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| Status |
Public on Feb 06, 2014 |
| Title |
Array-based assay detects genome-wide 5-methylcytosine and 5-hydroxymethlycytosine in non-human primates and mice |
| Platform organism |
Homo sapiens |
| Sample organisms |
Macaca mulatta; Pan troglodytes; Homo sapiens; Mus musculus |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Murine and non-human primates (e.g. rhesus monkeys) represent excellent model systems to study human health and disease. However, use of these model systems for genomic studies is limited, particularly with array-based tools, as most have only been developed to survey the human genome. Here we present the optimization of a widely used human DNA methylation array, designed to detect 5-methylcytosine (5-mC), and show that non-human data generated using the optimized array reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99). Genome-wide methylation analysis, using this approach, reveals 6,102 differentially methylated loci between rhesus placental and fetal tissues with pathways analysis significantly overrepresented for developmental processes. Restricting the analysis to oncogenes and tumor suppressors genes finds 125 differentially methylated loci, suggesting that rhesus placental tissue carries a cancer epigenetic signature. Moreover, we adapted the assay to detect 5-hydroxymethylcytosine (5-hmC) and find highly reproducible 5-hmC levels within human, rhesus, and mouse brain tissue that is species-specific with a hierarchical abundance among the three species (human > rhesus >> mouse). Together, these data show that this array-based methylation assay is generalizable to all mammals for the detection of both 5-mC and 5-hmC, greatly improving the utility of mammalian model systems to study the role of epigenetics in human health, disease, and evolution.
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| Overall design |
Here we present the optimization of a widely used human DNA methylation array, designed to detect 5-methylcytosine (5-mC), and show that non-human data generated using the optimized array reproducibly distinguishes tissue types within and between chimpanzee, rhesus, and mouse, with correlations near the human DNA level (R2 > 0.99).
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| Contributor(s) |
Alisch R, Chopra P |
| Citation(s) |
24524199 |
| Submission date |
Jul 24, 2013 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Pankaj Chopra |
| E-mail(s) |
pchopr4@emory.edu
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| Phone |
404 727 0405
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| Organization name |
Emory University
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| Department |
Human Genetics
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| Lab |
Warren Lab
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| Street address |
615 Michael St. NE, Ste. 375
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (61)
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| Relations |
| BioProject |
PRJNA213232 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE49177_RAW.tar |
183.1 Mb |
(http)(custom) |
TAR |
| GSE49177_signal_intensities.txt.gz |
204.8 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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