Mining plant endogenous target mimics from miRNA-lncRNA interactions based on dual-path parallel ensemble pruning method.

The interactions between microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) play important roles in biological activities. Specially, lncRNAs as endogenous target mimics (eTMs) can bind miRNAs to regulate the expressions of target messenger RNAs (mRNAs). A growing number of studies focus on animals, but the studies on plants are scarce and many functions of plant eTMs are unknown. This study proposes a novel ensemble pruning protocol for predicting plant miRNA-lncRNA interactions at first. It adaptively prunes the base models based on dual-path parallel ensemble method to meet the challenge of cross-species prediction. Then potential eTMs are mined from predicted results. The expression levels of RNAs are identified through biological experiment to construct the lncRNA-miRNA-mRNA regulatory network, and the functions of potential eTMs are inferred through enrichment analysis. Experiment results show that the proposed protocol outperforms existing methods and state-of-the-art predictors on various plant species. A total of 17 potential eTMs are verified by biological experiment to involve in 22 regulations, and 14 potential eTMs are inferred by Gene Ontology enrichment analysis to involve in 63 functions, which is significant for further research.

Long noncoding RNA lncRNA354 functions as a competing endogenous RNA of miR160b to regulate ARF genes in response to salt stress in upland cotton.

Long non-coding RNAs (lncRNAs) play important roles in response to biotic and abiotic stress through acting as competing endogenous RNAs (ceRNAs) to decoy mature miRNAs. However, whether this mechanism is involved in cotton salt stress response remains unknown. We report the characterization of an endogenous lncRNA, lncRNA354, whose expression was reduced in salt-treated cotton and was localized at the nucleus and cytoplasm. Using endogenous target mimic (eTM) analysis, we predicted that lncRNA354 had a potential binding site for miR160b. Transient expression in tobacco demonstrated that lncRNA354 was a miR160b eTM and attenuated miR160b suppression of its target genes, including auxin response factors (ARFs). Silencing or overexpressing lncRNA354 affected the expression of miR160b and target ARFs. Silencing lncRNA354 and targets GhARF17/18 resulted in taller cotton plants and enhanced the resistant to salt stress. Overexpression of lncRNA354 and targets GhARF17/18 in Arabidopsis led to dwarf plants, decreased root dry weight and reduced salt tolerance. Our results show that the lncRNA354-miR160b effect on GhARF17/18 expression may modulate auxin signalling and thus affect growth. These results also shed new light on a mechanism of lncRNA-associated responses to salt stress.

Functions of long intergenic non-coding (linc) RNAs in plants.

Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants. Recent advances in RNA-seq and tiling microarray technologies have revealed the presence of many lincRNAs across plant species. This review focuses on the functions of lincRNAs that have been recently reported in plants. One of the most well characterized functions of lincRNAs is to epigenetically regulate gene expression by recruiting proteins for chromosome modification to specific loci. Second, lincRNAs are known to inhibit the physical interaction between microRNAs (miRNAs) and their target mRNAs thus controling protein levels of the target mRNAs. Lastly, lincRNAs control alternative splicing by binding and sequestering the proteins required for alternative splicing.

Transcript Profiling Analysis and ncRNAs' Identification of Male-Sterile Systems of Brassica campestris Reveal New Insights Into the Mechanism Underlying Anther and Pollen Development.

Male-sterile mutants are useful materials to study the anther and pollen development. Here, whole transcriptome sequencing was performed for inflorescences in three sterile lines of Chinese cabbage (Brassica campestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis), the genic male-sterile line (A line), the Polima cytoplasmic male-sterile (CMS) line (P line), and the Ogura CMS line (O line) along with their maintainer line (B line). In total, 7,136 differentially expressed genes (DEGs), 361 differentially expressed long non-coding RNAs (lncRNAs) (DELs), 56 differentially expressed microRNAs (miRNAs) (DEMs) were selected out. Specific regulatory networks related to anther cell differentiation, meiosis cytokinesis, pollen wall formation, and tapetum development were constructed based on the abortion characteristics of male-sterile lines. Candidate genes and lncRNAs related to cell differentiation were identified in sporocyteless P line, sixteen of which were common to the DEGs in Arabidopsis spl/nzz mutant. Genes and lncRNAs concerning cell plate formation were selected in A line that is defected in meiosis cytokinesis. Also, the orthologs of pollen wall formation and tapetum development genes in Arabidopsis showed distinct expression patterns in the three different sterile lines. Among 361 DELs, 35 were predicted to interact with miRNAs, including 28 targets, 47 endogenous target mimics, and five precursors for miRNAs. Two lncRNAs were further proved to be functional precursors for bra-miR156 and bra-miR5718, respectively. Overexpression of bra-miR5718HG in B. campestris slowed down the growth of pollen tubes, caused shorter pollen tubes, and ultimately affected the seed set. Our study provides new insights into molecular regulation especially the ncRNA interaction during pollen development in Brassica crops.

Integrated Analysis of Long Non-coding RNAs (lncRNAs) and mRNAs Reveals the Regulatory Role of lncRNAs Associated With Salt Resistance in Camellia sinensis.

Tea plant (Camellia sinensis), an important economic crop, is seriously affected by various abiotic stresses, including salt stress, which severely diminishes its widespread planting. However, little is known about the roles of long non-coding RNAs (lncRNAs) in transcriptional regulation under salt stress. In this study, high-throughput sequencing of tea shoots under salt-stress and control conditions was performed. Through sequencing analysis, 16,452 unique lncRNAs were identified, including 172 differentially expressed lncRNAs (DE-lncRNAs). The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of their cis- and trans-target genes showed that these DE-lncRNAs play important roles in many pathways such as the galactinol synthase (GOLS), calcium signaling pathway, and interact with transcription factors (TFs) under salt stress. The data from the gene-specific antisense oligodeoxynucleotide-mediated reduction in the lncRNA MSTRG.139242.1 and its predicted interacting gene, TEA027212.1 (Ca2+-ATPase 13), in tea leaves revealed that MSTRG.139242.1 may function in the response of tea plants to high salinity. In addition, 12 lncRNAs were predicted to be target mimics of 17 known mature miRNAs, such as miR156, that are related to the salt-stress response in C. sinensis. Our results provide new insights into lncRNAs as ubiquitous regulators in response to salt stress in tea plants.

Genome-wide identification and characterization of lncRNAs and miRNAs in cluster bean (Cyamopsis tetragonoloba).

Long non coding RNAs (lncRNAs) are a class of non-protein coding RNAs that play a crucial role in most of the biological activities like nodule metabolism, flowering time and male sterility. Quite often, the function of lncRNAs is species-specific in nature. Thus an attempt has been made in cluster bean (Cyamopsis tetragonoloba) for the first time to computationally identify lncRNAs based on a proposed index and study their targeted genes. Further, these targeted genes of lncRNAs were identified and characterized for their role in various biological processes like stress mechanisms, DNA damage repair, cell wall synthesis. Besides, lncRNAs and miRNAs bearing Simple Sequence Repeats (SSRs) were identified that contribute towards biogenesis of small non-coding RNAs. Moreover, five novel endogenous Target Mimic lncRNAs (eTMs) were identified that may disrupt the miRNA-mRNA regulations. For easy understanding and usability, a database CbLncRNAdb has been developed and made available at http://cabgrid.res.in/cblncrnadb.