A comprehensive study of Z-DNA density and its evolutionary implications in birds.
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| Format: | Artículo científico |
| Sprache: | en |
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BMC genomics
2024
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| author | Wang, Yu-Ren Chang, Shao-Ming Lin, Jinn-Jy Chen, Hsiao-Chian Lee, Lo-Tung Tsai, Dien-Yu Lee, Shih-Da Lan, Chung-Yu Chang, Chuang-Rung Chen, Chih-Feng Ng, Chen Siang |
| author_facet | Wang, Yu-Ren Chang, Shao-Ming Lin, Jinn-Jy Chen, Hsiao-Chian Lee, Lo-Tung Tsai, Dien-Yu Lee, Shih-Da Lan, Chung-Yu Chang, Chuang-Rung Chen, Chih-Feng Ng, Chen Siang Wang, Yu-Ren Chang, Shao-Ming Lin, Jinn-Jy Chen, Hsiao-Chian Lee, Lo-Tung Tsai, Dien-Yu Lee, Shih-Da Lan, Chung-Yu Chang, Chuang-Rung Chen, Chih-Feng Ng, Chen Siang |
| collection | PubMed - marine biology |
| contents | A comprehensive study of Z-DNA density and its evolutionary implications in birds. Wang, Yu-Ren Chang, Shao-Ming Lin, Jinn-Jy Chen, Hsiao-Chian Lee, Lo-Tung Tsai, Dien-Yu Lee, Shih-Da Lan, Chung-Yu Chang, Chuang-Rung Chen, Chih-Feng Ng, Chen Siang Animals Birds Evolution, Molecular DNA, Z-Form Genome Nucleotide Motifs Genomics Promoter Regions, Genetic Base Composition Z-DNA, a left-handed helical form of DNA, plays a significant role in genomic stability and gene regulation. Its formation, associated with high GC content and repetitive sequences, is linked to genomic instability, potentially leading to large-scale deletions and contributing to phenotypic diversity and evolutionary adaptation. In this study, we analyzed the density of Z-DNA-prone motifs of 154 avian genomes using the non-B DNA Motif Search Tool (nBMST). Our findings indicate a higher prevalence of Z-DNA motifs in promoter regions across all avian species compared to other genomic regions. A negative correlation was observed between Z-DNA density and developmental time in birds, suggesting that species with shorter developmental periods tend to have higher Z-DNA densities. This relationship implies that Z-DNA may influence the timing and regulation of development in avian species. Furthermore, Z-DNA density showed associations with traits such as body mass, egg mass, and genome size, highlighting the complex interactions between genome architecture and phenotypic characteristics. Gene Ontology (GO) analysis revealed that Z-DNA motifs are enriched in genes involved in nucleic acid binding, kinase activity, and translation regulation, suggesting a role in fine-tuning gene expression essential for cellular functions and responses to environmental changes. Additionally, the potential of Z-DNA to drive genomic instability and facilitate adaptive evolution underscores its importance in shaping phenotypic diversity. This study emphasizes the role of Z-DNA as a dynamic genomic element contributing to gene regulation, genomic stability, and phenotypic diversity in avian species. Future research should experimentally validate these associations and explore the molecular mechanisms by which Z-DNA influences avian biology. |
| format | Artículo científico |
| id | pubmed_39573987 |
| institution | PubMed |
| language | en |
| publishDate | 2024 |
| publisher | BMC genomics |
| record_format | pubmed |
| spellingShingle | A comprehensive study of Z-DNA density and its evolutionary implications in birds. Wang, Yu-Ren Chang, Shao-Ming Lin, Jinn-Jy Chen, Hsiao-Chian Lee, Lo-Tung Tsai, Dien-Yu Lee, Shih-Da Lan, Chung-Yu Chang, Chuang-Rung Chen, Chih-Feng Ng, Chen Siang Animals Birds Evolution, Molecular DNA, Z-Form Genome Nucleotide Motifs Genomics Promoter Regions, Genetic Base Composition A comprehensive study of Z-DNA density and its evolutionary implications in birds. Wang, Yu-Ren Chang, Shao-Ming Lin, Jinn-Jy Chen, Hsiao-Chian Lee, Lo-Tung Tsai, Dien-Yu Lee, Shih-Da Lan, Chung-Yu Chang, Chuang-Rung Chen, Chih-Feng Ng, Chen Siang Animals Birds Evolution, Molecular DNA, Z-Form Genome Nucleotide Motifs Genomics Promoter Regions, Genetic Base Composition Z-DNA, a left-handed helical form of DNA, plays a significant role in genomic stability and gene regulation. Its formation, associated with high GC content and repetitive sequences, is linked to genomic instability, potentially leading to large-scale deletions and contributing to phenotypic diversity and evolutionary adaptation. In this study, we analyzed the density of Z-DNA-prone motifs of 154 avian genomes using the non-B DNA Motif Search Tool (nBMST). Our findings indicate a higher prevalence of Z-DNA motifs in promoter regions across all avian species compared to other genomic regions. A negative correlation was observed between Z-DNA density and developmental time in birds, suggesting that species with shorter developmental periods tend to have higher Z-DNA densities. This relationship implies that Z-DNA may influence the timing and regulation of development in avian species. Furthermore, Z-DNA density showed associations with traits such as body mass, egg mass, and genome size, highlighting the complex interactions between genome architecture and phenotypic characteristics. Gene Ontology (GO) analysis revealed that Z-DNA motifs are enriched in genes involved in nucleic acid binding, kinase activity, and translation regulation, suggesting a role in fine-tuning gene expression essential for cellular functions and responses to environmental changes. Additionally, the potential of Z-DNA to drive genomic instability and facilitate adaptive evolution underscores its importance in shaping phenotypic diversity. This study emphasizes the role of Z-DNA as a dynamic genomic element contributing to gene regulation, genomic stability, and phenotypic diversity in avian species. Future research should experimentally validate these associations and explore the molecular mechanisms by which Z-DNA influences avian biology. |
| title | A comprehensive study of Z-DNA density and its evolutionary implications in birds. |
| topic | Animals Birds Evolution, Molecular DNA, Z-Form Genome Nucleotide Motifs Genomics Promoter Regions, Genetic Base Composition |
| url | https://pubmed.ncbi.nlm.nih.gov/39573987/ |