Epigenetics Evolution and Replacement Histones: Evolutionary Changes at Drosophila H4r

Abstract

Histone 4 replacement (H4r) can replace replication-dependent H4 in Drosophila. To study the evolution of epigenetic mechanisms, the H4 and H4r genes from 14 Drosophila species were compared with regard to gene arrangement, codon bias and flanking sequences. Although the amino acid sequences of H4 and H4r are identical or nearly identical, the gene structures are quite different. The H4r gene is a single copy gene located 3R88C9 in D. melanogaster between punt and CEP78K, as it is in 11 closely related Drosophila species, but not in the three distantly related species. The H4r gene, unlike the H4 gene, has two introns and generates polyadenylated transcripts. The codon usage bias at particular sites differed between H4r and H4. The H4r gene had more GC pairs at 3 rd codon position. Strongly conserved signal sequence was not found in the 5'-region or 3'-region of the H4r gene. These results suggested that the post transcriptional process such as modifying histone at or after translation will be important for replacing histones and remodeling the chromatin. The evolutionary changes that affect gene structure and codon usage might be a key step to develop epigenetic systems by replacement histones.

Concerted Evolution of the Replication-Dependent Histone Gene Family in Drosophila immigrans

“…There is also a large difference in the gene structures of the two types of histones [25][26][27][28]. Two types of histone genes have been evolved independently [29][30][31].…”

Epigenetics and Codon Usage of the Histone Genes in 12 Drosophila Species

“…The relationship between codon usage and histone modification (at Lys, Arg, Thr, or Ser) was analysed for four histones in Drosophila [87][88][89]. The modification pattern of Lys was complicated because of many sites of modification; several kinds of modifications such as methylation, acetylation, phosphorylation, and ubiquitylation; and multiple modifications at a single site such as 1-3 methylations, methylation and acetylation [20,45,46,51,52,94].…”

“…On the other hand, the genes for the replacement type histones are either single copy (H2AvD and H4r) or a few copies (H3.3A and H3.3B) [65][66][67][68], and have evolved independently of those for the canonical type [87][88][89]. These histone genes are split by 1-4 introns [65][66][67][68] (Figure 2) and a poly(A) tail is added to the transcripts [65,67].…”

“…Therefore, control of histone expression by splicing is only possible for the replacement type. Although the detailed mechanisms regarding the control of histone expression by splicing remains unknown, several conserved sequences at splicing sites have been found for the replacement type [87][88][89]. Transcriptional control plays an important role in controlling the expression of the canonical type [19,69].…”

“…The GC content at the 3 rd codon position of the genes for the canonical and replacement histone types was analysed and compared for 12 Drosophila species [87][88][89] for which the genome project has already been completed. Analyses for the H1 and H2B genes have not been presented before because of the absence of corresponding replacement histones.…”