Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana

Functions of microRNAs in plant stress responses

The discovery of microRNAs (miRNAs) as gene regulators has led to a paradigm shift in the understanding of post-transcriptional gene regulation in plants and animals. miRNAs have emerged as master regulators of plant growth and development. Evidence suggesting that miRNAs play a role in plant stress responses arises from the discovery that miR398 targets genes with known roles in stress tolerance. In addition, the expression profiles of most miRNAs that are implicated in plant growth and development are significantly altered during stress. These later findings imply that attenuated plant growth and development under stress may be under the control of stress-responsive miRNAs. Here we review recent progress in the understanding of miRNA-mediated plant stress tolerance.

microRNAs responsive to ozone-induced oxidative stress in Arabidopsis thaliana

Ozone is a model abiotic elicitor of reactive oxygen species (ROS). ROS are important oxidative signaling molecules coordinating plant development and responses to biotic and abiotic stresses. Recently, microRNAs have been described as important players in regulating stress responses in plants. In this research we examined the miRNAs that are differentially expressed early in response to ozone in the Arabidopsis thaliana ecotype Col-0 that is tolerant to this oxidant. We used a plant miRNA array to identify 22 miRNA families that are differentially expressed within one hour of ozone fumigation. Majority of these miRNAs were also reported in response to UV-B stress. Analysis of the miRNA target genes showed a strong negative correlation to the miRNA expression. In silico promoter analysis of miRNA genes identified several stress responsive cis-elements that were enriched in the promoters of ozone responsive genes. Majority of the target genes of ozone responsive miRNAs were associated with developmental processes. Based on these results we suggest that post-transcriptional gene regulation via miRNAs may aid in resource allocation by downregulating developmental processes to cater to the oxidative stress demands on plants.

MicroRNA expression analysis in the cellulosic biofuel crop switchgrass (Panicum virgatum) under abiotic stress

Switchgrass has increasingly been recognized as a dedicated biofuel crop for its broad adaptation to marginal lands and high biomass. However, little is known about the basic biology and the regulatory mechanisms of gene expression in switchgrass, particularly under stress conditions. In this study, we investigated the effect of salt and drought stress on switchgrass germination, growth and the expression of small regulatory RNAs. The results indicate that salt stress had a gradual but significant negative effect on switchgrass growth and development. The germination rate was significantly decreased from 82% for control to 36% under 1% NaCl treatment. However, drought stress had little effect on the germination rate but had a significant effect on the growth of switchgrass under the severest salinity stress. Both salt and drought stresses altered the expression pattern of miRNAs in a dose-dependent manner. However, each miRNA responded to drought stress in a different pattern. Salt and drought stress changed the expression level of miRNAs mainly from 0.9-fold up-regulation to 0.7-fold down-regulation. miRNAs were less sensitive to drought treatment than salinity treatment, as evidenced by the narrow fold change in expression levels. Although the range of change in expression level of miRNAs was similar under salt and drought stress, no miRNAs displayed significant change in expression level under all tested salt conditions. Two miRNAs, miR156 and miR162, showed significantly change in expression level under high drought stress. This suggests that miR156 and miR162 may attribute to the adaption of switchgrass to drought stress and are good candidates for improving switchgrass as a biofuel crop by transgenic technology.

Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress

MicroRNAs (miRNAs) are a class of small, non-coding RNAs that play important downregulation roles in plants growth, development, and stress responses. To better identify Populus tomentosa miRNAs and understand the functions of miRNAs in response to water stress (drought and flooding), 152 conserved miRNAs belonging to 36 miRNA families, 8 known but non-conserved miRNAs and 64 candidate novel miRNAs belonging to 54 miRNA families were identified and analyzed from three small RNA (sRNA) libraries (drought treatment, flooding treatment, and control) by high-throughput sequencing combined with qRT-PCR. Significant changes in the expression of 17 conserved miRNA families and nine novel miRNAs were observed in response to drought stress, and in seven conserved miRNA families and five novel miRNAs in response to flooding stress. Both miRNA and miRNA*s were involved in the regulation of plant stress responses. The annotation of the potential targets of miRNAs with differential expression indicate that many types of genes encoding transcription factors, enzymes, and signal transduction components are implicated in the abiotic stress response..

Ethylene-responsive miRNAs in roots of Medicago truncatula identified by high-throughput sequencing at whole genome level

Ethylene is one of the classical plant hormones with a diverse function in plant growth and development. Root elongation is sensitive to ethylene such that treatments with ethylene and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) inhibit root growth. MicroRNA as one type of endogenous, non-coding small RNAs, plays an important role in regulation of plant growth, development and hormonal signaling by affecting expression of target genes. However, there has been no detailed study to evaluate the role of microRNAs in mediation of ethylene-dependent physiological processes in plants. Medicago truncatula is a model plant widely used for investigation of molecular biology in legume species. In this study, we constructed two small RNA libraries from roots of M. truncatula treated with and without ACC. High-throughput sequencing was employed to sequence the small RNA libraries, and more than 30 M raw reads were obtained. We annotated 301 known miRNAs and identified 3 new miRNAs in the two libraries. Treatment of M. truncatula with 10 μM ACC led to changes in expression of 8 miRNAs. The targets of the ethylene-responsive miRNAs were predicted by bioinformatic approach. The potential role of the ethylene-responsive miRNAs in the ethylene-induced inhibition of root elongation is discussed. These results are useful for functional characterization of miRNAs in mediation of ethylene-dependent physiological processes in general and root elongation in particular.

