Genome-wide identification of phasiRNAs in Arabidopsis thaliana, and insights into biogenesis, temperature sensitivity, and organ specificity

The knowledge of biogenesis and target regulation of the phased small interfering RNAs (phasiRNAs) needs continuous update, since the phasiRNA loci are dynamically evolved in plants. Here, hundreds of phasiRNA loci of Arabidopsis thaliana were identified in distinct tissues and under different temperature. In flowers, most of the 24-nt loci are RNA-dependent RNA polymerase 2 (RDR2)-dependent, while the 21-nt loci are RDR6-dependent. Among the RDR-dependent loci, a significant portion is Dicer-like 1-dependent, indicating the involvement of microRNAs in their expression. Besides, two TAS candidates were discovered. Some interesting features of the phasiRNA loci were observed, such as the strong strand bias of phasiRNA generation, and the capacity of one locus for producing phasiRNAs by different increments. Both organ specificity and temperature sensitivity were observed for phasiRNA expression. In leaves, the TAS genes are highly activated under low temperature. Several trans-acting siRNA-target pairs are also temperature-sensitive. In many cases, the phasiRNA expression patterns correlate well with those of the processing signals. Analysis of the rRNA-depleted degradome uncovered several phasiRNA loci to be RNA polymerase II-independent. Our results should advance the understanding on phasiRNA biogenesis and regulation in plants.

Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network

Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants.

Drugging non-coding RNAs-A new light of hope in senescence-related cancer therapy

Cancer is the most prevalent disease of concern worldwide for several decades. Diverse therapeutic aspects are in applications to control this phenomenal disease and also for decennaries. Among many causes and consequences of cancer, senescence has gained much interest in recent times. Senescence, also termed aging, is the natural process that induces cancer in neighboring cells through Senescence-Associated-Secretory Phenotypes (SASPs) production. As a cure or preventive measure of cancer progression, studies already light upon multiple proteins and their roles in associated pathways but the aspect of different non-coding RNAs (ncRNAs) is emerging recently and is under extensive research. Different approaches toward controlling senescence and inhibiting senescent cell accumulation are other aspects of cancer procurement. Thus, the role of ncRNA molecules in senescence and aging is getting much more interest as an alternate therapy for cancer treatment. In this review, at first, the roles of different ncRNAs related to several cellular processes are described. Then we tried to highlight the roles of different non-coding RNAs in senescence-induced cancer formation that extends with increasing age and emphasized non-coding RNAs as a therapeutic target solely or in combination with small molecules where drugging of small molecules targeting these non-coding RNAs can control cancer development.

Integrated analysis of small RNAs, transcriptome and degradome sequencing reveal the drought stress network in Agropyron mongolicum Keng

Agropyron mongolicum (A. mongolicum) is an excellent gramineous forage with extreme drought tolerance, which lives in arid and semiarid desert areas. However, the mechanism that underlies the response of microRNAs (miRNAs) and their targets in A. mongolicum to drought stress is not well understood. In this study, we analyzed the transcriptome, small RNAome (specifically the miRNAome) and degradome to generate a comprehensive resource that focused on identifying key regulatory miRNA-target circuits under drought stress. The most extended transcript in each collection is known as the UniGene, and a total of 41,792 UniGenes and 1,104 miRNAs were identified, and 99 differentially expressed miRNAs negatively regulated 1,474 differentially expressed target genes. Among them, eight miRNAs were unique to A. mongolicum, and there were 36 target genes. A weighted gene co-expression network analysis identified five hub genes. The miRNAs of five hub genes were screened with an integration analysis of the degradome and sRNAs, such as osa-miR444a-3p.2-MADS47, bdi-miR408-5p_1ss19TA-CCX1, tae-miR9774_L-2R-1_1ss11GT-carC, ata-miR169a-3p-PAO2, and bdi-miR528-p3_2ss15TG20CA-HOX24. The functional annotations revealed that they were involved in mediating the brassinosteroid signal pathway, transporting and exchanging sodium and potassium ions and regulating the oxidation-reduction process, hydrolase activity, plant response to water deprivation, abscisic acid (ABA) and the ABA-activated signaling pathway to regulate drought stress. Five hub genes were discovered, which could play central roles in the regulation of drought-responsive genes. These results show that the combined analysis of miRNA, the transcriptome and degradation group provides a useful platform to investigate the molecular mechanism of drought resistance in A. mongolicum and could provide new insights into the genetic engineering of Poaceae crops in the future.

An organ-specific transcriptomic atlas of the medicinal plant Bletilla striata: Protein-coding genes, microRNAs, and regulatory networks

As one of the important species belonging to the Bletilla genus of Orchidaceae, Bletilla striata (Thunb.) Rchb. f., possesses both ornamental and medicinal values. Its dried tubers are used as a traditional Chinese medicine, and several secondary metabolites have been indicated to be the active ingredients. However, the molecular mechanisms related to the regulation of secondary metabolism have not been characterized in B. striata. In this study, integrated analysis of RNA sequencing (RNA-seq), small RNA sequencing (sRNA-seq), and degradome sequencing (degradome-seq) data from three organs (leaf, root, and tuber) of B. striata provided us with a comprehensive view of the microRNA (miRNA)-mediated regulatory network. Firstly, based on the RNA-seq data, the organ-specific expression patterns of the protein-coding genes, especially for those related to secondary metabolism, were investigated. Secondly, 342 conserved miRNA candidates were identified from B. striata. These miRNAs were assigned to 88 families, some of which were selected for expression pattern analysis. Additionally, 31 hairpin-structured precursors encoding 23 novel miRNAs were uncovered from the transcriptome assembly. Thirdly, based on the degradome signatures, 1,142 validated miRNA-target pairs (involving 167 conserved miRNAs and six novel miRNAs and 51 target genes) were included in the regulatory network. Organ-specific expression level comparison between the miRNAs and their targets revealed some interesting miRNA-target pairs. Fourthly, some valuable subnetworks were extracted for further functional studies. Additionally, some regulatory pathways were indicated to be monocot specific. Summarily, our results lay a solid basis for in-depth studies on the regulatory mechanisms underlying the production of the medicinal ingredients in B. striata.

