Yoshinori Matsuo and Norikazu Kakubayashi
Histone modification and replacement in variant histones result in nucleosome remodeling and play an important role in epigenetics. The evolutionary mechanism of epigenetics was investigated by analysing the variant histone 3 genes, H3.3A and H3.3B, in 12 Drosophila species. A U11-48K-like gene coding for a zinc finger domain was located in the region upstream of the H3.3A gene in all Drosophila species studied. The U11-48K-like and H3.3A genes may be co-regulated, as is the case for the H3-H4 gene pair. However, no strongly conserved nucleotide sequence was found in the 5`- regions of the two genes. Various combinations of gene pairs were found upstream or downstream of the H3.3B gene but none were conserved amongst a broad range of Drosophila species. Moderately conserved DNA sequences were found in the H3.3B gene regions around the first intron and outside the coding region of the fifth exon, but DNA sequences in the upstream or downstream regions of the H3.3B genes were not strongly conserved. Different codon usages for three H3 genes (H3, H3.3A and H3.3B) were found for 13 of 18 amino acids and codon usages characteristic of replacement histones (H4r, H3.3A and H3.3B) were found for several amino acids. Several histone modification sites in H3, H3.3A and H3.3B showed extraordinarily biased codon usages. These results suggested the importance of the translational step for histone modification and for the development of epigenetic systems.
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