Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development

Abstract

BackgroundLeaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to noncoding RNAs (ncRNAs). Moreover, increasing evidence indicates that an intricate interplay among RNA species, including protein-coding RNAs and ncRNAs, exists in eukaryotic transcriptomes, however, it remains elusive in plant leaves.ResultsWe detected novel ncRNAs, such as circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs), and further constructed and analyzed their associated competitive endogenous RNA (ceRNA) networks in Arabidopsis leaves. Transcriptome profiling showed extensive changes during leaf development. In addition, comprehensive detection of circRNAs in other plant leaves suggested that circRNAs are widespread in plant leaves. To investigate the complex post-transcriptional interactions in Arabidopsis leaves, we constructed a global circRNA/lncRNA-associated ceRNA network. Functional analysis revealed that ceRNAs were highly correlated with leaf development. These ceRNAs could be divided into six clusters, which were enriched for different functional classes. Stage-specific ceRNA networks were further constructed and comparative analysis revealed different roles of stage common and specific hub ceRNAs.ConclusionsOur results demonstrate that understanding the ceRNA interactions will lead insights into gene regulations implicated in leaf development.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4993-2) contains supplementary material, which is available to authorized users.

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). To assess the regulatory patterns of non-coding RNA-related ceRNA interactions in sweet sorghum roots, lncRNA-miRNA-mRNA pairs were predicted in the treated and control of M-81E and Roma samples.…”

“…Additionally, some natural antisense lncRNAs help regulate target gene expression (Swiezewski et al, 2009;Huanca-Mamani et al, 2018). Although ceRNAs have been well studied in animals (Qu et al, 2015;Meng et al, 2018), relatively little is known about ceRNAs in plants, beyond the current research on the associated regulatory mechanism.…”

Splicing conservation signals in plant long non-coding RNAs

“…Competing endogenous RNAs (ceRNAs) acts as "sponges" for miRNAs. In plants, ceRNAs are a large class of lncRNAs (Yuan et al, 2017;Paschoal et al, 2018) and form extensive regulatory networks (Meng et al, 2018;Zhang et al, 2018). The paradigmatic examples in A. thaliana is IPS1, which sequesters miR399 (Franco-Zorrilla et al, 2007).…”

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.…”

“…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].…”