In planta transcriptome analysis reveals tissue-specific expression of pathogenicity genes and microRNAs during rice-Magnaporthe interactions

Transcriptional re-programming in host and pathogen upon leaf and neck infection is an evolving area of research for the rice blast community. Analysis of in planta rice transcriptome in leaf and neck tissues revealed tissue-specific and infection-specific expression of rice and Magnaporthe oryzae genes in host and pathogen. The glycosyl hydrolase, isocitrate lyase, cupin domain containing protein, TF2, CMPG1, CHIT17 and OsCML14 genes were uniquely expressed in leaf infection. Genes like cytochrome P450, inhibitor I family protein, GSTU6, abscisic stress ripening, and cupin domain containing protein were up-regulated during neck infection. In our microRNA sequencing study, Osa-miR166n-3p was highly expressed in upon Magnaporthe leaf infection, whereas osa-miR1661-3p, osa-miR166n-3p and osa-miR159b were overexpressed in neck infection. Here we report several transcripts being targeted by up and down regulated microRNAs during infection. The putative genes expressed upon infection in leaf and neck could be used in understanding the dual-epidemics of blast disease.

Molecular and Hormonal Regulation of Leaf Morphogenesis in Arabidopsis

Shoot apical meristems (SAM) are tissues that function as a site of continuous organogenesis, which indicates that a small pool of pluripotent stem cells replenishes into lateral organs. The coordination of intercellular and intracellular networks is essential for maintaining SAM structure and size and also leads to patterning and formation of lateral organs. Leaves initiate from the flanks of SAM and then develop into a flattened structure with variable sizes and forms. This process is mainly regulated by the transcriptional regulators and mechanical properties that modulate leaf development. Leaf initiation along with proper orientation is necessary for photosynthesis and thus vital for plant survival. Leaf development is controlled by different components such as hormones, transcription factors, miRNAs, small peptides, and epigenetic marks. Moreover, the adaxial/abaxial cell fate, lamina growth, and shape of margins are determined by certain regulatory mechanisms. The over-expression and repression of various factors responsible for leaf initiation, development, and shape have been previously studied in several mutants. However, in this review, we collectively discuss how these factors modulate leaf development in the context of leaf initiation, polarity establishment, leaf flattening and shape.

The RNA degradome: a precious resource for deciphering RNA processing and regulation codes in plants

The plant RNA degradome was defined as an aggregate of the RNA fragments degraded from various biochemical pathways, such as RNA turnover, maturation and quality surveillance. In recent years, the degradome sequencing (degradome-seq) libraries became a rich storehouse for researchers to study on RNA processing and regulation. Here, we provided a brief overview of the uses of degradome-seq data in plant RNA biology, especially on non-coding RNA processing and small RNA-guided target cleavages. Some novel applications in RNA research area, such as in vivo mapping of the endoribonucleolytic cleavage sites, identification of conserved motifs at the 5' ends of the uncapped RNA fragments, and searching for the protein-binding regions on the transcripts, were also mentioned. More importantly, we proposed a model for the biologists to deduce the contributions of transcriptional and/or post-transcriptional regulation to gene differential expression based on degradome-seq data. Finally, we hope that the degradome-based analytical methods could be widely applied for the studies on RNA biology in eukaryotes.

Si vis pacem para bellum: A prospective in silico analysis of miRNA-based plant defenses against fungal infections

Fungal pathogens are an important threat for plant crops, being responsible for important reductions of production yields and a consequent economic impact. Among the molecular mediators of fungal infections of plant crops, non-coding RNAs (ncRNAs) have been described as relevant players either in the plant immune responses and mechanism of defense or in the colonization of plant tissues by fungi. Acting as a mechanism of defense, some plant small ncRNAs such as miRNAs and tasiRNAs can be secreted by cells and directed to target the transcriptome of pathogenic fungi, triggering an RNAi-like interference mechanism able to silence the expression of specific fungal genes. The detailed knowledge of this mechanism of defense against fungal pathogens could open new possibilities for the protection of human important crops. To infer putative functional relationships mediated by ncRNA communication, we performed a prospective analysis to determine potential plant miRNAs able to target the genome of fungal pathogens, which resulted in the description of enriched specific plant miRNA families and their putative fungal targets that could be further studied in the context of plant-fungi interactions. The expression profile of specific members of the enriched miRNAs families showed an infection-dependent behavior in laboratory models of infection. Plant miRNAs showed sequence complementarity with coding genes of their cognate fungal pathogens. Plant miRNAs could potentially target fungal genes belonging to functional families related to stress response, membrane architecture, vacuolar transport, membrane traffic, and anabolic processes. Families of specific infection-responsive miRNAs are included in the putative plant defense mechanism.

Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing

Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA and transcriptome sequencing were performed based on the highly resistant material (Gantai-2-2) and highly susceptible material (Wan 82-178) of soybean. The results showed that, when comparing 48 h feeding with 0 h feeding, 55 differentially expressed miRNAs were identified in Gantai-2-2 and 58 differentially expressed miRNAs were identified in Wan82-178. When comparing Gantai-2-2 with Wan82-178, 77 differentially expressed miRNAs were identified at 0 h feeding, and 70 differentially expressed miRNAs were identified at 48 h feeding. The pathway analysis of the predicted target genes revealed that the plant hormone signal transduction, RNA transport, protein processing in the endoplasmic reticulum, zeatin biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and isoquinoline alkaloid biosynthesis may play important roles in soybean's defense against the stress caused by bean pyralid larvae. According to conjoint analysis of the miRNA/mRNA, a total of 20 differentially expressed miRNAs were negatively correlated with 26 differentially expressed target genes. The qRT-PCR analysis verified that the small RNA sequencing results were credible. According to the analyses of the differentially expressed miRNAs, we speculated that miRNAs are more likely to play key roles in the resistance to insects. Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p, Gma-miR396e, and so on-as well as their negatively regulated differentially expressed target genes-may be involved in the regulation of soybean resistance to bean pyralid larvae. These results laid a foundation for further in-depth research regarding the action mechanisms of insect resistance.

