Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, 330045, Jiangxi Province, China.
Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang City, 330045, Jiangxi Province, China.
Plant Mol Biol. 2021 Apr;105(6):655-684. doi: 10.1007/s11103-021-01121-3. Epub 2021 Feb 11.
This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation-reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.
本研究系统鉴定了与水稻旗叶衰老相关的长非编码 RNA（lncRNA），为叶片衰老过程中 lncRNA-mRNA 调控关系和 lncRNA-miRNA-mRNA ceRNA 网络提供了可能。lncRNA 已被报道在多种生物学过程中发挥关键作用。然而，尚未有研究系统地鉴定与植物叶片衰老相关的 lncRNA。在本研究中，我们使用来自正常衰老的水稻旗叶进行了全基因组高通量测序分析。共鉴定到 3953 个 lncRNA 和 38757 个 mRNA，其中 343 个 lncRNA 和 9412 个 mRNA 差异表达。通过加权基因共表达网络分析（WGCNA），我们认为 22 个连续下调的 lncRNA 靶向 812 个共表达的 mRNA，以及 48 个连续上调的 lncRNA 靶向 1209 个共表达的 mRNA，与旗叶衰老显著相关。GO 结果表明，与衰老相关的 lncRNA 靶向的 mRNAs 涉及许多生物学过程，包括转录、激素反应、氧化还原过程和物质代谢。此外，43 个与衰老相关的 lncRNA 被预测靶向 111 个共表达的转录因子。有趣的是，8 个下调的 lncRNA 和 29 个上调的 lncRNA 分别靶向 12 个和 20 个研究充分的衰老相关基因（SAG）。此外，对竞争性内源 RNA（CeRNA）网络的分析表明，6 个下调的 lncRNA 可能通过 15 个 miRNA 调控 51 个共表达的 mRNAs，14 个上调的 lncRNA 可能通过 21 个 miRNA 调控 117 个共表达的 mRNAs。重要的是，通过表达验证，发现保守的 miR164-NAC 调控途径可能参与叶片衰老，其中 lncRNA MSTRG.62092.1 可能作为 ceRNA 与 miR164a 和 miR164e 结合，调控三个转录因子。两个关键的 lncRNA MSTRG.31014.21 和 MSTRG.31014.36 也可以通过 osa-miR5809 调节 ABA 生物合成基因 BGIOSGA025169（OsNCED4）和 BGIOSGA016313（NAC 家族）。讨论了涉及叶片衰老的 lncRNA 的可能调控网络，并推荐了几个候选 lncRNA 进行转基因分析。这些发现将扩展对 lncRNA 在叶片衰老中调控作用的理解，并为候选 lncRNA 的功能研究奠定基础。
