Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber (Cucumis sativus L.)

Abstract

Researchers have shown that long non‐coding RNAs (lncRNAs) and circular RNAs (circRNAs) act as competitive endogenous RNAs (ceRNAs) and are mutually regulated by competition for binding to common microRNA response elements (MREs). However, a comprehensive identification and analysis of lncRNAs and circRNAs as ceRNAs have not yet been completed in cucumber (Cucumis sativus L.) exposed to high‐temperature stress. In our study, 32 663 coding transcripts, 2085 lncRNAs, 2477 circRNAs and 348 differentially expressed miRNAs were identified using RNA sequencing. In addition, six heat‐stress‐responsive miRNAs (five known and one novel miRNAs) and eight lncRNAs were selected for qPCR to confirm their expression profiles. By analyzing the cis effects of lncRNAs, we constructed a lncRNA‐mRNA co‐expression network. Based on the results, the corresponding lncRNAs play a regulatory role in the stress response in cucumber plants. In our study, the PatMatch software was used to predict the potential function of lncRNAs and circRNAs as ceRNAs. A total of 18 lncRNAs and seven circRNAs were predicted to bind to 114 differentially expressed miRNAs and compete with 359 mRNAs for miRNA binding sites. These mRNAs are predicted to be involved in various pathways, such as plant hormone signal transduction, plant–pathogen interaction and glutathione metabolism. Among them, TCONS_00031790, TCONS_00014332, TCONS_00014717, TCONS_00005674, novel_circ_001543 and novel_circ_000876 may interact with miR9748 by plant hormone signal transduction pathways in response to high‐temperature stress. Moreover, indole‐3‐acetic acid (IAA) and 1‐aminocyclopropane‐l‐carboxylic acid (ACC) levels decreased in the high‐temperature treatment group, indicating that IAA and ethylene signaling might be involved in response to high‐temperature stress. In this study, we conducted a full transcriptomic analysis in response to high‐temperature stress in cucumber and, for the first time, integrated the potential ceRNA functions of lncRNAs/circRNAs. The results provide a basis for studying the potential functions of lncRNAs/circRNAs in response to high‐temperature stress.

Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum

“…Previous studies proved that lncRNAs can function as ceRNAs and regulate gene expression at the post-transcriptional level He et al, 2019). Additionally, lncRNAs serve as target mimics that interact with miRNAs thereby preventing miRNAs from completely degrading their targets (Wu et al, 2013;Deng et al, 2018;Meng et al, 2018).…”

Construction of a ceRNA regulatory network in Ziyang xiangcheng (Citrus junos Sieb. ex Tanaka) based on whole-genome transcriptome profiling of mRNAs, lncRNAs, miRNAs and circRNAs under Cu toxicity

“…A large number of circRNAs was found in the ethylene pathway of tomato, possibly acting as ceRNAs 69 . Recently, a ceRNA network was also reported in A. thaliana leaf development, tomato flowering, and cucumber heat stress 35,37,39,57 . Our study constructed a possible ceRNA regulatory network in response to citrus Cu toxicity, which described the global molecular network among mRNAs, miRNAs, and lncRNAs.…”

“…A survey of 10 plants by Deng et al 56 found that the number of lncRNAs varied from 2986 (A. thaliana) to 18031 (maize). Moreover, He et al 57 identified 2085 lncRNAs in cucumber, and Feng et al 58 identified 2546 lncRNAs in Brassica napus. The number of lncRNAs often ranges from thousands to tens of thousands in plants 55 .…”

Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development

“…Currently, ceRNET is mainly used to solve human cancer treatment, among which the typical representative is the construction of PTEN's ceRNET. In addition, ceRNET has also been applied to explore biological characteristics in animal and plant research (Qiu et al, 2018;Bai et al, 2019;He et al, 2019;Li et al, 2019;Wang et al, 2019a). It is reasonable to hypothesized that ceRNET would be an exactly effective methods to reflect the complete and accurate regulate process of the antler rapidly development.…”