文献类型： 外文期刊

作者： He, Zexue ¹ ; Run, Yonghang ¹ ; Feng, Yilong ¹ ; Yang, Ying ¹ ; Tavakoli, Mahmoud ¹ ; Ahmed, Asgar ¹ ; Ariel, Federico ⁴ ; Zhang, Wenli ¹ ;

作者机构： 1.Nanjing Agr Univ, CIC MCP, State Key Lab Crop Genet & Germplasm Enhancement &, Nanjing, Jiangsu, Peoples R China

2.Ningxia Acad Agr & Forestry Sci, Key Lab Agr Biotechnol Ningxia, Yinchuan, Peoples R China

3.Bangladesh Wheat & Maize Res Inst BWMRI, Dinajpur, Bangladesh

4.Univ Buenos Aires UBA, Fac Ciencias Exactas & Nat, Buenos Aires, Argentina

5.UBA, CONICET, Inst Fisiol Biol Mol & Neurociencias IFIBYNE, Buenos Aires, Argentina

关键词： Z-DNA; genomic and epigenetic features; gene transcription; TEs; rice

期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：10.5； 五年影响因子：12.4 ）

ISSN： 1467-7644

年卷期： 2025 年 23 卷 4 期

页码：

收录情况： SCI

摘要： Z-DNA is a left-handed double helix form of DNA that is believed to be involved in various DNA transactions. However, comprehensive investigations aimed at global profiling of Z-DNA landscapes are still missing in both humans and plants. We here report the development of two techniques: anti-Z-DNA antibody-based immunoprecipitation followed by sequencing (ZIP-seq), and cleavage under targets and tagmentation (CUT&TAG) for characterizing Z-DNA in nipponbare rice (Oryza sativa L., Japonica). We found that Z-DNA-IP+ (Z-DNA recognized by the antibody) exhibits distinct genomic features as compared to Z-DNA-IP- (Z-DNA not recognized by the antibody). The concomitant presence of G-quadruplexes (G4s) and i-motifs (iMs) may promote Z-DNA formation. DNA modifications such as DNA-6mA/-4acC generally disfavours Z-DNA formation, while modifications like DNA-5mC (CHH) and 8-oxodG promote it, highlighting the distinct roles of DNA base modifications in modulating Z-DNA formation. Importantly, Z-DNA located at transcription start sites (TSSs) enhances gene expression, whereas Z-DNA in genic regions represses it, underscoring its dual roles in regulating the expression of genes involved in fundamental biological functions and responses to salt stress. Furthermore, Z-DNA may play a role in transcriptional initiation and termination rather than in transcriptional elongation. Finally, the presence of Z-DNA in promoters is correlated with the coevolution of overlapping genes, thereby regulating gene domestication. Consequently, our study represents as a pivotal point and a solid foundation for reliably launching genome-wide investigations of Z-DNA, thereby advancing the understanding of Z-DNA biology in both plants and non-plant systems.