Luo Yi, Zhai Hang, Zhong Xiu, Yang Bo, Xu Yang, Liu Tianhong, Wang Qi, Zhou Yang, Mao Yan, Liu Yaxi, Tang Qi, Lu Yanli, Wang Yao, Xu Jie
Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
BMC Genomics. 2025 Jan 20;26(1):46. doi: 10.1186/s12864-025-11221-9.
Conserved non-coding sequences (CNS) are islands of non-coding sequences conserved across species and play an important role in regulating the spatiotemporal expression of genes. Identification of CNS provides valuable information about potentially functional genomic elements, regulatory regions, and helps to gain insights into the genetic basis of crop agronomic traits.
Here, we comprehensively analyze CNS in maize, by comparing the genomes of maize inbred line B73 (Zea mays ssp. mays), its close wild relative Zea mays spp. mexicana, and other grasses in Poaceae, including sorghum (Sorghum bicolor), foxtail millet (Setaria italica) and two adlay (Coix lacryma) cultivars. There were 289,931 CNS found in two syntenic gene pairs, while 51,701 CNS were conserved within at least three species. To explore the regulatory characteristics of the CNS identified, the flanking regions of CNS were compared with the peaks called using both transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) data of histone modifications. It was found that CNS in maize were enriched in open chromatin regions compared with randomly selected non-coding regions of similar length. A significant enrichment of transcription factor binding sites was found within CNS sequences, including different transcription factors involved in abiotic stress response, such as OBP (OBF-BINDING PROTEIN) family and Adof1 (Encodes dof zinc finger protein). To investigate the epigenetic modification patterns in CNS, ChIP-Seq data for histone modifications H3K9ac, H3K4me3, H3K36me3, H3K9me3, and H3K27ac were further analyzed to depict the changes along CNS. Our findings revealed significantly elevated levels of transcription-promoting histone modifications in the CNS regions compared to randomly selected non-coding sequences with an equal number and similar length. Notably, CNS were also identified on both Vgt1 (Vegetative to generative transition 1) and ZmCCT10. In addition, CNS with potential functions were identified based on SNPs within CNS significantly associated with various agronomic traits in maize, which holds potential utility in molecular breeding for maize.
In summary, we identified and characterized CNS in maize through genomic comparative analysis, which provides valuable insights into their potential regulatory effects on gene expression and phenotypic variation.
保守非编码序列（CNS）是跨物种保守的非编码序列区域，在调控基因的时空表达中发挥重要作用。鉴定CNS可为潜在的功能基因组元件、调控区域提供有价值的信息，并有助于深入了解作物农艺性状的遗传基础。
在此，我们通过比较玉米自交系B73（玉米 Zea mays ssp. mays）、其近缘野生种玉米 Zea mays spp. mexicana以及禾本科其他禾本科植物（包括高粱（Sorghum bicolor）、谷子（Setaria italica）和两个薏苡（Coix lacryma）品种）的基因组，全面分析了玉米中的CNS。在两个同线基因对中发现了289,931个CNS，而在至少三个物种中保守的CNS有51,701个。为了探究所鉴定的CNS的调控特征，将CNS的侧翼区域与使用转座酶可及染色质高通量测序（ATAC-seq）和组蛋白修饰染色质免疫沉淀高通量测序（ChIP-Seq）数据所调用的峰进行了比较。结果发现，与随机选择的长度相似的非编码区域相比，玉米中的CNS富集于开放染色质区域。在CNS序列中发现转录因子结合位点显著富集，包括参与非生物胁迫响应的不同转录因子，如OBP（OBF结合蛋白）家族和Adof1（编码dof锌指蛋白）。为了研究CNS中的表观遗传修饰模式，进一步分析了组蛋白修饰H3K9ac、H3K4me3、H3K36me3、H3K9me3和H3K27ac的ChIP-Seq数据，以描绘沿CNS的变化。我们的研究结果表明，与随机选择的数量相等且长度相似的非编码序列相比，CNS区域中促进转录的组蛋白修饰水平显著升高。值得注意的是，在Vgt1（营养生长向生殖生长转变1）和ZmCCT10上也鉴定出了CNS。此外，基于与玉米各种农艺性状显著相关的CNS内的单核苷酸多态性（SNP）鉴定出了具有潜在功能的CNS，这在玉米分子育种中具有潜在应用价值。
总之，我们通过基因组比较分析鉴定并表征了玉米中的CNS，这为它们对基因表达和表型变异的潜在调控作用提供了有价值的见解。