Transcriptional regulation of Arabidopsis MIR168a and argonaute1 homeostasis in abscisic acid and abiotic stress responses

The accumulation of a number of small RNAs in plants is affected by abscisic acid (ABA) and abiotic stresses, but the underlying mechanisms are poorly understood. The miR168-mediated feedback regulatory loop regulates ARGONAUTE1 (AGO1) homeostasis, which is crucial for gene expression modulation and plant development. Here, we reveal a transcriptional regulatory mechanism by which MIR168 controls AGO1 homeostasis during ABA treatment and abiotic stress responses in Arabidopsis (Arabidopsis thaliana). Plants overexpressing MIR168a and the AGO1 loss-of-function mutant ago1-27 display ABA hypersensitivity and drought tolerance, while the mir168a-2 mutant shows ABA hyposensitivity and drought hypersensitivity. Both the precursor and mature miR168 were induced under ABA and several abiotic stress treatments, but no obvious decrease for the target of miR168, AGO1, was shown under the same conditions. However, promoter activity analysis indicated that AGO1 transcription activity was increased under ABA and drought treatments, suggesting that transcriptional elevation of MIR168a is required for maintaining a stable AGO1 transcript level during the stress response. Furthermore, we showed both in vitro and in vivo that the transcription of MIR168a is directly regulated by four abscisic acid-responsive element (ABRE) binding factors, which bind to the ABRE cis-element within the MIR168a promoter. This ABRE motif is also found in the promoter of MIR168a homologs in diverse plant species. Our findings suggest that transcriptional regulation of miR168 and posttranscriptional control of AGO1 homeostasis may play an important and conserved role in stress response and signal transduction in plants.

Regulation of miR319 during cold stress in sugarcane

MicroRNAs (miRNAs) are part of a novel mechanism of gene regulation that is active in plants under abiotic stress conditions. In the present study, 12 miRNAs were analysed to identify miRNAs differentially expressed in sugarcane subjected to cold stress (4 °C). The expression of miRNAs assayed by stem-loop RT-PCR showed that miR319 is up-regulated in sugarcane plantlets exposed to 4 °C for 24 h. The induction of miR319 expression during cold stress was observed in both roots and shoots. Sugarcane miR319 was also regulated by treatment with abscisic acid. Putative targets of this miRNA were identified and their expression levels were decreased in sugarcane plantlets exposed to cold. The cleavage sites of two targets were mapped using a 5' RACE PCR assay confirming the regulation of these genes by miR319. When sugarcane cultivars contrasting in cold tolerance were subjected to 4 °C, we observed up-regulation of miR319 and down-regulation of the targets in both varieties; however, the changes in expression were delayed in the cold-tolerant cultivar. These results suggest that differences in timing and levels of the expression of miR319 and its targets could be tested as markers for selection of cold-tolerant sugarcane cultivars.

Bioinformatic identification of cassava miRNAs differentially expressed in response to infection by Xanthomonas axonopodis pv. manihotis

BACKGROUND

microRNAs (miRNAs) are short RNA molecules that control gene expression by silencing complementary mRNA. They play a crucial role in stress response in plants, including biotic stress. Some miRNAs are known to respond to bacterial infection in Arabidopsis thaliana but it is currently unknown whether these responses are conserved in other plants and whether novel species-specific miRNAs could have a role in defense.

RESULTS

This work addresses the role of miRNAs in the Manihot esculenta (cassava)-Xanthomonas axonopodis pv. manihotis (Xam) interaction. Next-generation sequencing was used for analyzing small RNA libraries from cassava tissue infected and non-infected with Xam. A full repertoire of cassava miRNAs was characterized, which included 56 conserved families and 12 novel cassava-specific families. Endogenous targets were predicted in the cassava genome for many miRNA families. Some miRNA families' expression was increased in response to bacterial infection, including miRNAs known to mediate defense by targeting auxin-responding factors as well as some cassava-specific miRNAs. Some bacteria-repressed miRNAs included families involved in copper regulation as well as families targeting disease resistance genes. Putative transcription factor binding sites (TFBS) were identified in the MIRNA genes promoter region and compared to promoter regions in miRNA target genes and protein coding genes, revealing differences between MIRNA gene transcriptional regulation and other genes.

CONCLUSIONS

Taken together these results suggest that miRNAs in cassava play a role in defense against Xam, and that the mechanism is similar to what's known in Arabidopsis and involves some of the same families.

Differential gene expression in different types of Hevea brasiliensis roots

Three types of roots (taproots, first order laterals and second order laterals) were functionally characterized on 7-month-old in vitro plantlets regenerated by somatic embryogenesis in Hevea brasiliensis. A histological analysis revealed different levels of differentiation depending on root diameter. A primary structure was found in first and second order lateral roots, while taproots displayed a secondary structure. The expression of 48 genes linked to some of the regulatory pathways acting in roots was compared in leaves, stems and the different types of roots by real-time RT-PCR. Thirteen genes were differentially expressed in the different organs studied in plants grown under control conditions. Nine additional other genes were differentially regulated between organs under water deficit conditions. In addition, 10 genes were significantly regulated in response to water deficit, including 8 regulated mainly in lateral roots types. Our results suggest that the regulation of gene expression in lateral roots is different than that in taproots, which have a main role in nutrient uptake and transport, respectively.

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs have a similar structure, function, and biogenesis as miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences. Besides their roles in growth and development and maintenance of genome integrity, small RNAs are also important components in plant stress responses. One way in which plants respond to environmental stress is by modifying their gene expression through the activity of small RNAs. Thus, understanding how small RNAs regulate gene expression will enable researchers to explore the role of small RNAs in biotic and abiotic stress responses. This review focuses on the regulatory roles of plant small RNAs in the adaptive response to stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

MicroRNAs (miRNAs) play important roles in response of plants to biotic and abiotic stresses. Aluminum (Al) toxicity is a major factor limiting plant growth in acidic soils. However, there has been limited report on the involvement of miRNAs in response of plants to toxic Al(3+). To identify Al(3+)-responsive miRNAs at whole-genome level, high-throughput sequencing technology was used to sequence libraries constructed from root apices of the model legume plant Medicago truncatula treated with and without Al(3+). High-throughput sequencing of the control and two Al(3+)-treated libraries led to generation of 17.1, 14.1 and 17.4 M primary reads, respectively. We identified 326 known miRNAs and 21 new miRNAs. Among the miRNAs, expression of 23 miRNAs was responsive to Al(3+), and the majority of Al(3+)-responsive mRNAs was down-regulated. We further classified the Al(3+)-responsive miRNAs into three groups based on their expression patterns: rapid-responsive, late-responsive and sustained-responsive miRNAs. The majority of Al(3+)-responsive miRNAs belonged to the 'rapid-responsive' category, i.e. they were responsive to short-term, but not long-term Al(3+) treatment. The Al(3+)-responsive miRNAs were also verified by quantitative real-time PCR. The potential targets of the 21 new miRNAs were predicted to be involved in diverse cellular processes in plants, and their potential roles in Al(3+)-induced inhibition of root growth were discussed. These findings provide valuable information for functional characterization of miRNAs in Al(3+) toxicity and tolerance.

