Splicing conservation signals in plant long noncoding RNAs

Abstract

Long 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.

A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs

“…Therefore, other features independent of the integrity of transcripts, such as MLCDS (the most-like coding domain sequence) and k-mers, were applied in lncRNA identification. In addition, lncRNA shows a distinct difference from mRNA in terms of sequence conservation, which can be measured from multiple sequence alignments (Corona-Gomez et al 2020). In brief, the exons of lncRNAs are far less conserved than the exons of mRNAs (Ulitsky 2016;Hon et al 2017).…”

Heavy metal stress in rice: Uptake, transport, signaling, and tolerance mechanisms

“…These lncRNAs are enriched in certain QTLs (Quantitative Trait Loci) containing genes regulating stress‐receptive pathways (Yuan et al, 2018). lncRNAs have important roles in the modulation of nutrient uptake, growth and development of plants, adaptation of resistance capability against disease and various environmental stresses, regulating some biological activities via modification of histone and chromatin disposition in plants (Corona‐Gomez et al, 2020; Nejat & Mantri 2018; Sun et al, 2020). Chen, Shi, et al (2018) demonstrated that lncRNAs regulate the expression of genes related to various amino acids metabolic pathways (phenylalanine, methionine, and cysteine), photosynthetic metabolism, and phenylpropanoids metabolic pathways to reduce the cadmium toxicity in rice.…”

Comparative genomics in the search for conserved long noncoding RNAs

“…MaxEntScan is based on maximum entropy distribution and is considered to offer the most unbiased approximation for modeling short sequence motifs [49]. Remarkably, it considers dependencies between both nonadjacent and adjacent positions and is used extensively in analyses of lncRNA splice-site conservation [50][51][52]. One such study was performed on vertebrate lncRNAs [50], in which multiple sequence alignment together with transcriptomics data were utilized to determine the homologous positions in splice sites, leading to the construction of a comparative map of splice sites.…”

“…The authors showed that in conserved human transcripts, 87% of splice sites are present in other species, including mice, rats, cows, and dogs, yet most of the novel splice sites originated during primate evolution. MaxEntScan has also been used in recent studies on lncRNA splicing conservation in 16 Brassica species [ 52 ]. These studies revealed that nearly 18% of lincRNAs display splicing conservation in at least one exon in Brassicaceae plant family members.…”