher
- FUTURE MEDICINE LTD
- Keywords
- WIDE DNA METHYLATION; CPG ISLAND SHORES; CYTOSINE METHYLATION; SINGLE-MOLECULE; HUMAN GENOME; 5-METHYLCYTOSINE RESIDUES; HUMAN-CELLS; CANCER; 5-HYDROXYMETHYLCYTOSINE; RESOLUTION
- Publisher's Version
- https://doi.org/10.2217/EPI.10.36
- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2010-08-01 12:00:00