Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Japan.
Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima, Japan.
Plant Cell Physiol. 2019 Sep 1;60(9):1961-1973. doi: 10.1093/pcp/pcz048.
Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.
长链非编码 RNA（lncRNA）在多种生物中基因表达的转录和转录后调控中发挥着关键作用。尽管植物基因组中已经鉴定出了数千种 lincRNA，但它们的功能仍大多未被阐明。在这里，我们报告了一个关于拟南芥对低营养条件反应的 lincRNA 的全基因组调查。我们使用了源自暴露于 12 种不同营养素低水平的拟南芥根的 RNA 测序数据。使用生物信息学方法，鉴定了 60 个差异表达的 lincRNA，这些 lincRNA在至少一种养分缺乏时显著上调或下调。为了阐明它们在养分反应中的作用，我们在 13 种条件下（12 种低养分条件和对照）检查了 lincRNA 和参考基因之间的表达模式相关性。这种分析允许我们鉴定具有高度正相关或负相关的 lincRNA-RNA 对。此外，计算这些对的相互作用能表明 lincRNA 可能作为调节相互作用因子发挥作用；例如，小干扰 RNA（siRNA）。其中，已知通过产生针对生长素反应因子 2、3 和 4 的 siRNA 促进侧根发育的反式作用 siRNA3（TAS3）被揭示为一种氮（N）响应性 lincRNA。此外，硝酸盐转运蛋白 2被鉴定为 TAS3 衍生的 siRNA 的潜在靶标，表明 TAS3 通过调节低 N 条件下的 N 转运和根系发育参与了多个途径。这项研究为植物中涉及多种养分反应的候选 lincRNA 提供了第一个资源。
