PceRBase: a database of plant competing endogenous RNA

Yuan, Chunhui; Meng, Xianwen; Li, Xue; Illing, Nicola; Ingle, Robert A.; Wang, Jingjing; Chen, Ming

doi:10.1093/nar/gkw916

Cited by 54 publications

(43 citation statements)

References 45 publications

(62 reference statements)

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“…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).…”

Section: Introductionmentioning

confidence: 99%

Splicing conservation signals in plant long non-coding RNAs

Corona-Gómez

Garcia-Lopez

Stadler

2019

Preprint

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AbstractLong non-coding RNAs (lncRNAs) have recently emerged as prominent regulators of gene expression in eukaryotes. LncRNAs often drive the modification and maintenance of gene activation or gene silencing states via chromatin conformation rearrangements. In plants, lncRNAs have been shown to participate in gene regulation, and are essential to processes such as vernalization and photomorphogenesis. Despite their prominent functions only over a dozen lncRNAs have been experimentally and functionally characterized.Similar to its animal counterparts, the rates of sequence divergence are much higher in plant lncRNAs than in protein coding mRNAs, making it difficult to identify lncRNA conservation using traditional sequence comparison methods. Beyond this, little is known about the evolutionary patterns of lncRNAs in plants. Here, we characterized the splicing conservation of lncRNAs in Brassicaceae. We generated a whole-genome alignment of 16 Brassica species and used it to identify synthenic lncRNA orthologues. Using a scoring system trained on transcriptomes from A. thaliana and B. oleracea, we identified splice sites across the whole alignment and measured their conservation. Our analysis revealed that 17.9% (112/627) of all intergenic lncRNAs display splicing conservation in at least one exon, an estimate that is substantially higher to previous estimates of lncRNA conservation in this group. Our findings agree with similar studies in vertebrates, demonstrating that splicing conservation can be evidence of stabilizing selection. We provide conclusive evidence for the existence of evolutionary deeply conserved lncRNAs in plants and describe a generally applicable computational workflow to identify functional lncRNAs in plants.

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Section: Introductionmentioning

confidence: 99%

Splicing conservation signals in plant long non-coding RNAs

Corona-Gómez

Garcia-Lopez

Stadler

2019

Preprint

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“…The computationally predicted ceRNAs can be further investigated and validated by biochemical methods. CeRNA-ceRNA network analysis, the emerging area of research can provide insights into normal and abnormal cell mechanism and in turn can assist in prediction of potential targets in therapeutics [76][77][78][79][80][81][82][83][84][85][86][87][88][89][90][91][92][93][94].…”

Section: Resultsmentioning

confidence: 99%

Review of Computational Prediction of Competing Endogenous RNA

Sherin¹,

Nair²

2019

J Proteomics Bioinform

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MicroRNAs (miRNAs) are the gene regulatory molecules that bind to microRNA response elements (MREs) in the 3' untranslated regions (UTRs) of mRNAs. The repressive activity of miRNA is counteracted by "miRNA sponges" or "competing endogenous RNAs (ceRNAs)" termed because of its competing nature of sequestering miRNA's effect. The ceRNAs with multiple MREs for a miRNA interact more, resulting in a regulatory gene network layer. The perturbation of ceRNA network causes various diseases including cancer. This discovery has increased the analysis of ceRNA interactions, networks and dynamics. Currently, a number of ceRNA-ceRNA interaction analysis and prediction tools are available online. This review focuses on computational prediction of mRNA-mRNA pairs acting as ceRNAs and its significance in RNA therapeutics. The computational prediction tools are compared with respect to the input data retrieved, features considered and the prediction method.

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“…19 The Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) contains potential ceRNAs, and ceRNA target-mimic pairs from 26 plant species. 17 lncRNAs potentially acting as ceRNAs of two key miRNAs, osa-miR156 and osa-miR396, were deduced and characterized in this study (Table 2). These two miRNAs regulate not only growth and development but also response to pathogen infection in plants.…”

Section: Discussionmentioning

confidence: 99%

“…15 Competing endogenous RNAs (ceRNAs) of miRNAs or miRNA target mimics have been shown to function in many biological processes through repression of miRNAs. 16,17 Plant ceRNAs can act as 'sponges' to sequester miRNAs complementary to ceRNAs resulting in unleashing miRNA targets mimics. 18,19 For instance, rice lncRNA XLOC_057324 is able to release more transcripts of the targets of miR160 and miR164 by decoying these two miRNAs.…”

Section: Introductionmentioning

confidence: 99%