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Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus.

Yoshihara M, Jiang L, Akatsuka S, Suyama M, Toyokuni S - DNA Res. (2014)

Bottom Line: 8-Oxoguanine (8-oxoG) is one of the most common DNA lesions generated by reactive oxygen species.Genome-wide mapping of 8-oxoG in normal rat kidney revealed that 8-oxoG is preferentially located at gene deserts.We did not observe differences in 8-oxoG levels between groups of genes with high and low expression, possibly because of the generally low 8-oxoG levels in genic regions compared with gene deserts.

View Article: PubMed Central - PubMed

Affiliation: Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.

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Distribution of 8-oxoG along the chromosomes. The vertical axis corresponds to log2 intensity of the array data. Distribution profile for 8-oxoG was calculated by averaging the intensities over a 1 Mb sliding window. Chromosome ideogram is shown under each plot.
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DSU023F2: Distribution of 8-oxoG along the chromosomes. The vertical axis corresponds to log2 intensity of the array data. Distribution profile for 8-oxoG was calculated by averaging the intensities over a 1 Mb sliding window. Chromosome ideogram is shown under each plot.

Mentions: To analyse the distribution of 8-oxoG, we plotted the signal of each probe of the microarray in the rat chromosomes. There are ∼244,000 probes (60-mer in length) on the microarray used in this study (Agilent Rat Genome CGH Microarray Kit 244A), corresponding to the average probe interval of 1 in 6,000 bases. The averaged 8-oxoG levels are plotted along the chromosomes and shown together with the ideogram in Figure 2. The plot reveals that the regions with high 8-oxoG level are not uniformly distributed; their size fluctuates around several Mb, with some 8-oxoG-rich regions larger than 10 Mb. For example, there is a broad peak spanning more than 10 Mb in the position of 50–60 Mb in chr14. However, there are also some 8-oxoG-depleted regions. We did not observe any clear correlation between the 8-oxoG levels and ideogram-banding patterns. The average probe interval of the microarray that we used in this experiment is 6,000 bases, while the 8-oxoG levels fluctuate with intervals of several Mb. This indicates that the probe density is high enough to depict the 8-oxoG profile along chromosomes.Figure 2.


Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus.

Yoshihara M, Jiang L, Akatsuka S, Suyama M, Toyokuni S - DNA Res. (2014)

Distribution of 8-oxoG along the chromosomes. The vertical axis corresponds to log2 intensity of the array data. Distribution profile for 8-oxoG was calculated by averaging the intensities over a 1 Mb sliding window. Chromosome ideogram is shown under each plot.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263294&req=5

DSU023F2: Distribution of 8-oxoG along the chromosomes. The vertical axis corresponds to log2 intensity of the array data. Distribution profile for 8-oxoG was calculated by averaging the intensities over a 1 Mb sliding window. Chromosome ideogram is shown under each plot.
Mentions: To analyse the distribution of 8-oxoG, we plotted the signal of each probe of the microarray in the rat chromosomes. There are ∼244,000 probes (60-mer in length) on the microarray used in this study (Agilent Rat Genome CGH Microarray Kit 244A), corresponding to the average probe interval of 1 in 6,000 bases. The averaged 8-oxoG levels are plotted along the chromosomes and shown together with the ideogram in Figure 2. The plot reveals that the regions with high 8-oxoG level are not uniformly distributed; their size fluctuates around several Mb, with some 8-oxoG-rich regions larger than 10 Mb. For example, there is a broad peak spanning more than 10 Mb in the position of 50–60 Mb in chr14. However, there are also some 8-oxoG-depleted regions. We did not observe any clear correlation between the 8-oxoG levels and ideogram-banding patterns. The average probe interval of the microarray that we used in this experiment is 6,000 bases, while the 8-oxoG levels fluctuate with intervals of several Mb. This indicates that the probe density is high enough to depict the 8-oxoG profile along chromosomes.Figure 2.

Bottom Line: 8-Oxoguanine (8-oxoG) is one of the most common DNA lesions generated by reactive oxygen species.Genome-wide mapping of 8-oxoG in normal rat kidney revealed that 8-oxoG is preferentially located at gene deserts.We did not observe differences in 8-oxoG levels between groups of genes with high and low expression, possibly because of the generally low 8-oxoG levels in genic regions compared with gene deserts.

View Article: PubMed Central - PubMed

Affiliation: Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.

Show MeSH
Related in: MedlinePlus