The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis

BACKGROUND

Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found. Due to low abundance, non conserved miRNAs are difficult to identify and isolate using conventional approaches. Conversely, deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs.No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots.

RESULTS

Conserved and novel miRNAs were discovered using accepted criteria. The expression level of selected miRNAs was monitored by quantitative real-time PCR. Targets were predicted and validated for their cleavage site. A total of 122 artichoke miRNAs were identified, 98 (25 families) of which were conserved with other plant species, and 24 were novel. Some miRNAs were differentially expressed according to tissue or condition, magnitude of variation after salt stress being more pronounced in roots. Target function was predicted by comparison to Arabidopsis proteins; the 43 targets (23 for novel miRNAs) identified included transcription factors and other genes, most of which involved in the response to various stresses. An unusual cleaved transcript was detected for miR393 target, transport inhibitor response 1.

CONCLUSIONS

The miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.

Genome-wide identification of cold-responsive and new microRNAs in Populus tomentosa by high-throughput sequencing

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate the expression of target mRNAs in plant growth, development, abiotic stress responses, and pathogen responses. Cold stress is one of the most common abiotic factors affecting plants, and it adversely affects plant growth, development, and spatial distribution. To understand the roles of miRNAs under cold stress in Populus tomentosa, we constructed two small RNA libraries from plantlets treated or not with cold conditions (4°C for 8 h). High-throughput sequencing of the two libraries identified 144 conserved miRNAs belonging to 33 miRNA families and 29 new miRNAs (as well as their corresponding miRNA(∗)s) belonging to 23 miRNA families. Differential expression analysis showed that 21 miRNAs were down-regulated and nine miRNAs were up-regulated in response to cold stress. Among them, 19 cold-responsive miRNAs, two new miRNAs and their corresponding miRNA(∗)s were validated by qRT-PCR. A total of 101 target genes of the new miRNAs were predicted using a bioinformatics approach. These target genes are involved in growth and resistance to various stresses. The results demonstrated that Populus miRNAs play critical roles in the cold stress response.

Metabolic and miRNA profiling of TMV infected plants reveals biphasic temporal changes

Plant viral infections induce changes including gene expression and metabolic components. Identification of metabolites and microRNAs (miRNAs) differing in abundance along infection may provide a broad view of the pathways involved in signaling and defense that orchestrate and execute the response in plant-pathogen interactions. We used a systemic approach by applying both liquid and gas chromatography coupled to mass spectrometry to determine the relative level of metabolites across the viral infection, together with a miRs profiling using a micro-array based procedure. Systemic changes in metabolites were characterized by a biphasic response after infection. The first phase, detected at one dpi, evidenced the action of a systemic signal since no virus was detected systemically. Several of the metabolites increased at this stage were hormone-related. miRs profiling after infection also revealed a biphasic alteration, showing miRs alteration at 5 dpi where no virus was detected systemically and a late phase correlating with virus accumulation. Correlation analyses revealed a massive increase in the density of correlation networks after infection indicating a complex reprogramming of the regulatory pathways, either in response to the plant defense mechanism or to the virus infection itself. Our data propose the involvement of a systemic signaling on early miRs alteration.

Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity

MicroRNAs (miRNAs) are a class of endogenous, non-coding small RNAs that play important roles in many developmental processes and stress responses in plants and animals. Cotton (Gossypium hirsutum L.) is considered a relatively salt-tolerant non-halophytic plant species. To study the role of miRNAs in salt adaptation, a salt-tolerant cotton cultivar SN-011 and a salt-sensitive cultivar LM-6 were used to detect differentially expressed miRNAs. Using miRNA microarray analysis and a computational approach, 17 cotton miRNAs belonging to eight families were identified. Although they are conserved, 12 of them showed a genotype-specific expression model in both the cultivars. Under salt stress treatment, miR156a/d/e, miR169, miR535a/b and miR827b were dramatically down-regulated in SN-011, while miR167a, miR397a/b and miR399a were up-regulated. Only miR159 was found to be down-regulated in LM-6 under salt stress. To gain insight into their functional significance, 26 target genes were predicted and their functional similarity was further analyzed. Quantitative real-time PCR showed that the expression of seven target genes showed a significant inverse correlation with corresponding miRNAs. These differentially expressed miRNAs can help in further study into the role of transcriptome homeostasis in the adaptation responses of cotton to salt.

Microarray-based identification of conserved microRNAs from Pinellia ternata

A large number of microRNAs (miRNAs) reportedly play important roles in plant development; however, scarcely any of these have been found in Pinellia ternata, a herbaceous plant with special physiologic characteristics and important medicinal value. To detect P. ternata miRNAs, an in situ synthesized custom microarray of plant miRNAs was employed, following verification of the presence of the miRNAs through reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR) in the current study. A total of 54 miRNAs belonging to 23 miRNA families were identified. RT-PCR applied to the eight miRNAs validated the microarray results. qRT-PCR that targeted eleven miRNAs showed the presence of miRNAs in different tissues with different expression levels, especially, miRNA319 expression level in the tubers is nearly 10 times higher than that in the stalks and leaves. This is the first report on the miRNAs in P. ternata, which will enable further investigation of their roles in P. ternata.

