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Complementary to this, one of the most important findings in the field of epigenetics in recent times is the discovery of DNA methylation variation between individuals at a genome-wide level [15].
We further looked at whether these 1296 genes showed DNA methylation variation between tissues as well.
Overall methylation variation between combined treatment-naïve samples and 2 treated UC samples was examined by correlation based principal component analysis (PCA).
By joining with transcriptome data measured by RNA-Seq, we were able to correlate most methylation variation between tissues with gene expression levels.
The results showed that the degree of DNA methylation variation between the two lines across the genome was greater than gene expression variation (Fig. 7).
Because the majority of genes that have methylation variation between tissues showed correlation between methylation and transcriptional levels, such number of correlations was so significant that it could not be generated by chance.
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But due to the lack of enough biological replicates, it was hard for us to carry out comprehensive analysis on methylation variations between different chicken breeds.
Xu et al reported the overall methylation differences between different tissues and strains of chicken [30], which provided the first attempt to elucidate the DNA methylation variations between chicken breeds with heterogeneous genetic background.
Using genome-scale methylome data, we examined the dynamics of methylation variations between different cell lines, and among different genomic regions including CpG islands, gene structures, and various types of repeats.
Differences in DNA methylation variations between genes related to the immune-inflammatory process and the other groups of genes are concentrated in sequences near the TSS, and variations in DNA methylation in genes related to the immune-inflammatory process are correlated with variations in mRNA levels.
These results indicated that more DNA methylation variation exhibited between groups with larger chronological ages distances in Moso bamboo.
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