To analyse the involvement of duplicated genes on tissue evolution, we initially focused on the relationship between gene expression breadth and gene duplication.
We observed the connection between gene expression breadth in humans and gene compactness to be significantly weaker than the connection between expression level and compactness, a result that is compatible with the selection hypothesis but not the genome design hypothesis.
They found that the connection between gene expression breadth in humans and gene compactness to be significantly weaker than the connection between expression level and compactness, which is compatible with the selection hypothesis but not the genome design hypothesis [ 13].
However, Lercher et al. reported that there is a strong correlation between gene expression breadth and GC content in human, suggesting that there might be selective pressure favoring the concentration of housekeeping genes in GC-rich isochors.
In the present study, we observed that the connection between gene expression breadth in chicken and gene compactness to be significantly stronger than the connection between expression level and compactness, and the tissue specificity of genes is positively correlated with first intron length (P < 0.0001, r = 0.07276).
Furthermore, genes with tissue-specific eCGIs in their promoters exhibit more tissue-specific expression than those with constitutive eCGIs (Supplementary Material, Fig. S9) and associate with tissue-specific GO categories (Supplementary Material, Table S5), indicating co-regulation between eCGI methylation and gene expression breadths.
Indeed, the correlation between DNA methylation breadth and gene expression breadth was about twice as stronger as that between promoter CpG contents and gene expression breadths (Supplementary Material, Table S4).
Second, we assessed the influence of gene expression breadths on the correlation between CpG O/E and gene lengths, using partial correlation (Kim and Yi 2006, 2007).
Given that the underlying idea for the association between promoter CpG content and gene expression breadth is DNA methylation, we hypothesized that DNA methylation characteristics of eCGIs in promoters may provide a better indicator of gene expression breadths than CpG content.