Identification of conserved microRNAs and their targets in Chinese cabbage (Brassica rapa subsp. pekinensis)

The microRNAs (miRNAs) are a new class of small nonprotein-coding RNAs that have been identified to regulate gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Until now, thousands of miRNAs have been identified in many plants species. However, only 23 miRNAs have been reported from the microRNA database in Chinese cabbage ( Brassica rapa subsp. pekinensis ), one of the most widely cultivated vegetables in China and East Asia. In the present study, 168 potential miRNAs, derived from 22 EST and 119 GSS sequences in Chinese cabbage were identified and classified into 38 miRNA families by well-defined computational analysis, in which most belonged to the miRNA1533, miRNA156, and miRNA2911 families. Totally, there are 129 identified miRNAs potentially targeting 1386 Chinese cabbage EST genes, which play roles in multiple biological and metabolic processes including metabolism, cell growth, signal transduction, stress response, and plant development. Gene ontology analysis, based on these target proteins, showed that 688, 532, and 287 genes were involved in molecular functions, biological processes, and cellular components, respectively. KEGG pathway analysis demonstrated that these miRNAs participated in 214 metabolism pathways, including, amongst others, plant–pathogen interaction, fatty acid metabolism, amino acid metabolism, nitrogen metabolism, plant hormone signal transduction.

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

Background

Higher plants exhibit remarkable phenotypic plasticity allowing them to adapt to an extensive range of environmental conditions. Sorghum is a cereal crop that exhibits exceptional tolerance to adverse conditions, in particular, water-limiting environments. This study utilized next generation sequencing (NGS) technology to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) in order to elucidate genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.

Results

RNA-Seq results revealed transcriptional activity of 28,335 unique genes from sorghum root and shoot tissues subjected to polyethylene glycol (PEG)-induced osmotic stress or exogenous ABA. Differential gene expression analyses in response to osmotic stress and ABA revealed a strong interplay among various metabolic pathways including abscisic acid and 13-lipoxygenase, salicylic acid, jasmonic acid, and plant defense pathways. Transcription factor analysis indicated that groups of genes may be co-regulated by similar regulatory sequences to which the expressed transcription factors bind. We successfully exploited the data presented here in conjunction with published transcriptome analyses for rice, maize, and Arabidopsis to discover more than 50 differentially expressed, drought-responsive gene orthologs for which no function had been previously ascribed.

Conclusions

The present study provides an initial assemblage of sorghum genes and gene networks regulated by osmotic stress and hormonal treatment. We are providing an RNA-Seq data set and an initial collection of transcription factors, which offer a preliminary look into the cascade of global gene expression patterns that arise in a drought tolerant crop subjected to abiotic stress. These resources will allow scientists to query gene expression and functional annotation in response to drought.

Salt and drought stresses induce the aberrant expression of microRNA genes in tobacco

Drought and salinity stresses significantly altered microRNA (miRNA) expression in a dose-dependent manner in tobacco. Salinity stress changed the miRNA expression levels from a 6.86-fold down-regulation to a 616.57-fold up-regulation. Alternatively, miRNAs were down-regulated by 2.68-fold and up-regulated 2810-fold under drought conditions. miR395 was most sensitive to both stresses and was up-regulated by 616 and 2810-folds by 1.00% PEG and 0.171 M NaCl, respectively. Salinity and drought stresses also changed the expression of protein-coding genes [alcohol dehydrogenase (ADH) and alcohol peroxidase (APX)]. The results suggest that miRNAs may play an important role in plant response to environmental abiotic stresses. Further investigation of miRNA-mediated gene regulation may elucidate the molecular mechanism of plant tolerance to abiotic stresses and has the potential to create a miRNA-based biotechnology for improving plant tolerance to drought and salinity stresses.

Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes

BACKGROUND

Cowpea (Vigna unguiculata) is an important crop in arid and semi-arid regions and is a good model for studying drought tolerance. MicroRNAs (miRNAs) are known to play critical roles in plant stress responses, but drought-associated miRNAs have not been identified in cowpea. In addition, it is not understood how miRNAs might contribute to different capacities of drought tolerance in different cowpea genotypes.

RESULTS

We generated deep sequencing small RNA reads from two cowpea genotypes (CB46, drought-sensitive, and IT93K503-1, drought-tolerant) that grew under well-watered and drought stress conditions. We mapped small RNA reads to cowpea genomic sequences and identified 157 miRNA genes that belong to 89 families. Among 44 drought-associated miRNAs, 30 were upregulated in drought condition and 14 were downregulated. Although miRNA expression was in general consistent in two genotypes, we found that nine miRNAs were predominantly or exclusively expressed in one of the two genotypes and that 11 miRNAs were drought-regulated in only one genotype, but not the other.

CONCLUSIONS

These results suggest that miRNAs may play important roles in drought tolerance in cowpea and may be a key factor in determining the level of drought tolerance in different cowpea genotypes.

MiR398 and plant stress responses

Because of their sessile nature, plants are constantly exposed to a multitude of abiotic and biotic stresses. Great progress has been made in elucidating the complex stress response mechanisms in plants. MicroRNAs (miRNAs), recently recognized as important regulators of gene expression at the posttranscriptional level, have been found to be involved in plant stress responses. Most plant miRNAs usually mediate cleavage of their target mRNAs. The observation that some miRNAs are up- or downregulated in response to stress implies that miRNAs play vital roles in plant resistance to abiotic and biotic stresses. Manipulation of miRNA-guided gene regulation may represent a new way to engineer plants with improved stress tolerance. Among stress-responsive miRNAs, miRNA398 (miR398) is a miRNA proposed to be directly linked to the plant stress regulatory network and regulates plant responses to oxidative stress, water deficit, salt stress, abscisic acid stress, ultraviolet stress, copper and phosphate deficiency, high sucrose and bacterial infection. This review highlights recent progress in understanding the crucial role of miR398 in plant stress responses, and also includes a discussion of miR398-centered gene regulatory network.

Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network

Understanding the responses of plants to the major environmental stressors drought and salt is an important topic for the biotechnological application of functional mechanisms of stress adaptation. Here, we review recent discoveries on regulatory systems that link sensing and signaling of these environmental cues focusing on the integrative function of transcription activators. Key components that control and modulate stress adaptive pathways include transcription factors (TFs) ranging from bZIP, AP2/ERF, and MYB proteins to general TFs. Recent studies indicate that molecular dynamics as specific homodimerizations and heterodimerizations as well as modular flexibility and posttranslational modifications determine the functional specificity of TFs in environmental adaptation. Function of central regulators as NAC, WRKY, and zinc finger proteins may be modulated by mechanisms as small RNA (miRNA)-mediated posttranscriptional silencing and reactive oxygen species signaling. In addition to the key function of hub factors of stress tolerance within hierarchical regulatory networks, epigenetic processes as DNA methylation and posttranslational modifications of histones highly influence the efficiency of stress-induced gene expression. Comprehensive elucidation of dynamic coordination of drought and salt responsive TFs in interacting pathways and their specific integration in the cellular network of stress adaptation will provide new opportunities for the engineering of plant tolerance to these environmental stressors.

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

BACKGROUND

MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in development and stress response in plants by negatively affecting gene expression post-transcriptionally. Identification of miRNAs at the global genome-level by high-throughout sequencing is essential to functionally characterize miRNAs in plants. Drought is one of the common environmental stresses limiting plant growth and development. To understand the role of miRNAs in response of plants to drought stress, drought-responsive miRNAs were identified by high-throughput sequencing in a legume model plant, Medicago truncatula.

RESULTS

Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 238 potential candidate miRNAs were identified, and among them 14 new miRNAs and 15 new members of known miRNA families whose complementary miRNA*s were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. Among the 29 new miRNAs/new members of known miRNA families, 8 miRNAs were responsive to drought stress with both 4 miRNAs being up- and down-regulated, respectively. The known and predicted targets of the drought-responsive miRNAs were found to be involved in diverse cellular processes in plants, including development, transcription, protein degradation, detoxification, nutrient status and cross adaptation.

CONCLUSIONS

We identified 32 known members of 10 miRNA families and 8 new miRNAs/new members of known miRNA families that were responsive to drought stress by high-throughput sequencing of small RNAs from M. truncatula. These findings are of importance for our understanding of the roles played by miRNAs in response of plants to abiotic stress in general and drought stress in particular.

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

BACKGROUND

MicroRNAs (miRNAs) are small, endogenous RNAs that play important regulatory roles in development and stress response in plants by negatively affecting gene expression post-transcriptionally. Identification of miRNAs at the global genome-level by high-throughout sequencing is essential to functionally characterize miRNAs in plants. Drought is one of the common environmental stresses limiting plant growth and development. To understand the role of miRNAs in response of plants to drought stress, drought-responsive miRNAs were identified by high-throughput sequencing in a legume model plant, Medicago truncatula.

RESULTS

Two hundreds eighty three and 293 known miRNAs were identified from the control and drought stress libraries, respectively. In addition, 238 potential candidate miRNAs were identified, and among them 14 new miRNAs and 15 new members of known miRNA families whose complementary miRNA*s were also detected. Both high-throughput sequencing and RT-qPCR confirmed that 22 members of 4 miRNA families were up-regulated and 10 members of 6 miRNA families were down-regulated in response to drought stress. Among the 29 new miRNAs/new members of known miRNA families, 8 miRNAs were responsive to drought stress with both 4 miRNAs being up- and down-regulated, respectively. The known and predicted targets of the drought-responsive miRNAs were found to be involved in diverse cellular processes in plants, including development, transcription, protein degradation, detoxification, nutrient status and cross adaptation.

CONCLUSIONS

We identified 32 known members of 10 miRNA families and 8 new miRNAs/new members of known miRNA families that were responsive to drought stress by high-throughput sequencing of small RNAs from M. truncatula. These findings are of importance for our understanding of the roles played by miRNAs in response of plants to abiotic stress in general and drought stress in particular.

The role of epigenetic processes in controlling flowering time in plants exposed to stress

Plants interact with their environment by modifying gene expression patterns. One mechanism for this interaction involves epigenetic modifications that affect a number of aspects of plant growth and development. Thus, the epigenome is highly dynamic in response to environmental cues and developmental changes. Flowering is controlled by a set of genes that are affected by environmental conditions through an alteration in their expression pattern. This ensures the production of flowers even when plants are growing under adverse conditions, and thereby enhances transgenerational seed production. In this review recent findings on the epigenetic changes associated with flowering in Arabidopsis thaliana grown under abiotic stress conditions such as cold, drought, and high salinity are discussed. These epigenetic modifications include DNA methylation, histone modifications, and the production of micro RNAs (miRNAs) that mediate epigenetic modifications. The roles played by the phytohormones abscisic acid (ABA) and auxin in chromatin remodelling are also discussed. It is shown that there is a crucial relationship between the epigenetic modifications associated with floral initiation and development and modifications associated with stress tolerance. This relationship is demonstrated by the common epigenetic pathways through which plants control both flowering and stress tolerance, and can be used to identify new epigenomic players.

Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa)

MicroRNAs (miRNAs) are a class of small non-coding RNAs that negatively regulate specific target mRNAs at the post-transcriptional level. Plant miRNAs have been implicated in developmental processes and adaptations to environmental stresses. Cadmium (Cd) is a non-essential heavy metal that is highly toxic to plants. To investigate the responsive functions of miRNAs under Cd stress, miRNA expression in Cd-stressed rice (Oryza sativa) was profiled using a microarray assay. A total of 19 Cd-responsive miRNAs were identified, of which six were further validated experimentally. Target genes were also predicted for these Cd-responsive miRNAs, which encoded transcription factors, and proteins associated with metabolic processes or stress responses. In addition, the mRNA levels of several targets were negatively correlated with the corresponding miRNAs under Cd stress. Promoter analysis showed that metal stress-responsive cis-elements tended to occur more frequently in the promoter regions of Cd-responsive miRNAs. These findings suggested that miRNAs played an important role in Cd tolerance in rice, and highlighted a novel molecular mechanism of heavy metal tolerance in plants.

