Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan.
National Center for High-performance Computing, National Applied Research Laboratories, Hsinchu, 300092, Taiwan.
BMC Genomics. 2024 Nov 21;25(1):1123. doi: 10.1186/s12864-024-11039-x.
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.
Z-DNA 是一种左手螺旋的 DNA 形式，在基因组稳定性和基因调控中发挥着重要作用。它的形成与高 GC 含量和重复序列有关，与基因组不稳定性有关，可能导致大规模缺失，并有助于表型多样性和进化适应。
在这项研究中，我们使用非 B DNA 基序搜索工具（nBMST）分析了 154 种鸟类基因组中 Z-DNA 倾向基序的密度。我们的研究结果表明，与其他基因组区域相比，所有鸟类物种的启动子区域中 Z-DNA 基序的出现频率更高。我们观察到 Z-DNA 密度与鸟类发育时间之间存在负相关关系，这表明发育时间较短的物种具有较高的 Z-DNA 密度。这种关系表明，Z-DNA 可能影响鸟类物种的发育时间和调控。此外，Z-DNA 密度与身体质量、蛋重和基因组大小等特征相关，突出了基因组结构与表型特征之间的复杂相互作用。基因本体论（GO）分析表明，Z-DNA 基序在参与核酸结合、激酶活性和翻译调节的基因中富集，这表明 Z-DNA 在精细调节细胞功能和对环境变化做出反应所必需的基因表达中发挥作用。此外，Z-DNA 驱动基因组不稳定性和促进适应性进化的潜力突显了其在塑造表型多样性方面的重要性。
本研究强调了 Z-DNA 作为一种动态基因组元件在调节基因表达、基因组稳定性和表型多样性方面的作用，有助于鸟类物种的进化。未来的研究应该通过实验验证这些关联，并探索 Z-DNA 影响鸟类生物学的分子机制。
