China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, China.
Center for Agroforestry Mega Data Science and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
BMC Genomics. 2018 Oct 4;19(1):730. doi: 10.1186/s12864-018-5103-1.
The majority of eukaryote genomes can be actively transcribed into non-coding RNAs (ncRNAs), which are functionally important in development and evolution. In the study of maize, an important crop for both humans and animals, aside from microRNAs and long non-coding RNAs, few studies have been conducted on intermediate-size ncRNAs.
We constructed a homogenized cDNA library of 50-500 nt RNAs in the maize inbred line Chang 7-2. Sequencing revealed 169 ncRNAs, which contained 58 known and 111 novel ncRNAs (including 70 snoRNAs, 27 snRNAs, 13 unclassified ncRNAs and one tRNA). Forty of the novel ncRNAs were specific to the Panicoideae, and 24% of them are located on sense-strand of the 5' or 3' terminus of protein coding genes on chromosome. Target site analysis found that 22 snoRNAs can guide to 38 2'-O-methylation and pseudouridylation modification sites of ribosomal RNAs and small nuclear RNAs. Expression analysis showed that 43 ncRNAs exhibited significantly altered expression in different tissues or developmental stages of maize seedlings, eight ncRNAs had tissue-specific expression and five ncRNAs were strictly accumulated in the early stage of leaf development. Further analysis showed that 3 of the 5 stage-specific ncRNAs (Zm-3, Zm-18, and Zm-73) can be highly induced under drought and salt stress, while one snoRNA Zm-8 can be repressed under PEG-simulated drought condition.
We provided a genome-wide identification and functional analysis of ncRNAs with a size range of 50-500 nt in maize. 111 novel ncRNAs were cloned and 40 ncRNAs were determined to be specific to Panicoideae. 43 ncRNAs changed significantly during maize development, three ncRNAs can be strongly induced under drought and salt stress, suggesting their roles in maize stress response. This work set a foundation for further study of intermediate-size ncRNAs in maize.
真核生物基因组的大部分都能被转录为非编码 RNA（ncRNA），ncRNA 在生物的发育和进化中具有重要的功能。在玉米这一重要的人类和动物作物的研究中，除了 microRNA 和长链非编码 RNA 之外，对中等大小的 ncRNA 的研究较少。
我们构建了玉米自交系 Chang 7-2 的 50-500nt RNA 均一 cDNA 文库。测序揭示了 169 个 ncRNA，其中包含 58 个已知和 111 个新的 ncRNA（包括 70 个 snoRNA、27 个 snRNA、13 个未分类的 ncRNA 和一个 tRNA）。40 个新的 ncRNA 是 Panicoideae 特有的，其中 24%位于染色体上蛋白编码基因 5'或 3'末端的正义链上。靶位点分析发现，22 个 snoRNA 可以指导核糖体 RNA 和小核 RNA 的 38 个 2'-O-甲基化和假尿嘧啶化修饰位点。表达分析表明，43 个 ncRNA 在玉米幼苗的不同组织或发育阶段的表达发生了显著改变，8 个 ncRNA 具有组织特异性表达，5 个 ncRNA 在叶片发育的早期阶段严格积累。进一步分析表明，5 个发育阶段特异的 ncRNA（Zm-3、Zm-18 和 Zm-73）中的 3 个可以在干旱和盐胁迫下被高度诱导，而一个 snoRNA Zm-8 在 PEG 模拟的干旱条件下被抑制。
我们提供了玉米基因组中 50-500nt 大小范围的 ncRNA 的全基因组鉴定和功能分析。克隆了 111 个新的 ncRNA，其中 40 个是 Panicoideae 特有的。43 个 ncRNA 在玉米发育过程中发生了显著变化，3 个 ncRNA 在干旱和盐胁迫下可以被强烈诱导，提示它们在玉米胁迫反应中的作用。这项工作为进一步研究玉米中等大小的 ncRNA 奠定了基础。