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs have a similar structure, function, and biogenesis as miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences. Besides their roles in growth and development and maintenance of genome integrity, small RNAs are also important components in plant stress responses. One way in which plants respond to environmental stress is by modifying their gene expression through the activity of small RNAs. Thus, understanding how small RNAs regulate gene expression will enable researchers to explore the role of small RNAs in biotic and abiotic stress responses. This review focuses on the regulatory roles of plant small RNAs in the adaptive response to stresses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in phalaenopsis orchid

Plant small RNAs (smRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate a group of genes involved in plant development and responses to environmental stimuli. Low temperature is necessary to initiate stalk development in the orchid Phalaenopsis aphrodite subsp. formosana. To identify smRNAs in Phalaenopsis responding to low temperatures, a smRNA profiling analysis using high-throughput sequencing technology was performed. Subsequent bioinformatic analysis was applied to categorize the miRNAs identified. A total of 37,533,509 smRNA reads yielded 11,129 independent orchid miRNA sequences, representing 329 known miRNA families identified in other plant species. Because the genomic resources available for Phalaenopsis are limited, a transcriptomic database was established using deep sequencing data sets to identify miRNAs precursors and their target transcripts. Comparing small RNAs and the transcriptomic database, 14 putative miRNA precursors of 10 miRNA families were identified, as were hundreds of putative targets. Comparing sequencing data and smRNA northern hybridization results identified miR156, miR162, miR528 and miR535 as low temperature-induced miRNAs. In addition, tissue-specific expression of these miRNAs was investigated. It was concluded that miR156 and miR172 may be components of a regulatory pathway mediating transition from the vegetative to the reproductive phase in Phalaenopsis. The smRNA and transcriptomic databases could be the foundations for further research aimed at elucidating the control of the flowering time in orchids.

Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato

To defend against invading pathogens, plants possess RNA silencing mechanisms involving small RNAs (miRNAs, siRNAs). Also viroids - plant infectious, non-coding, unencapsidated RNA - cause the production of viroid-specific small RNAs (vsRNA), but viroids do escape the cytoplasmic silencing mechanism. Viroids with minor sequence variations can produce different symptoms in infected plants, suggesting an involvement of vsRNAs in symptom production. We analyzed by deep sequencing the spectrum of vsRNAs induced by the PSTVd strain AS1, which causes strong symptoms such as dwarfing and necrosis upon infection of tomato plants cv Rutgers. Indeed, vsRNAs found with highest frequency mapped to the pathogenicity-modulating domain of PSTVd, supporting an involvement of vsRNAs in symptom production. Furthermore, in PSTVd AS1-infected plants the accumulation of some endogenous miRNAs, which are involved in leaf development via regulation of transcription factors, is suppressed. The latter finding supports the hypothesis that a miRNA-dependent (mis)regulation of transcription factors causes the viroid symptoms.

miRNA expression patterns of Triticum dicoccoides in response to shock drought stress

Drought is a major environmental stress factor that affects plant growth and development worldwide. Wild emmer wheat (Triticum turgidum ssp. dicoccoides), the ancestor of domesticated durum wheat (Triticum turgidum ssp. durum), has great potential for improving the understanding of the wheat drought response. MicroRNAs (miRNAs) are a recently discovered class of gene expression regulators that have also been linked to several plant stress responses; however, this relationship is just beginning to be understood. miRNA expression patterns of drought-resistant wild emmer wheat in response to drought stress were investigated using a plant miRNA microarray platform. Expression was detected to be 205 miRNAs in control and 438 miRNAs in drought-stressed leaf and root tissues. Of these miRNAs, the following 13 were differentially regulated in response to drought: miR1867, miR896, miR398, miR528, miR474, miR1450, miR396, miR1881, miR894, miR156, miR1432, miR166 and miR171. Regulation of miRNAs upon 4 and 8 h drought stress applications observed by qRT-PCR. Target transcripts of differentially regulated miRNAs were computationally predicted. In addition to miRNA microarray study, five new conserved T. turgidum miRNAs were identified through a homology-based approach, and their secondary structures and putative targets were predicted. These findings both computationally and experimentally highlight the presence of miRNAs in T. dicoccoides and further extend the role of miRNAs under shock drought stress conditions.

The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana

Mediator is a conserved multi-subunit complex known to promote the transcription of protein-coding genes by RNA polymerase II (Pol II) in eukaryotes. It has been increasingly realized that Pol II transcribes a large number of intergenic loci to generate noncoding RNAs, but the role of Mediator in Pol II-mediated noncoding RNA production has been largely unexplored. The role of Mediator in noncoding RNA production in plants is particularly intriguing given that plants have evolved from Pol II two additional polymerases, Pol IV and Pol V, to specialize in noncoding RNA production and transcriptional gene silencing at heterochromatic loci. Here, we show that Mediator is required for microRNA (miRNA) biogenesis by recruiting Pol II to promoters of miRNA genes. We also show that several well-characterized heterochromatic loci are de-repressed in Mediator mutants and that Mediator promotes Pol II-mediated production of long noncoding scaffold RNAs, which serve to recruit Pol V to these loci. This study expands the function of Mediator to include Pol II-mediated intergenic transcription and implicates a role of Mediator in genome stability.

