Title |
Differential DNA Methylation Analysis without a Reference Genome
|
---|---|
Published in |
Cell Reports, December 2015
|
DOI | 10.1016/j.celrep.2015.11.024 |
Pubmed ID | |
Authors |
Johanna Klughammer, Paul Datlinger, Dieter Printz, Nathan C. Sheffield, Matthias Farlik, Johanna Hadler, Gerhard Fritsch, Christoph Bock |
Abstract |
Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Austria | 4 | 21% |
United States | 3 | 16% |
France | 2 | 11% |
Spain | 2 | 11% |
United Kingdom | 1 | 5% |
Switzerland | 1 | 5% |
Unknown | 6 | 32% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 10 | 53% |
Scientists | 8 | 42% |
Science communicators (journalists, bloggers, editors) | 1 | 5% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 2% |
United Kingdom | 2 | 1% |
Germany | 1 | <1% |
Canada | 1 | <1% |
Portugal | 1 | <1% |
Unknown | 173 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 52 | 29% |
Researcher | 31 | 17% |
Student > Master | 25 | 14% |
Student > Bachelor | 15 | 8% |
Student > Doctoral Student | 13 | 7% |
Other | 23 | 13% |
Unknown | 22 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 85 | 47% |
Biochemistry, Genetics and Molecular Biology | 44 | 24% |
Computer Science | 6 | 3% |
Neuroscience | 4 | 2% |
Medicine and Dentistry | 3 | 2% |
Other | 12 | 7% |
Unknown | 27 | 15% |