Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development

Abstract

Long non-coding RNAs (lncRNAs) have been reported to be involved in the development of maize plant. However, few focused on seed development of maize. Here, we identified 753 lncRNA candidates in maize genome from six seed samples. Similar to the mRNAs, lncRNAs showed tissue developmental stage specific and differential expression, indicating their putative role in seed development. Increasing evidence shows that crosstalk among RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in plant development. Functional roles and regulatory mechanisms of lncRNAs as competing endogenous RNAs (ceRNA) in plants, particularly in maize seed development, are unclear. We combined analyses of consistently altered 17 lncRNAs, 840 mRNAs and known miRNA to genome-wide investigate potential lncRNA-mediated ceRNA based on “ceRNA hypothesis”. The results uncovered seven novel lncRNAs as potential functional ceRNAs. Functional analyses based on their competitive coding-gene partners by Gene Ontology (GO) and KEGG biological pathway demonstrated that combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in maize seed. These findings provided a useful platform for uncovering novel mechanisms of maize seed development and may provide opportunities for the functional characterization of individual lncRNA in future studies.

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

“…For example, Xu et al 32 constructed a ceRNA network to explain the function of lncRNAs in phosphate starvation of rice. Zhu et al 33 reported a complex ceRNA network consisting of lncRNAs, mRNAs, and miRNAs in maize seed development. A large number of circRNAs was found in the ethylene pathway of tomato, possibly acting as ceRNAs 69 .…”

“…CircRNAs are a class of endogenous, covalently closed, circular RNAs generated by alternative circularization [30]. Increasing numbers of studies in animals, humans, and plants have proved that lncRNAs and circRNAs can act as competing endogenous RNAs (ceRNAs) to regulate a wide range of biological and developmental processes [31][32][33][34][35][36][37]. CeRNAs, including mRNAs, lncRNAs, circRNAs, and pseudogenes, are the transcripts that can competitive bind common miRNA response elements (MREs), and which are also named miRNA sponges to sequester specific miRNAs and suppress their function [30,31,34,35].…”

Computational mapping of the differentially expressed gene-lncRNA pairs present at the root nodule developmental stages of Arachis hypogaea

“…LncRNAs show the response to external and internal stimuli [17] and have the role in the tissue development in the plants [18]. Genome-wide computational techniques are • Ahsan Z. Rizvi is with Institute of Human Genetics, CNRS, Montpellier,…”

Peer Review #2 of "Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus (v0.1)"

“…Due to the rapid advance of next-generation sequencing (NGS) techniques and bioinformatics tools, a large number of lncRNAs have been identified from various organisms such as animals and plants (Sun et al 2017b). However, lncRNAs have been identified in a limited number of plant species such as Arabidopsis thaliana, medicago, potato, rice, strawberry, tomato (Solanum lycopersicum), and maize (Guo & Liu 2017;Kang et al 2017;Nejat & Mantri 2017;Scarano et al 2017;Zheng et al 2017;Zhu et al 2017). Furthermore, studies revealing functional roles of identified lncRNAs in plants are rare.…”