Pol II-directed short RNAs suppress the nuclear export of mRNA

The synthesis and subsequent nuclear export of non-coding RNA (ncRNA) directed by RNA polymerase (Pol) II is very sensitive to abiotic and biotic external stimuli including pathogen challenges. To assess whether stress-induced ncRNAs may suppress the nuclear export of mRNA, we exploited the ability of Agrobacterium tumefaciens to co-deliver Pol I, II and III promoter-based vectors for the transcription of short (s) ncRNAs, GFP mRNA or genomic RNA of plant viruses (Tobacco mosaic virus, TMV; or Potato virus X, PVX) into the nucleus of Nicotiana benthamiana cells. We showed that, in contrast to Pol I- and Pol III-derived sncRNAs, all tested Pol II-derived sncRNAs (U6 RNA, tRNA or artificial RNAs) resulted in decreased expression of GFP and host mRNA. The level of this inhibitory effect depended on the non-coding transcript length and promoter strength. Short coding RNA (scRNA) can also compete with mRNA for nuclear export. We showed that scRNA, an artificial 117-nt short sequence encoding Elastin-Like peptide element tandems with FLAG sequence (ELF) and the 318-nt N. benthamiana antimicrobial peptide thionin (defensin) gene efficiently decreased GFP expression. The stress-induced export of Pol II-derived sncRNA and scRNA into the cytoplasm via the mRNA export pathway may block nucleocytoplasmic traffic including the export of mRNA responsible for antivirus protection. Consistent with this model, we observed that Pol II-derived sncRNAs as well as scRNA, thionin and ELF strongly enhanced the cytoplasmic reproduction of TMV and PVX RNA.

[Advances in plant microRNA and stresses response.]

MicroRNAs (miRNAs) are endogenous 16-29 nt non-coding small RNAs that were are generally found in species and typically encoded by endogenous genes. They play an important regulatory role at post-transcription level by targeting mRNA cleavage and translation repression. More and more plant miRNAs had been predicted and identified along with the development of bioinformatics and experimental techniques. At stress conditions, plant miRNAs also play a role in adaptation by up-regulating or down-regulating the miRNA expression. The biogenesis, action mode with target genes, bio-logical functions of plant miRNAs, as well as the stress-responsive miRNAs, were reviewed and the methodologies of miRNA study were also briefly summarized in this paper.

Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.)

Phosphorus is one of the major factors controlling plant growth and productivity. Although physiological and molecular processes of P deficiency have been intensively investigated, our current understanding of the coordinated regulation of phosphate-responsive genes and signal networks is limited. In the present study, we performed a microarray-based genome-wide transcriptional analysis of miRNAs from soybean (Glycine max L.) under phosphate deficiency. miRNAs extracted from P-deficient and P-sufficient soybean were hybridized to an array containing 853 known plant miRNA sequences. An induction ratio significant at p<0.01 was observed for 57 miRNAs belonging to 27 families. Among these miRNA families, which differentially expressed, 7 and 8 were found to be up-regulated, whereas 17 and 6 were down-regulated in leaves and roots, respectively. Seven representative individual miRNAs were selected for qRT-PCR validation, and most showed an expression pattern similar to that on microarray. We further predicted P-responsive cis-elements from the promoters of miRNAs in response to and non-responding to P deficiency. In total, 125 putative cis-elements were identified for 24 soybean P-deficient responsive miRNAs. Interestingly, those miRNAs (54) not responding to P deficiency were also found to contain the same P-responsive motifs. A comparative analysis revealed that the frequency of the motif occurrence in the promoters of miRNA genes in response to P deficiency was higher than that of miRNA genes not responding to P deficiency. Our study provides initial evidence in soybean that a set of miRNAs with a high frequency of P-responsive cis-elements may coordinately regulate the plant response to P deficiency.

Global expression profiling of rice microRNAs by one-tube stem-loop reverse transcription quantitative PCR revealed important roles of microRNAs in abiotic stress responses

MicroRNAs are a class of endogenous small RNA molecules (20-24 nucleotides) that have pivotal roles in regulating gene expression mostly at posttranscriptional levels in plants. Plant microRNAs have been implicated in the regulation of diverse biological processes including growth and stress responses. However, the information about microRNAs in regulating abiotic stress responses in rice is limited. We optimized a one-tube stem-loop reverse transcription quantitative PCR (ST-RT qPCR) for high-throughput expression profiling analysis of microRNAs in rice under normal and stress conditions. The optimized ST-RT qPCR method was as accurate as small RNA gel blotting and was more convenient and time-saving than other methods in quantifying microRNAs. With this method, 41 rice microRNAs were quantified for their relative expression levels after drought, salt, cold, and abscisic acid (ABA) treatments. Thirty-two microRNAs showed induced or suppressed expression after stress or ABA treatment. Further analysis suggested that stress-responsive cis-elements were enriched in the promoters of stress-responsive microRNA genes. The expressions of five and seven microRNAs were significantly affected in the rice plant with defects in stress tolerance regulatory genes OsSKIPa and OsbZIP23, respectively. Some of the predicted target genes of these microRNAs were also related to abiotic stresses. We conclude that ST-RT qPCR is an efficient and reliable method for expression profiling of microRNAs and a significant portion of rice microRNAs participate in abiotic stress response and regulation.

A set of miRNAs from Brassica napus in response to sulphate deficiency and cadmium stress

MicroRNAs (miRNAs) are a class of short endogenous non-coding small RNAs that can base pair their target mRNAs to repress their translation or induce their degradation in organisms. However, whether miRNAs are involved in the global response to sulphate deficiency and heavy metal stress is unknown. In this study, we constructed a small RNA library from rapeseed (Brassica napus) treated with sulphate deficiency and cadmium (Cd²+), respectively. Sequencing analysis revealed 13 conserved miRNAs representing nine families, with five new miRNAs that have not been cloned before. Transcriptional analysis with RT-PCR showed the differential expression of these miRNAs under sulphate deficiency and Cd exposure. We have cloned five genes BnSultr2;1 and BnAPS1-4, which encode a low-affinity sulphate transporter and a family of ATP sulphurylases in B. napus, respectively. BnSultr2;1, BnAPS3 and BnAPS4 were first cloned from B. napus, and BnSultr2;1, BnAPS1, BnAPS3 and BnAPS4 were identified as the targets of miR395. Analysis with 5'-RACE and transformation of MIR395d into B. napus confirmed that all of them were the authentic targets of miR395. Our results support the importance of miRNAs in regulating plant responses to abiotic stresses and suggest that identification of a set of miRNAs would facilitate our understanding of regulatory mechanisms for plant tolerance to sulphate deficiency and heavy metal stress.

