Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China.
Int J Mol Sci. 2023 Oct 10;24(20):15039. doi: 10.3390/ijms242015039.
Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was significantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modifications of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (mA), it was found that the enrichment of histone modifications associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These findings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress.
长链非编码 RNA（lncRNA）是长度超过 200nt 且具有有限蛋白编码潜力的转录本。它们被发现于植物应激反应中发挥重要作用。在这项研究中，选择了耐旱自交系 AC7643 和敏感自交系 AC7729/TZSRW 及其重组自交系（RIL），以鉴定根中对干旱响应的 lncRNA。与非响应 lncRNA 相比，干旱响应 lncRNA 在基因长度和外显子数量上具有不同的序列特征。受干旱诱导的下调 lncRNA 与编码基因的比例显著更高；并且 lncRNA 在 RIL 中的重组位点更广泛地表达。此外，通过整合 DNA 5-甲基胞嘧啶（5mC）、组蛋白和 RNA N6-甲基腺苷（mA）的修饰，发现与产生 lncRNA 的基因相关的转录激活的组蛋白修饰的富集程度低于编码基因。构建了 lncRNA-mRNA 共表达网络，包含 15340 个编码基因和 953 个 lncRNA，以研究 lncRNA 的分子功能。发现有 13 个模块与干旱下的存活率相关。我们在与干旱下植物存活相关的模块中发现了九个位于 lncRNA 中的 SNPs。总之，我们通过多组学研究揭示了玉米根中响应干旱的 lncRNA 的特征。这些发现丰富了我们对干旱下 lncRNA 的理解，并阐明了非编码 RNA 响应干旱胁迫时协调的复杂调控网络。
