EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

Abstract

Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database. The first release of such a database (EVLncRNAs) was made using the literature prior to 1 May 2016. Since then (till 15 May 2020), 19 245 articles related to lncRNAs have been published. In EVLncRNAs 2.0, these articles were manually examined for a major expansion of the data collected. Specifically, the number of annotated EVlncRNAs, associated diseases, lncRNA-disease associations, and interaction records were increased by 260%, 320%, 484% and 537%, respectively. Moreover, the database has added several new categories: 8 lncRNA structures, 33 exosomal lncRNAs, 188 circular RNAs, and 1079 drug-resistant, chemoresistant, and stress-resistant lncRNAs. All records have checked against known retraction and fake articles. This release also comes with a highly interactive visual interaction network that facilitates users to track the underlying relations among lncRNAs, miRNAs, proteins, genes and other functional elements. Furthermore, it provides links to four new bioinformatics tools with improved data browsing and searching functionality. EVLncRNAs 2.0 is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/.

From “Dark Matter” to “Star”: Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

“…These fundamental studies are practically important because these lncRNAs are implicated in plant yield and quality and disease resistance. According to the current experimental identification technology, such as CRISPR/Cas9, RNAi, and loss and gain functions, the rate of functional lncRNA verified by the biological experiments is ~600 per year (Zhou et al, 2020 ). It will be a long journey to fully understand the role of the massive amount of potential functional lncRNAs in the living organisms.…”

“…The association between lncRNAs and small RNAs is perhaps the most reported relationship in plants. MicroRNAs (miRNAs) that FIGURE 1 | Statistics of the number of functional lncRNAs in top 10 plant species based on the experimentally validated functional lncRNAs in plants, according to EVLncRNA2.0 (Zhou et al, 2020).…”

“…If lncRNAs are calculated on the order of millions, there are more than 200,000 predicted functional lncRNAs based on predictions (Zhou et al, 2019 ). By comparison, only 506 functional lncRNAs in 56 plant species are curated in the database of EVLncRNAs2.0 (Zhou et al, 2020 ). The majority of these EVLncRNAs belong to the model plant Arabidopsis thaliana ( Figure 1 ).…”

“… Statistics of the number of functional lncRNAs in top 10 plant species based on the experimentally validated functional lncRNAs in plants, according to EVLncRNA2.0 (Zhou et al, 2020 ). …”

“…So far, only a small number of lncRNAs have been analyzed by the low-throughput biochemical and molecular biology functional assays. In fact, only 506 functional lncRNAs and 41 interactions of lncRNAs biomolecules in 56 plant species have been recorded in the recent update of the database for EVLncRNAs ( https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/ ) (Zhou et al, 2020 ). These data are only a tiny fraction of what can be possibly found.…”