Deciphering the non-coding RNA-level response to arsenic stress in rice (Oryza sativa)

Arsenic (As) contamination in subsoil and groundwater is a big problem, especially in many South-East Asian countries. As a staple crop growing under flooded condition in these areas, rice (Oryza sativa L.) becomes a big threat to human health through the food chain since As is highly accumulated in grains. Thus, reducing As accumulation in rice through molecular breeding and identification of rice varieties with low As content are the pressing issues. However, the current understanding on the molecular mechanism of As stress response is still limited for rice. In this study, we performed a comprehensive search for the As-responsive small RNAs (sRNAs) of rice. Briefly, 4,762 and 18,152 sRNAs were identified to be highly activated under As stress in roots and shoots respectively, while 14,603 and 8,308 sRNAs were intensively repressed by As treatment in roots and shoots, respectively. A number of the As-responsive sRNAs found their loci on tRNAs, rRNAs or long non-coding RNAs (lncRNAs). Interestingly, these loci preferentially distributed on the 5' halves of the tRNA, rRNA or lncRNA precursors. Among the above-identified As-responsive sRNAs, 252 Argonaute 1 (AGO1)-enriched sRNAs were extracted for target identification, resulting in 200 pairs of sRNA-protein-coding target interactions. Many targets are functionally involved in the development, stress response, reproduction, or lipid metabolism. Additionally, 56 lncRNAs were discovered to be targeted by nine AGO1-enriched sRNAs, indicating the potential involvement of these lncRNAs in As signaling. Taken together, our results could expand the understanding on the non-coding RNA-mediated As stress response in rice.

Transcriptome-wide identification and functional investigation of the RDR2- and DCL3-dependent small RNAs encoded by long non-coding RNAs in Arabidopsis thaliana

The involvement of the long non-coding RNAs (lncRNAs) in small RNA (sRNA)-related pathways remains elusive. Taking advantage of the public sRNA sequencing data, we searched for RNA-dependent RNA polymerase 2 (RDR2)- and Dicer-like 3 (DCL3)-dependent sRNAs generated from the lncRNAs of Arabidopsis thaliana. First, 55,162 sRNAs were identified to be RDR2- and DCL3-dependent. These sRNAs were then mapped onto the lncRNAs. As a result, a total of 26,643 sRNAs found their loci on 3,834 lncRNAs, and 29,388 sRNAs found their loci on 4,174 reverse complementary (RC) sequences of the lncRNAs. To support the formation of the double-stranded precursors for sRNA generation, double-stranded RNA sequencing (dsRNA-seq) reads were mapped onto the sense and antisense strands of the lncRNAs with RDR2- and DCL3-dependent sRNA loci. As a result, 1,075 regions longer than 100 nt were identified to be covered by dsRNA-seq reads on 390 sense strands of the lncRNAs, and 1,352 regions were identified on 544 RC strands. Besides, 2,238 out of 3,211 dsRNA-seq read-covered sRNA loci were supported by degradome sequencing data on the sense strands of the lncRNAs. Interestingly, dozens of dsRNA-seq read-covered regions with AGO4-associated sRNA loci showed site-specific chromatin modification patterns. Thus, some of the lncRNAs were integrated into the RDR2- and DCL3-dependent sRNA biogenesis pathway. Moreover, our results indicated that the site-specific chromatin modifications mediated by the AGO4-associated sRNAs might play a regulatory role on the transcription activity of the lncRNA genes.

Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing

microRNAs represent small endogenous RNAs which are known to play a crucial role in various plant metabolic processes. Carrot being an important vegetable crop, represents one of the richest sources of carotenoids and anthocyanins. Most of the studies on microRNAs have been conducted in the aerial parts of the plants. However, carrot has the rare distinction of storing these compounds in roots. Therefore, carrot represents a good model system to unveil the regulatory roles of miRNAs in the underground edible part of the plant. For the first time, we report the genome wide identification and expression profiling of miRNAs in two contrasting color variants of carrot namely Orange Red and Purple Black using RNA-seq. Illumina sequencing resulted in the generation of 25.5M and 18.9M reads in Orange Red and Purple Black libraries, respectively. In total, 144 and 98 (read count >10), conserved microRNAs and 36 and 66 novel microRNAs were identified in Orange Red and Purple Black, respectively. Functional categorization and differential gene expression revealed the presence of several miRNA genes targeting various secondary metabolic pathways including carotenoid and anthocyanin biosynthetic pathways in the two libraries. 11 known and 2 novel microRNAs were further validated using Stem-Loop PCR and qRT-PCR. Also, target validation was performed for selected miRNA genes using RLM-RACE approach. The present work has laid a foundation towards understanding of various metabolic processes, particularly the color development in carrot. This information can be further employed in targeted gene expression for increasing the carotenoid and anthocyanin content in crop plants.

Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants

Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.

Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow

Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs. The nuclear-localized regulatory mode was also reported for the plant miRNAs. However, evidence is still lacking to show the universality and conservation of the miRNA-mediated regulation in the plant nuclei. Here, we introduced a bioinformatics workflow for genome-wide investigation of miRNA-guided, cleavage-based regulation of the nascent nuclear transcripts. Facilitated by the tool package PmiRNTSA (Plant microRNA-mediated nascent transcript slicing analyzer), plant biologists could perform a comprehensive search for the miRNA slicing sites located within the introns or the exon-intron/intron-exon junctions of the target transcripts, which are supported by degradome sequencing data. The results enable the researchers to examine the co-transcriptional regulatory model of the miRNAs for a specific plant species. Moreover, a case study was performed to search for the slicing sites located within the exon-intron/intron-exon junctions in two model plants. A case study was performed to show the feasibility and reliability of our workflow. Together, we hope that this work could inspire much more innovative research efforts to expand the current understanding of the miRNA action modes in plants.

Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs

The next-generation sequencing (NGS) technology has revolutionized our previous understanding of the plant genomes, relying on its innate advantages, such as high throughput and deep sequencing depth. In addition to the protein-coding gene loci, massive transcription signals have been detected within intergenic or intragenic regions. Most of these signals belong to non-coding ones, considering their weak protein-coding potential. Generally, these transcripts could be divided into long non-coding RNAs and small non-coding RNAs (sRNAs) based on their sequence length. In addition to the well-known microRNAs (miRNAs), many plant endogenous sRNAs were collectively referred to as small interfering RNAs. However, an increasing number of unclassified sRNA species are being discovered by NGS. The high heterogeneity of these novel sRNAs greatly hampered the mechanistic studies, especially on the clear description of their biogenesis and action pathways. Fortunately, public databases, bioinformatics softwares and NGS datasets are increasingly available for plant sRNA research. Here, by summarizing these valuable resources, we proposed a general workflow to decipher the RDR (RNA-dependent RNA polymerase)- and DCL (Dicer-like)-dependent biogenesis pathways, and the Argonaute-mediated action modes (such as target cleavages and chromatin modifications) for specific sRNA species in plants. Taken together, we hope that by summarizing a list of the public resources, this work will facilitate the plant biologists to perform classification and functional characterization of the interesting sRNA species.

Abiotic Stress Responsive miRNA-Target Network and Related Markers (SNP, SSR) in Brassica juncea

Abiotic stress is one of the major factors responsible for huge yield loss in crop plants. MicroRNAs play a key role in adaptive responses of plants under abiotic stress conditions through post-transcriptional gene regulations. In present study, 95 potential miRNAs were predicted in Brassica juncea using comparative genomics approach. It was noted that these miRNAs, target several transcription factors (TFs), transporter family proteins, signaling related genes, and protease encoding genes. Nineteen distinct miRNA-target regulatory networks were observed with significant involvement in regulation of transcription, response to stimulus, hormone and auxin mediated signaling pathway related gene ontology (GO) term. The sucrose-starch metabolism and pentose-gluconate interconversion pathways were found significantly enriched for these target genes. Molecular markers such as Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNPs) were identified on miRNAs (miR-SSRs and miR-SNPs) and their target genes in B. juncea. Notably, one of the miR-SNP (C/T) was found at the 5^th position on mature region of miR2926. This C/T transition led to the distorted and unstable hairpin structure of miR2926, consequently complete loss of target function. Hence, findings from this study will lay a foundation for marker assisted breeding for abiotic stress tolerant varieties of B. juncea.

Computational Identification of MicroRNAs and Their Transcript Target(s) in Field Mustard (Brassica rapa L.)

BACKGROUND

Micro RNAs (miRNAs) are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally.

OBJECTIVE

In the present study, we report the results of a systemic search for identification of new miRNAs in B. rapa using homology-based ESTs (Expressed Sequence Tags) analysis and considering a series of fi ltration criteria.

MATERIALS AND METHODS

Plant mature miRNA sequences were searched in non-protein coding ESTs registered in NCBI EST database. Zuker RNA folding algorithm was used to generate the secondary structures of the ESTs. Potential sequences were candidate as miRNA genes and characterized evolutionarily only and if only they fi t some described criteria. Also, the web tool psRNATarget was applied to predict candidate B. rapa miRNA targets.

RESULTS

In this study, 10 novel miRNAs from B. rapa belonging to 6 miRNA families were identified using EST-based homology analysis by considering a series of fi ltration criteria. All potent miRNAs appropriate fold back structure. Several potential targets with known/unknown functions for these novel miRNAs were identified. The target genes mainly encode transcription factors, enzymes, DNA binding proteins, disease resistance proteins, carrier proteins and other biological processes.

CONCLUSIONS

MicroRNA having diverse functions in plant species growth, development and evolution by posttranscriptionally regulating the levels of specific transcriptome so by effecting on their translation products. Research in miRNA led to the identification of many miRNAs and their regulating genes from diverse plant species.

Investigating the regulatory roles of the microRNAs and the Argonaute 1-enriched small RNAs in plant metabolism

The biological roles of small RNAs (sRNAs) in metabolic processes are emerging. However, a systemic study is needed to investigate the wide-spread involvement of the sRNAs in plant metabolism. By using the metabolism-related transcripts retrieved from the public database Plant Metabolic Network, and the publicly available sRNA high-throughput sequencing data, large-scale target identification was performed for microRNAs (miRNAs) and Argonaute 1 (AGO1)-enriched sRNAs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Based on the publicly available degradome sequencing data, 200 miRNA/sRNA-target pairs involving 19 miRNAs, 111 AGO1-enriched sRNAs and 58 target transcripts in Arabidopsis, and 151 pairs involving 62 miRNAs, 33 AGO1-enriched sRNAs and 69 target transcripts in rice were identified. After considering protein-protein interactions for the above identified target genes, a total of 251 pairs involving 21 miRNAs, 120 AGO1-enriched sRNAs and 75 target transcripts exist within the regulatory network of Arabidopsis, and 168 pairs involving 64 miRNAs, 38 AGO1-enriched sRNAs and 80 target transcripts exist in rice. Based on GO (Gene Ontology) term enrichment analysis, the targets within the networks of both plants are enriched in "metabolic process" and "catalytic activity", pointing to the high relevance of the established networks to metabolism. Several functionally conserved subnetworks were identified between the two plant species. Our study provides a basis for studies on metabolism-related sRNAs in plants.

tRNA Derived smallRNAs: smallRNAs Repertoire Has Yet to Be Decoded in Plants

Among several smallRNAs classes, microRNAs play an important role in controlling the post-transcriptional events. Next generation sequencing has played a major role in extending the landscape of miRNAs and revealing their spatio-temporal roles in development and abiotic stress. Lateral evolution of these smallRNAs classes have widely been seen with the recently emerging knowledge on tRNA derived smallRNAs. In the present perspective, we discussed classification, identification and roles of tRNA derived smallRNAs across plants and their potential involvement in abiotic and biotic stresses.

The pivotal role of small non-coding RNAs in the regulation of seed development

Seeds represent a crucial stage of the seed plants life cycle. It is during seed development that the foundations of the future plant body, and the ability to give rise to a new plant capable of growing under sometimes adverse environmental conditions, are established. Small non-coding RNAs are major regulators of gene expression both at the post-transcriptional and transcriptional levels and, not surprisingly, these elements play major roles in seed development and germination. We review here the current knowledge about small RNA expression and functions in seed development, going from the morphogenesis phase comprehending embryo development and patterning, to the several steps of the maturation phase, ending in the transition to the germination. A special focus is given to the small RNAs for which functional studies have been conducted and their participation in regulatory networks operating in seeds. Many challenges remain ahead for dissecting the complex small RNA landscape in seeds, but this is a highly relevant issue in plant biology and advances in this area will most certainly impact plant breeding.

MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network

Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF, and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signaling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.

A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb

Dendrobium officinale is an important traditional Chinese herb. Here, we did a transcriptome-wide, organ-specific study on this valuable plant by combining RNA, small RNA (sRNA) and degradome sequencing. RNA sequencing of four organs (flower, root, leaf and stem) of Dendrobium officinale enabled us to obtain 536,558 assembled transcripts, from which 2,645, 256, 42 and 54 were identified to be highly expressed in the four organs respectively. Based on sRNA sequencing, 2,038, 2, 21 and 24 sRNAs were identified to be specifically accumulated in the four organs respectively. A total of 1,047 mature microRNA (miRNA) candidates were detected. Based on secondary structure predictions and sequencing, tens of potential miRNA precursors were identified from the assembled transcripts. Interestingly, phase-distributed sRNAs with degradome-based processing evidences were discovered on the long-stem structures of two precursors. Target identification was performed for the 1,047 miRNA candidates, resulting in the discovery of 1,257 miRNA--target pairs. Finally, some biological meaningful subnetworks involving hormone signaling, development, secondary metabolism and Argonaute 1-related regulation were established. All of the sequencing data sets are available at NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/). Summarily, our study provides a valuable resource for the in-depth molecular and functional studies on this important Chinese orchid herb.

High-Throughput Sequencing Reveals H2O2 Stress-Associated MicroRNAs and a Potential Regulatory Network in Brachypodium distachyon Seedlings

Oxidative stress in plants can be triggered by many environmental stress factors, such as drought and salinity. Brachypodium distachyon is a model organism for the study of biofuel plants and crops, such as wheat. Although recent studies have found many oxidative stress response-related proteins, the mechanism of microRNA (miRNA)-mediated oxidative stress response is still unclear. Using next generation high-throughput sequencing technology, the small RNAs were sequenced from the model plant B. distachyon 21 (Bd21) under H₂O₂ stress and normal growth conditions. In total, 144 known B. distachyon miRNAs and 221 potential new miRNAs were identified. Further analysis of potential new miRNAs suggested that 36 could be clustered into known miRNA families, while the remaining 185 were identified as B. distachyon-specific new miRNAs. Differential analysis of miRNAs from the normal and H₂O₂ stress libraries identified 31 known and 30 new H₂O₂ stress responsive miRNAs. The expression patterns of seven representative miRNAs were verified by reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis, which produced results consistent with those of the deep sequencing method. Moreover, we also performed RT-qPCR analysis to verify the expression levels of 13 target genes and the cleavage site of 5 target genes by known or novel miRNAs were validated experimentally by 5' RACE. Additionally, a miRNA-mediated gene regulatory network for H₂O₂ stress response was constructed. Our study identifies a set of H₂O₂-responsive miRNAs and their target genes and reveals the mechanism of oxidative stress response and defense at the post-transcriptional regulatory level.

Construction of regulatory networks mediated by small RNAs responsive to abiotic stresses in rice (Oryza sativa)

Plants have evolved exquisite molecular mechanisms to adapt to diverse abiotic stresses. MicroRNAs play an important role in stress response in plants. However, whether the other small RNAs (sRNAs) possess stress-related roles remains elusive. In this study, thousands of sRNAs responsive to cold, drought and salt stresses were identified in rice seedlings and panicles by using high-throughput sequencing data. These sRNAs were classified into 12 categories, including "Panicle_Cold_Down", "Panicle_Cold_Up", "Panicle_Drought_Down", "Panicle_Drought_Up", "Panicle_Salt_Down", "Panicle_Salt_Up", "Seedling_Cold_Down", "Seedling_Cold_Up", "Seedling_Drought_Down", "Seedling_Drought_Up", "Seedling_Salt_Down" and "Seedling_Salt_Up". The stress-responsive sRNAs enriched in Argonaute 1 were extracted for target prediction and degradome sequencing data-based validation, which enabled network construction. Within certain subnetworks, some target genes were further supported by microarray data. Literature mining indicated that certain targets were potentially involved in stress response. These results demonstrate that the established networks are biologically meaningful. We discovered that in some cases, one sRNA sequence could be assigned to two or more categories. Moreover, within certain target-centered subnetworks, one transcript was regulated by several stress-responsive sRNAs assigned to different categories. It implies that these subnetworks are potentially implicated in stress signal crosstalk. Together, our results could advance the current understanding of the biological role of plant sRNAs in stress signaling.

Manipulating microRNAs for improved biomass and biofuels from plant feedstocks

Petroleum-based fuels are nonrenewable and unsustainable. Renewable sources of energy, such as lignocellulosic biofuels and plant metabolite-based drop-in fuels, can offset fossil fuel use and reverse environmental degradation through carbon sequestration. Despite these benefits, the lignocellulosic biofuels industry still faces many challenges, including the availability of economically viable crop plants. Cell wall recalcitrance is a major economic barrier for lignocellulosic biofuels production from biomass crops. Sustainability and biomass yield are two additional, yet interrelated, foci for biomass crop improvement. Many scientists are searching for solutions to these problems within biomass crop genomes. MicroRNAs (miRNAs) are involved in almost all biological and metabolic process in plants including plant development, cell wall biosynthesis and plant stress responses. Because of the broad functions of their targets (e.g. auxin response factors), the alteration of plant miRNA expression often results in pleiotropic effects. A specific miRNA usually regulates a biologically relevant bioenergy trait. For example, relatively low miR156 overexpression leads to a transgenic feedstock with enhanced biomass and decreased recalcitrance. miRNAs have been overexpressed in dedicated bioenergy feedstocks such as poplar and switchgrass yielding promising results for lignin reduction, increased plant biomass, the timing of flowering and response to harsh environments. In this review, we present the status of miRNA-related research in several major biofuel crops and relevant model plants. We critically assess published research and suggest next steps for miRNA manipulation in feedstocks for increased biomass and sustainability for biofuels and bioproducts.

