全基因组环状 RNA 谱分析和竞争性内源性 RNA 调控网络分析为龙眼早期体细胞胚胎发生的分子机制提供了新的见解。

Genome-wide circular RNA profiling and competing endogenous RNA regulatory network analysis provide new insights into the molecular mechanisms underlying early somatic embryogenesis in Dimocarpus longan Lour.

机构信息

Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China.

Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France.

出版信息

Tree Physiol. 2022 Sep 8;42(9):1876-1898. doi: 10.1093/treephys/tpac032.

DOI:10.1093/treephys/tpac032

PMID:35313353

Abstract

Circular RNAs (circRNAs) are widely involved in plant growth and development. However, the function of circRNAs in plant somatic embryogenesis (SE) remains elusive. Here, by using high-throughput sequencing, a total of 5029 circRNAs were identified in the three stages of longan (Dimocarpus longan Lour.) early SE. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed (DE) circRNA host genes were enriched in the 'non-homologous end-joining' (NHEJ) and 'butanoate metabolism' pathways. In addition, the reactive oxygen species (ROS) content during longan early SE was determined. The results indicated that ROS-induced DNA double-strand breaks may not depend on the NHEJ repair pathway. Correlation analyses of the levels of related metabolites (glutamate, γ-aminobutyrate and pyruvate) and the expression levels of circRNAs and their host genes involved in butanoate metabolism were performed. The results suggested that circRNAs may act as regulators of the expression of cognate mRNAs, thereby affecting the accumulation of related compounds. A competing endogenous RNA (ceRNA) network of DE circRNAs, DE mRNAs, DE long noncoding RNAs (lncRNAs) and DE microRNAs (miRNAs) was constructed. The results showed that the putative targets of the noncoding RNA (ncRNAs) were significantly enriched in the KEGG pathways 'mitogen-activated protein kinase signaling' and 'nitrogen metabolism'. Furthermore, the expression patterns of the candidate circRNAs, lncRNAs, miRNAs and mRNAs confirmed the negative correlation between miRNAs and ceRNAs. In addition, two circRNA overexpression vectors were constructed to further verify the ceRNA network correlations in longan early SE. Our study revealed the potential role of circRNAs in longan early SE, providing new insights into the intricate regulatory mechanism underlying plant SE.

摘要

环状 RNA（circRNAs）广泛参与植物的生长和发育。然而，circRNAs 在植物体细胞胚胎发生（SE）中的功能仍然难以捉摸。在这里，通过高通量测序，在龙眼早期 SE 的三个阶段共鉴定出 5029 个 circRNAs。京都基因与基因组百科全书（KEGG）分析表明，差异表达（DE）circRNA 宿主基因富集在“非同源末端连接”（NHEJ）和“丁酸代谢”途径中。此外，还确定了龙眼早期 SE 过程中的活性氧（ROS）含量。结果表明，ROS 诱导的 DNA 双链断裂可能不依赖于 NHEJ 修复途径。对与丁酸代谢相关的相关代谢物（谷氨酸、γ-氨基丁酸和丙酮酸）的水平以及 circRNAs 及其宿主基因的表达水平进行了相关分析。结果表明，circRNAs 可能作为同源 mRNA 表达的调节剂，从而影响相关化合物的积累。构建了 DE circRNAs、DE mRNAs、DE 长非编码 RNA（lncRNA）和 DE 微小 RNA（miRNA）的竞争性内源 RNA（ceRNA）网络。结果表明，ncRNA 的假定靶标在 KEGG 途径“丝裂原活化蛋白激酶信号”和“氮代谢”中显著富集。此外，候选 circRNAs、lncRNA、miRNA 和 mRNA 的表达模式证实了 miRNA 和 ceRNA 之间的负相关关系。此外，构建了两个 circRNA 过表达载体，以进一步验证龙眼早期 SE 中的 ceRNA 网络相关性。我们的研究揭示了 circRNAs 在龙眼早期 SE 中的潜在作用，为植物 SE 复杂的调控机制提供了新的见解。