title: Underrepresentation of active histone modification marks in evolutionarily young genes.
abstract: It is known that evolutionarily new genes can rapidly evolve essential roles in fundamental biological processes. Nevertheless, the underlying molecular mechanism of how they acquire their novel transcriptional pattern is less characterized except for the role of cis-regulatory evolution. Epigenetic modification offers an alternative possibility. Here, we examined how histone modifications have changed among different gene age groups in Drosophila melanogaster by integrative analyses of an updated new gene dataset and published epigenomic data. We found a robust pattern across various datasets where both the coverage and intensity of active histone modifications, histone 3 lysine 4 trimethylation and lysine 36 trimethylation, increased with evolutionary age. Such a temporal correlation is negative and much weaker for the repressive histone mark, lysine 9 trimethylation, which is expected given its major association with heterochromatin. By further comparison with neighboring old genes, the depletion of active marks of new genes could be only partially explained by the local epigenetic context. All these data are consistent with the observation that older genes bear relatively higher expression levels and suggest that the evolution of histone modifications could be implicated in transcriptional evolution after gene birth.
authors.affiliation: State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Daqi
authors.initials: D
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Wenwen
authors.initials: W
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yong E
authors.initials: YE
authors.lastname: Zhang
mesh_terms: D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D005260:Female; D042421:Histone Code / Q000235:genetics*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D007814:Larva / Q000235:genetics; D008297:Male; D010802:Phylogeny
chemical_list: D006657:Histones
keywords: Drosophila; H3K36me3; H3K4me3; H3K9me3; epigenetic evolution; new gene evolution