Elucidating circRNA-miRNA-mRNA competing endogenous regulatory RNA network during leaf rust pathogenesis in wheat (Triticum aestivum L.)

IF 3.9 4区生物学 Q1 GENETICS & HEREDITY

Functional & Integrative Genomics Pub Date : 2025-01-16 DOI:10.1007/s10142-024-01520-x

Umang Kumar Dhandhanya, Uzma Afreen, Shailendra Kumar Jha, Kunal Mukhopadhyay, Manish Kumar

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引用次数: 0

Abstract

Advancements in bioinformatic tools and breakthroughs in high throughput RNA sequencing have unveiled the potential role of non-coding RNAs in influencing the overall expression of disease-responsive genes. Owing to the increasing need to develop resilient crop varieties against environmental constraints, our study explores the functional relationship of various non-coding RNAs in wheat during leaf rust pathogenesis. MicroRNAs (miRNAs) and circular RNAs (circRNAs) were retrieved from SAGE and RNA-Seq libraries, respectively, in the susceptible (HD2329) and resistant (HD2329 + Lr28) wheat Near-Isogenic Lines (NILs). Here we explored the previously published circRNAs for their differential expression and correlated the data with the differentially expressed miRNAs (DEMs) through various in silico methods to acquire the target miRNAs of circRNAs and the downstream target mRNAs of miRNAs. Finally, a competing endogenous RNA (ceRNAs) regulatory network was constructed and validated through RT-qPCR method. We have identified the ceRNA regulatory network of four differentially expressed circRNAs (DECs) and five DEMs to highlight their crucial roles in the robust enhancement of the temporal expression profiles of five defense responsive genes (mRNAs) in wheat NILs against leaf rust infection. The study confirms the synergistic expression of circRNAs and mRNAs with an antagonistic correlation with the expression profile of the corresponding miRNAs. The vital role of leaf rust-resistant gene Lr28 has also been highlighted for driving the efficiency of the circRNAs to upregulate target gene expression. Thus, understanding the circRNA-miRNA-target gene interaction during leaf rust pathogenesis can help to identify stress-specific regulatory biomarkers to enhance defense responses in wheat for improved resilience through multi-omics integration of transcriptomics, proteomics and metabolomics.

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小麦叶锈病发病机制中circRNA-miRNA-mRNA竞争内源调控RNA网络的研究

生物信息学工具的进步和高通量RNA测序的突破揭示了非编码RNA在影响疾病应答基因整体表达中的潜在作用。由于越来越需要开发抗环境约束的作物品种，我们的研究探索了小麦叶锈病发病过程中各种非编码rna的功能关系。从SAGE和RNA-Seq文库中分别检索易感（HD2329）和抗性（HD2329 + Lr28）小麦近等基因系（NILs）的MicroRNAs （miRNAs）和环状rna （circRNAs）。在这里，我们探索了之前发表的circRNAs的差异表达，并通过各种硅化方法将数据与差异表达的miRNAs （dem）相关联，以获得circRNAs的靶miRNAs和miRNAs的下游靶mrna。最后，构建了竞争性内源RNA （ceRNAs）调控网络，并通过RT-qPCR方法进行了验证。我们鉴定了4个差异表达环状rna （DECs）和5个差异表达环状rna （dem）的ceRNA调控网络，以突出它们在增强小麦NILs中5个防御应答基因（mrna）的时间表达谱中发挥的关键作用。该研究证实了circRNAs和mrna的协同表达与相应miRNAs的表达谱具有拮抗相关性。抗叶锈病基因Lr28的重要作用也被强调为驱动环状rna提高靶基因表达的效率。因此，了解叶锈病发病过程中circrna - mirna -靶基因的相互作用有助于通过转录组学、蛋白质组学和代谢组学的多组学整合，识别胁迫特异性调控生物标志物，增强小麦的防御反应，提高小麦的抗灾能力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Functional & Integrative Genomics 生物-遗传学

CiteScore

3.50

自引率

3.40%

发文量

审稿时长

2 months

期刊介绍： Functional & Integrative Genomics is devoted to large-scale studies of genomes and their functions, including systems analyses of biological processes. The journal will provide the research community an integrated platform where researchers can share, review and discuss their findings on important biological questions that will ultimately enable us to answer the fundamental question: How do genomes work?