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

In Arabidopsis thaliana, four different dicer-like (DCL) proteins have distinct but partially overlapping functions in the biogenesis of microRNAs (miRNAs) and siRNAs from longer, noncoding precursor RNAs. To analyze the impact of different components of the small RNA biogenesis machinery on the transcriptome, we subjected dcl and other mutants impaired in small RNA biogenesis to whole-genome tiling array analysis. We compared both protein-coding genes and noncoding transcripts, including most pri-miRNAs, in two tissues and several stress conditions. Our analysis revealed a surprising number of common targets in dcl1 and dcl2 dcl3 dcl4 triple mutants. Furthermore, our results suggest that the DCL1 is not only involved in miRNA action but also contributes to silencing of a subset of transposons, apparently through an effect on DNA methylation.

MicroRNA171c-targeted SCL6-II, SCL6-III, and SCL6-IV genes regulate shoot branching in Arabidopsis

MicroRNAs (miRNAs) are ∼21-nucleotide noncoding RNAs that play critical roles in regulating plant growth and development through directing the degradation of target mRNAs. Axillary meristem activity, and hence shoot branching, is influenced by a complicated network that involves phytohormones such as auxin, cytokinin, and strigolactone. GAI, RGA, and SCR (GRAS) family members take part in a variety of developmental processes, including axillary bud growth. Here, we show that the Arabidopsis thaliana microRNA171c (miR171c) acts to negatively regulate shoot branching through targeting GRAS gene family members SCARECROW-LIKE6-II (SCL6-II), SCL6-III, and SCL6-IV for cleavage. Transgenic plants overexpressing MIR171c (35Spro-MIR171c) and scl6-II scl6-III scl6-IV triple mutant plants exhibit a similar reduced shoot branching phenotype. Expression of any one of the miR171c-resistant versions of SCL6-II, SCL6-III, and SCL6-IV in 35Spro-MIR171c plants rescues the reduced shoot branching phenotype. Scl6-II scl6-III scl6-IV mutant plants exhibit pleiotropic phenotypes such as increased chlorophyll accumulation, decreased primary root elongation, and abnormal leaf and flower patterning. SCL6-II, SCL6-III, and SCL6-IV are located to the nucleus, and show transcriptional activation activity. Our results suggest that miR171c-targeted SCL6-II, SCL6-III, and SCL6-IV play an important role in the regulation of shoot branch production.

Global analysis of microRNA in Arabidopsis in response to phosphate starvation as studied by locked nucleic acid-based microarrays

MicroRNAs (miRNAs) are short RNA chains (20-24 bp) which are emerging as important regulators of gene expression. miRNAs are encoded by specific genes, and in Arabidopsis, 190 genes have presently been identified. It has been shown that miR399 is essential for the phosphate starvation response, and recent studies have shown transcriptional changes in a number of additional miRNAs in response to a shortage of phosphate. In this study, global profiles of the miRNA in shoots of Arabidopsis plants grown on limited phosphate or full nutrient in combination with sucrose feed were analysed using the miRCURY LNA microRNA Array system. Furthermore, changes in miRNA transcript were compared between a mutant lacking the transcription factor phosphate starvation responses 1 (PHR1) and wild-type plants. The global analysis identified miRNAs belonging to nine families to respond to P deprivation, sucrose or PHR1. Among these, miR399d, miR827, miR866, miR391 and miR163 were most prominently induced upon P starvation, whereas miR169b/c was strongly induced in previously starved plants when provided with sufficient P and more so when combined with an addition of sucrose. This study shows that array analysis is in general agreement with data obtained by other high-throughput technologies. The array data were confirmed by real-time reverse transcriptase-polymerase chain reaction analyses of selected pri-miRNAs. Our data corroborate the implication that several miRNAs are involved in the P-starvation response and further identify miR866 and miR163 as new candidates of miRNAs associated with the regulation of the P-starvation response.

Why is ethylene involved in selective promotion of female flower development in cucumber?

Our recent work by Wang et al (2010), together with previous studies published in the last decade, have provided evidence suggesting a link between ethylene signaling and primordial anther specific DNA damage in female cucumber flowers. These findings explained ethylene promotion of female flower by ethylene inhibition of stamen development. However, it is not determined if ethylene promotes carpel development. In addition, an explanation of why the naturally occurring gas ethylene was selected to be involved in such developmental events remains elusive. In this study, we carried out a phylogenetic analysis of cucumber ACS genes, and analyzed the expression levels of some pre-miRNAs in male, female and hermaphrodite flowers. We found the M gene might have evolved prior to, or "co-opted" into unisexual flower development before the F gene, and miRNA might be involved in carpel development regulation. Based on these observations, we propose a new hypothesis to explain why ethylene was selected to be involved in the evolution of the unisexual cucumber flower.

Regulation of barley miRNAs upon dehydration stress correlated with target gene expression

We aim to identify conserved and dehydration responsive microRNAs (miRNAs) in Hordeum vulgare (barley). A total of 28 new barley miRNAs belonging to 18 distinct miRNA families were identified. Detailed nucleotide analyses revealed that barley pre-miRNAs are in the range of 46-114 nucleotides with average of 77.14. Using 28 newly detected miRNAs as queries, 445 potential target mRNAs were predicted. The predicted miRNAs were differentially expressed and some of them behaved similarly in leaf and root tissues upon stress treatment. Hvu-MIR156, Hvu-MIR166, Hvu-MIR171, and Hvu-MIR408 were detected as dehydration stress-responsive barley miRNAs. To discover target transcripts of barley miRNAs a modified 5' RLM-RACE was performed and seven cleaved miRNA transcripts were retrieved from drought stressed leaf samples. In silico analysis indicated 15 potential EST targets. Measurement of expression levels showed a positive correlation between levels of miRNA expression and suppression of their target mRNA transcripts in dehydration-stress-treated barley.