Is Argonaute 1 the only effective slicer of small RNA-mediated regulation of gene expression in plants?

To maintain normal growth and development in a plant, gene expression must be under strict surveillance. One of the post-transcriptional regulatory pathways involves small RNA (sRNA)-guided, Argonaute (AGO) protein complex-mediated target cleavages. MicroRNAs (miRNAs) are the well-known sRNA species participating in the cleavage-based regulation of gene expression. In plants, most miRNAs are incorporated into AGO1-associated silencing complexes. Thus, the AGO1 protein is considered to be the most important slicer for sRNA-mediated target cleavages. Previous phylogenetic analysis revealed that AGO1, AGO5, and AGO10 belonged to the same clade in Arabidopsis (Arabidopsis thaliana). In addition, experimental evidence pointed to the possibility that AGO2, AGO7, and AGO10 were implicated in specific miRNA-mediated regulatory pathways. To investigate the potential slicer activities of AGO2, AGO5, AGO7, and AGO10, a comprehensive search was performed for the sRNAs enriched in the four AGO proteins in Arabidopsis. A total of 3 499, 1 618, 4 632, and 63 sRNAs are enriched in AGO2, AGO5, AGO7, and AGO10, respectively. Interestingly, several miRNAs were found to be enriched in AGO2 or AGO5. Transcriptome-wide target identification based on degradome sequencing data uncovered that a number of sRNAs enriched in the four AGOs could perform target cleavages like AGO1-associated miRNAs in plants. Based on the above results, the opinion was put forward that not only AGO1, but also AGO2, AGO5, AGO7, and AGO10 might be essential for the sRNA-mediated regulation of gene expression in plants.

Long non-coding RNAs: a novel endogenous source for the generation of Dicer-like 1-dependent small RNAs in Arabidopsis thaliana

The biological relevance of long non-coding RNAs (lncRNAs) is emerging. Whether the lncRNAs could form structured precursors for small RNAs (sRNAs) production remains elusive. Here, 172 713 DCL1 (Dicer-like 1)-dependent sRNAs were identified in Arabidopsis. Except for the sRNAs mapped onto the microRNA precursors, the remaining ones led us to investigate their originations. Intriguingly, 65 006 sRNAs found their loci on 5891 lncRNAs. These sRNAs were sent to AGO (Argonaute) enrichment analysis. As a result, 1264 sRNAs were enriched in AGO1, which were then subjected to target prediction. Based on degradome sequencing data, 109 transcripts were validated to be targeted by 96 sRNAs. Besides, 44 lncRNAs were targeted by 23 sRNAs. To further support the origination of the DCL1-dependent sRNAs from lncRNAs, we searched for the degradome-based cleavage signals at either ends of the sRNA loci, which were supposed to be produced during DCL1-mediated processing of the long-stem structures. As a result, 63 612 loci were supported by degradome signatures. Among these loci, 6606 reside within the dsRNA-seq (double-stranded RNA sequencing) read-covered regions of 100 nt or longer. These regions were subjected to secondary structure prediction. And, 43 regions were identified to be capable of forming highly complementary long-stem structures. We proposed that these local long-stem structures could be recognized by DCL1 for cropping, thus serving as the sRNA precursors. We hope that our study could inspire more research efforts to study on the biological roles of the lncRNAs in plants.

Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz.)

MicroRNAs (miRNAs) are a newly discovered class of noncoding endogenous small RNAs involved in plant growth and development as well as response to environmental stresses. miRNAs have been extensively studied in various plant species, however, only few information are available in cassava, which serves as one of the staple food crops, a biofuel crop, animal feed and industrial raw materials. In this study, the 169 potential cassava miRNAs belonging to 34 miRNA families were identified by computational approach. Interestingly, mes-miR319b was represented as the first putative mirtron demonstrated in cassava. A total of 15 miRNA clusters involving 7 miRNA families, and 12 pairs of sense and antisense strand cassava miRNAs belonging to six different miRNA families were discovered. Prediction of potential miRNA target genes revealed their functions involved in various important plant biological processes. The cis-regulatory elements relevant to drought stress and plant hormone response were identified in the promoter regions of those miRNA genes. The results provided a foundation for further investigation of the functional role of known transcription factors in the regulation of cassava miRNAs. The better understandings of the complexity of miRNA-mediated genes network in cassava would unravel cassava complex biology in storage root development and in coping with environmental stresses, thus providing more insights for future exploitation in cassava improvement.

Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa)

Background

The root systems play essential roles for plants to anchorage to the soil, and to exploit the mineral and water resources. The molecular mechanisms underlying root development have been extensively studied to improve root system architecture, especially for the crops. Several microRNA (miRNA) families have been demonstrated to be involved in plant root development. However, whether the other small RNA (sRNA) species, which occupy a dominant portion of the plant endogenous sRNA population, possess potential roles in root development remains unclear.

Results

In this study, by using sRNA high-throughput sequencing data, we made a comparison of the sRNA accumulation levels between the rice root tips and the whole roots. The sRNAs highly accumulated in the root tips and in the whole roots were extracted respectively. After Argonaute 1 (AGO1) enrichment analysis, the sRNAs with great potential of performing target cleavages were included for target prediction and degradome sequencing data-based validation. As a result, lists of the targets regulated by the AGO1-enriched sRNAs were obtained for both the root tips and the whole roots. Further evidences were identified from microarray data of the target genes to support some of the sRNA—target interactions. Specifically, the expression patterns of certain target genes in the root tips and the whole roots were contrary to those of the regulating sRNAs. Besides, several targets were indicated to play important roles in root development based on literature mining.

Conclusions

Taken together, the regulatory networks mediated by the sRNAs highly accumulated in the root tips or in the whole roots could advance our current understanding of the sRNA-involved molecular mechanisms underlying rice root development. And, the sRNA—target lists could serve as the basis for further functional investigations.

Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice

BACKGROUND

MiRNAs are key regulators in the miRNA-mediated regulatory networks. Single nucleotide polymorphisms (SNPs) that occur at miRNA-related regions may cause serious phenotype changes. To gain new insights into the evolution of miRNAs after SNP variation, we performed a genome-wide scan of miRNA-related SNPs, and analyzed their effects on the stability of miRNAs structure and the alteration of target spectrum in rice.

RESULTS

We find that the SNP density in pre-miRNAs is significantly higher than that in the flanking regions, owing to the rapid evolution of a large number of species-specific miRNAs in rice. In contrast, it is obvious that deeply conserved miRNAs are under strong purifying selection during evolution. In most cases, the SNPs in stem regions may result in the miRNA hairpin structures changing from stable to unstable status; And SNPs in mature miRNAs have great potential to have either newly created or disrupted the miRNA-target interactions. However, the total number of gained targets is over 2.5 times greater than that are lost after mutation. Notably, 12 putative domestication-related miRNAs have been identified, where the SNP density is significantly lower.

CONCLUSIONS

The present study provides the first outline of SNP variations occurred in rice pre-miRNAs at the whole genome-wide level. These analyses may deepen our understanding on the effects of SNPs on the evolution of miRNAs in the rice genome.

Introns targeted by plant microRNAs: a possible novel mechanism of gene regulation

BACKGROUND

In plant cells, most microRNAs (miRNAs) perform cleavages of target mature mRNAs in the cytoplasm. A recent report of a miRNA pathway involved in DNA methylation in the rice nucleus raises the possibility that plant miRNAs could cleave intron-containing pre-mRNAs (the precursor of messenger RNAs) located in the nucleus.

RESULTS

In this study, we searched for the miRNA binding sites present within the introns of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genes. All miRNA-intron interactions predicted to result in cleavages were validated by using the public degradome sequencing data. As a result, 40 miRNA-intron pairs involving 25 miRNAs in Arabidopsis and 1912 pairs involving 91 miRNAs in rice were identified. For several rice genes, not all transcription forms (alternative splicing variants) were under similar regulation by specific miRNAs. Certain transcripts could escape cleavages due to the absence of intronic miRNA binding sites within these sequences. In some instances, specific cleaved intron remnants could be converted to double-stranded RNAs (dsRNAs) by RNA-dependent RNA polymerase 2. These dsRNAs could then be processed into 21- and 24-nt phased sRNAs by the activity of Dicer-like 1 and 3, respectively. The resultant siRNAs have the potential to be incorporated into Argonaute (AGO)-associated silencing complexes and result in cleavages of target pre-mRNA sequences.

CONCLUSIONS

A regulatory model, miRNA-targeting of intron-containing pre-mRNAs-phased sRNAs-targeting of mature mRNAs is proposed, which further expands the potential modes of action of plant miRNAs.

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step.

Construction of gene regulatory networks mediated by vegetative and reproductive stage-specific small RNAs in rice (Oryza sativa)

Although huge amounts of high-throughput sequencing (HTS) data are available, limited systematic analyses have been performed by integrating these valuable resources. Based on small RNA (sRNA), RNA and degradome HTS data, the sRNAs specifically expressed at vegetative and reproductive stages were identified separately in rice. Two distinct groups of sRNA HTS data, which were prepared during the vegetative and the reproductive stages, were utilized to extract stage-specific sRNAs. Degradome sequencing data were employed for sRNA target validation. RNA sequencing data were used to construct expression-based, sRNA-mediated networks. As a result, 26 microRNAs and 413 sRNAs were specifically expressed at the vegetative stage, and 79 microRNAs and 539 sRNAs were specifically expressed at the reproductive stage. In addition to the microRNAs, numerous stage-specific sRNAs enriched in ARGONAUTE1 showed great potential to perform cleavage-based repression on the targets. Several stage-specific sRNAs were indicated to result from the wobble effect of Dicer-like 1-mediated processing of microRNA precursors. The expression patterns of the sRNA targets, and the stage-specific cleavage signals strongly indicated the reliability of the constructed networks. A set of rice stage-specific sRNAs along with the regulatory cascades, which have great potential in regulating specific developmental stages, were provided for further investigation.

Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis

MicroRNAs (miRNAs) play a pivotal role in plant development. The expression patterns of the miRNA genes significantly influence their regulatory activities. By utilizing small RNA (sRNA) high-throughput sequencing (HTS) data, the miRNA expression patterns were investigated in four organs (flowers, leaves, roots and seedlings) of Arabidopsis. Based on a set of criteria, dozens of organ-specific miRNAs were discovered. A dominant portion of the organ-specific miRNAs identified from the ARGONAUTE 4-enriched sRNA HTS libraries were highly expressed in flowers. Additionally, the expression of the precursors of the organ-specific miRNAs was analyzed. Degradome sequencing data-based approach was employed to identify the targets of the organ-specific miRNAs. The miRNA–target interactions were used for network construction. Subnetwork analysis unraveled some novel regulatory cascades, such as the feedback regulation mediated by miR161, the potential self-regulation of the genes miR172, miR396, miR398 and miR860, and the miR863-guided cleavage of the SERRATE transcript. Our bioinformatics survey expanded the organ-specific miRNA–target list in Arabidopsis, and could deepen the biological view of the miRNA expression and their regulatory roles.

Identification of the highly accumulated microRNA*s in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa)

Plant microRNAs (miRNAs) are crucial for the regulation of gene expression, which is involved in almost all the important biological processes. In the cytoplasm, the miRNA strand is selectively incorporated into a specific Argonaute (AGO)-associated gene silencing complex, while the miRNA* is degraded rapidly. Thus, most miRNA*s were thought to be biologically meaningless. Interestingly, several recent reports in both plants and animals have shaken this notion. Many miRNA*s were demonstrated to possess regulatory roles in gene expression. However, the low accumulation levels of most miRNA*s raise the question whether the activities of this small RNA (sRNA) species are widespread in plants. Here, by using publicly available sRNA high-throughput sequencing data, we found that the accumulation levels of several miRNA*s could be much higher than those of their miRNA partners in certain organs, mutants and/or AGO-associated silencing complexes of both Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Based on target prediction and degradome sequencing data-based validation, some of these highly accumulated miRNA*s were indicated to possess cleavage-based potential regulatory role on certain targets. Besides, some interesting biological interpretations were obtained based on the accumulation patterns of the miRNA*s, the annotations of the target genes, and literature mining. Taken together, the expanded list of the highly accumulated miRNA*s along with their potential target genes discovered in this study further strengthened the current notion that certain members of the miRNA* species are biologically relevant, which needs further inspection.

