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| Status |
Public on Jan 13, 2014 |
| Title |
Immunoprecipitation from rat kidney with 8-oxoguanine |
| Organism |
Rattus norvegicus |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
8-oxoguanine (8-oxoG) is one of the most common DNA lesions generated by reactive oxygen species. Here we show the genome-wide distribution of 8-oxoG by coupling immunoprecipitation by antibodies specific for the DNA fragments containing 8-oxoG with microarray that covers rat genome. Genome-wide mapping of 8-oxoG in rat kidney reveals that 8-oxoG preferentially located at gene deserts and depleted in genic regions. We did not observe the difference in 8-oxoG level between highly- and lowly-expressed groups of genes, may be because of the low level of 8-oxoG in genic regions in general comparing to gene deserts. Rather, the distribution of 8-oxoG highly correlates with the distribution of lamina associated domains (LADs), suggesting that the spatial location of the genomic regions in the nucleus is the major determinant for the susceptibility to oxidative modifications. One possible explanation for the enrichment of 8-oxoG in LADs is that the nuclear periphery is more susceptible to the oxidative damage coming from outside the nucleus. Another explanation is that LADs take rather compact conformation, which might prevent the recruitment of the repairing complex to the modified bases.
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| Overall design |
Normal condition. Biological replicate 2
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| Contributor(s) |
Yoshihara M, Suyama M, Toyokuni S |
| Citation(s) |
25008760 |
| Submission date |
Jan 12, 2014 |
| Last update date |
Aug 01, 2014 |
| Contact name |
Minako Yoshihara |
| E-mail(s) |
y_minako@bioreg.kyushu-u.ac.jp
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| Organization name |
Medical institute of Bioregulation, Kyushu University
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| Department |
Division of Bioinformatics
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| Street address |
3-1-1 Maidashi
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| City |
Higashi-ku, Fukuoka |
| State/province |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
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| Platforms (1) |
| GPL15358 |
Agilent-015223 Rat Genome CGH Microarray 244A |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA234331 |
