State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China.
ICARDA-NWSUAF Joint Research Center, Yangling 712100, China.
Int J Mol Sci. 2022 Jan 26;23(3):1405. doi: 10.3390/ijms23031405.
RNA/DNA difference (RDD) is a post-transcriptional RNA modification to enrich genetic information, widely involved in regulating diverse biological processes in eukaryotes. RDDs in the wheat nuclear genome, especially those associated with drought response or tolerance, were not well studied up to now. In this study, we investigated the RDDs related to drought response based on the RNA-seq data of drought-stressed and control samples in wheat. In total, 21,782 unique RDDs were identified, of which 265 were found to be drought-induced, representing the first drought-responsive RDD landscape in the wheat nuclear genome. The drought-responsive RDDs were located in 69 genes, of which 35 were differentially expressed under drought stress. Furthermore, the effects of RNA/DNA differences were investigated, showing that they could result in changes of RNA secondary structure, miRNA-target binding as well as protein conserved domains in the RDD-containing genes. In particular, the A to C mutation in TraesCS2A02G053100 (orthology to ) led to the loss of tae-miR9657b-5p targeting, indicating that RNA/DNA difference might mediate miRNA to regulate the drought-response process. This study reported the first drought-responsive RDDs in the wheat nuclear genome. It sheds light on the roles of RDD in drought tolerance, and may also contribute to wheat genetic improvement based on epi-transcriptome methods.
RNA/DNA 差异（RDD）是一种转录后 RNA 修饰，可丰富遗传信息，广泛参与真核生物多种生物过程的调控。小麦核基因组中的 RDD，尤其是那些与干旱响应或耐受相关的 RDD，到目前为止还没有得到很好的研究。在本研究中，我们基于小麦干旱胁迫和对照样本的 RNA-seq 数据，研究了与干旱响应相关的 RDD。总共鉴定出 21782 个独特的 RDD，其中 265 个被发现是干旱诱导的，这代表了小麦核基因组中第一个干旱响应的 RDD 景观。干旱响应的 RDD 位于 69 个基因中，其中 35 个在干旱胁迫下表达差异。此外，还研究了 RNA/DNA 差异的影响，表明它们可能导致 RDD 含基因中 RNA 二级结构、miRNA 靶标结合以及蛋白质保守结构域的变化。特别是，TraesCS2A02G053100（与同源）中的 A 到 C 突变导致 tae-miR9657b-5p 靶向的丧失，表明 RNA/DNA 差异可能通过 miRNA 来调节干旱响应过程。本研究报道了小麦核基因组中第一个干旱响应的 RDD。它揭示了 RDD 在耐旱性中的作用，并且也可能为基于 epi-transcriptome 方法的小麦遗传改良做出贡献。
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