Genome-wide identification of reverse complementary microRNA genes in plants

MicroRNAs (miRNAs) are ∼21-nucleotide small RNAs (sRNAs) with essential regulatory roles in plants. They are generated from stem-loop-structured precursors through two sequential Dicer-like 1 (DCL1)-mediated cleavages. To date, hundreds of plant miRNAs have been uncovered. However, the question, whether the sequences reverse complementary (RC) to the miRNA precursors could form hairpin-like structures and produce sRNA duplexes similar to the miRNA/miRNA* pairs has not been solved yet. Here, we interrogated this possibility in 16 plant species based on sRNA high-throughput sequencing data and secondary structure prediction. A total of 59 RC sequences with great potential to form stem-loop structures and generate miRNA/miRNA*-like duplexes were identified in ten plants, which were named as RC-miRNA precursors. Unlike the canonical miRNAs, only a few cleavage targets of the RC-miRNAs were identified in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), and none in Soybean (Glycine max) based on degradome data. Surprisingly, the genomic regions surrounding some of the RC-miRNA target recognition sites were observed to be specifically methylated in both Arabidopsis and rice. Taken together, we reported a new class of miRNAs, called RC-miRNAs, which were generated from the antisense strands of the miRNA precursors. Based on the results, we speculated that the mature RC-miRNAs might have subtle regulatory activity through target cleavages, but might possess short interfering RNA-like activity by guiding sequence-specific DNA methylation.

A reversed framework for the identification of microRNA-target pairs in plants

Most plant microRNAs (miRNAs) perform their repressive regulation through target cleavages. The resulting slicing sites on the target transcripts could be mapped by sequencing of the 3'-cleavage remnants, called degradome sequencing. The high sequence complementarity between miRNAs and their targets has greatly facilitated the development of the target prediction tools for plant miRNAs. The prediction results were then subjected to degradome sequencing data-based validation, through which numerous miRNA-target interactions have been extracted. However, some drawbacks are unavoidable when using this forward approach. Essentially, a known list of plant miRNAs should be obtained in advance of target prediction and validation. This becomes an obstacle to discover novel miRNAs and their targets. Here, after reviewing the current available algorithms for reverse identification of miRNA-target pairs in plants, a case study was performed by using a newly established framework with adjustable parameters. In this workflow, integration of degradome and ARGONAUTE 1-enriched small RNA sequencing data was recommended to do a relatively comprehensive and reliable search. Besides, several computational algorithms such as BLAST, target plots and RNA secondary structure prediction were used. The results demonstrated the prevalent utility of the reversed approach for uncovering miRNA-target interactions in plants.

Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants

Background

MicroRNAs (miRNAs) play an essential role in gene regulation in plants. At the same time, the expression of miRNA genes is also tightly controlled. Recently, a novel mechanism called “target mimicry” was discovered, providing another layer for modulating miRNA activities. However, except for the artificial target mimics manipulated for functional studies on certain miRNA genes, only one example, IPS1 (Induced by Phosphate Starvation 1)—miR399 was experimentally confirmed in planta. To date, few analyses for comprehensive identification of natural target mimics have been performed in plants. Thus, limited evidences are available to provide detailed information for interrogating the questionable issue whether target mimicry was widespread in planta, and implicated in certain biological processes.

Results

In this study, genome-wide computational prediction of endogenous miRNA mimics was performed in Arabidopsis and rice, and dozens of target mimics were identified. In contrast to a recent report, the densities of target mimic sites were found to be much higher within the untranslated regions (UTRs) when compared to those within the coding sequences (CDSs) in both plants. Some novel sequence characteristics were observed for the miRNAs that were potentially regulated by the target mimics. GO (Gene Ontology) term enrichment analysis revealed some functional insights into the predicted mimics. After degradome sequencing data-based identification of miRNA targets, the regulatory networks constituted by target mimics, miRNAs and their downstream targets were constructed, and some intriguing subnetworks were further exploited.

Conclusions

These results together suggest that target mimicry may be widely implicated in regulating miRNA activities in planta, and we hope this study could expand the current understanding of miRNA-involved regulatory networks.

On the complexity of miRNA-mediated regulation in plants: novel insights into the genomic organization of plant miRNAs

MicroRNAs (miRNAs) are endogenous small non-coding RNAs of about 20–24 nt, known to play key roles in post-transcriptional gene regulation, that can be coded either by intergenic or intragenic loci. Intragenic (exonic and intronic) miRNAs can exert a role in the transcriptional regulation and RNA processing of their host gene. Moreover, the possibility that the biogenesis of exonic miRNAs could destabilize the corresponding protein-coding transcript and reduce protein synthesis makes their characterization very intriguing and suggests a possible novel mechanism of post-transcriptional regulation of gene expression.

This work was designed to carry out the computational identification of putative exonic miRNAs in 30 plant species and the analysis of possible mechanisms involved in their regulation.

The results obtained represent a useful starting point for future studies on the complex networks involved in microRNA-mediated gene regulation in plants.

Large-scale identification of mirtrons in Arabidopsis and rice

A new catalog of microRNA (miRNA) species called mirtrons has been discovered in animals recently, which originate from spliced introns of the gene transcripts. However, only one putative mirtron, osa-MIR1429, has been identified in rice (Oryza sativa). We employed a high-throughput sequencing (HTS) data- and structure-based approach to do a genome-wide search for the mirtron candidate in both Arabidopsis (Arabidopsis thaliana) and rice. Five and eighteen candidates were discovered in the two plants respectively. To investigate their biological roles, the targets of these mirtrons were predicted and validated based on degradome sequencing data. The result indicates that the mirtrons could guide target cleavages to exert their regulatory roles post-transcriptionally, which needs further experimental validation.

psRNATarget: a plant small RNA target analysis server

Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/.