MicroRNAS and their regulatory roles in plants

Differential expression of microRNAs by arsenate and arsenite stress in natural accessions of rice

Arsenic (As) contamination of rice (Oryza sativa) imposes a serious threat to human health worldwide. Understanding the molecular mechanisms of As transport and accumulation in rice may provide promising solutions to the problem. MicroRNAs (miRNAs) are a novel class of short, endogenous, non-coding small RNA molecules involved in a wide variety of biological processes such as organ polarity, morphogenesis, floral transition, hormone signalling and adaptation to environment. In the past, a few studies led to the identification of differentially expressed miRNAs in rice in response to arsenite (As(III)) stress. However, studies related to differential miRNA expression involving natural rice accessions exposed to different species of As have not been carried out. Such studies are required to identify As-species responsive miRNAs in different rice accessions. In this study, we have carried out miRNA profiling in contrasting As accumulating rice accessions using miRNA Array. We report identification of differentially expressed miRNAs in contrasting As accumulating rice cultivars in response to As(III) (25 μM) and As(v) (50 μM) stress. A significant up-regulation in expression was observed among members of the miR396, miR399, miR408, miR528, miR1861, miR2102 and miR2907 families in response to As(III) and As(v) stress in both cultivars. In addition, members of the miR164, miR171, miR395, miR529, miR820, miR1432 and miR1846 families were down-regulated. The differentially expressed miRNAs were subjected to validation of expression and bioinformatic analyses to predict and categorise the key miRNAs and their target genes involved in As stress. Analysis suggests that As-species and rice accession specific miRNA might be responsible for the differential response of contrasting rice accessions towards As(III) and As(v) stress. Study of the proximal promoter sequences of the As-responsive miRNAs suggests that these identified miRNAs contain metal-responsive cis-acting motifs and other elicitor and hormonal related motifs. Our study suggests a miRNA-dependent regulatory mechanism during As species-specific stress in different rice accessions. Further analysis based on results obtained will be helpful in dissecting the molecular mechanism behind As responses in different rice accessions.

MicroRNA-mediated gene silencing: are we close to a unifying model?

Abstract MicroRNAs (miRNAs) comprise a group of small non-coding RNA -21 nucleotides in length. They act as post-transcriptional regulators of gene expression by forming base pairing interactions with target messenger RNA (mRNA). At least 1000 miRNAs are predicted to be expressed in humans and are encoded for in the genome of almost all organisms. Functional studies indicate that every cellular process studied thus far is regulated at some level by miRNAs. Given this expansive role, it is not surprising that disruption of this crucial pathway underlies the initiation of, or in the least, contributes to the development and progression of numerous human diseases and physiological disorders. This review will focus on the latest developments in uncovering the mechanism(s) of miRNA-mediated silencing with specific reference to the function of terminal effector proteins, how translation of target mRNA is inhibited and whether we are moving towards understanding this fundamental gene silencing paradigm.

Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis

The experimental induction of RNA silencing in plants often involves expression of transgenes encoding inverted repeat (IR) sequences to produce abundant dsRNAs that are processed into small RNAs (sRNAs). These sRNAs are key mediators of post-transcriptional gene silencing (PTGS) and determine its specificity. Despite its application in agriculture and broad utility in plant research, the mechanism of IR-PTGS is incompletely understood. We generated four sets of 60 Arabidopsis plants, each containing IR transgenes expressing different configurations of uidA and CHALCONE Synthase (At-CHS) gene fragments. Levels of PTGS were found to depend on the orientation and position of the fragment in the IR construct. Deep sequencing and mapping of sRNAs to corresponding transgene-derived and endogenous transcripts identified distinctive patterns of differential sRNA accumulation that revealed similarities among sRNAs associated with IR-PTGS and endogenous sRNAs linked to uncapped mRNA decay. Detailed analyses of poly-A cleavage products from At-CHS mRNA confirmed this hypothesis. We also found unexpected associations between sRNA accumulation and the presence of predicted open reading frames in the trigger sequence. In addition, strong IR-PTGS affected the prevalence of endogenous sRNAs, which has implications for the use of PTGS for experimental or applied purposes.

Epigenetic regulation in plants

The study of epigenetics in plants has a long and rich history, from initial descriptions of non-Mendelian gene behaviors to seminal discoveries of chromatin-modifying proteins and RNAs that mediate gene silencing in most eukaryotes, including humans. Genetic screens in the model plant Arabidopsis have been particularly rewarding, identifying more than 130 epigenetic regulators thus far. The diversity of epigenetic pathways in plants is remarkable, presumably contributing to the phenotypic plasticity of plant postembryonic development and the ability to survive and reproduce in unpredictable environments.

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.

Expression profile of maize microRNAs corresponding to their target genes under drought stress

Microarray assay of four inbred lines was used to identify 303 microRNAs differentially expressed under drought stress. The microRNAs were used for bioinformatics prediction of their target genes. The majority of the differentially expressed microRNA families showed different expression profiles at different time points of the stress process among the four inbred lines. Digital gene expression profiling revealed 54 genes targeted by 128 of the microRNAs differentially expressed under the same stress conditions. The differential expression of miR159 and miR168 was further validated by locked nucleic acid northern hybridization. These results indicated that miR159 and miR168, as well as numerous other microRNAs, play critical roles in signaling pathways of maize response to drought stress. However, the level of the post-transcriptional regulation mediated by microRNAs had different responses among genotypes, and the gene expression related to signaling pathways under drought stress is also regulated, possibly by multiple mechanisms.

Identification of microRNAs in six solanaceous plants and their potential link with phosphate and mycorrhizal signaling

To date, only a limited number of solanaceous miRNAs have been deposited in the miRNA database. Here, genome-wide bioinformatic identification of miRNAs was performed in six solanaceous plants (potato, tomato, tobacco, eggplant, pepper, and petunia). A total of 2,239 miRNAs were identified following a range of criteria, of which 982 were from potato, 496 from tomato, 655 from tobacco, 46 from eggplant, 45 were from pepper, and 15 from petunia. The sizes of miRNA families and miRNA precursor length differ in all the species. Accordingly, 620 targets were predicted, which could be functionally classified as transcription factors, metabolic enzymes, RNA and protein processing proteins, and other proteins for plant growth and development. We also showed evidence for miRNA clusters and sense and antisense miRNAs. Additionally, five Pi starvation- and one arbuscular mycorrhiza (AM)-related cis-elements were found widely distributed in the putative promoter regions of the miRNA genes. Selected miRNAs were classified into three groups based on the presence or absence of P1BS and MYCS cis-elements, and their expression in response to Pi starvation and AM symbiosis was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). These results show that conserved miRNAs exist in solanaceous species and they might play pivotal roles in plant growth, development, and stress responses.

Rice miR172 induces flowering by suppressing OsIDS1 and SNB, two AP2 genes that negatively regulate expression of Ehd1 and florigens

BACKGROUND

Rice is a facultative short-day plant that flowers under long days (LD) after a lengthy vegetative phase. Although several inhibitors that delay flowering have been identified, the process by which rice eventually flowers under non-permissive LD conditions is not well understood.

RESULTS

Overexpression of miR172 reduced flowering time significantly, suggesting its role as an inducer. Levels of miR172 increased as plants aged, further supporting our findings. Transcripts of SNB and OsIDS1, two members of the AP2 family that have the miR172 target site, were reduced in older plants as the level of miR172 rose. Overexpression of those AP2 genes delayed flowering; overexpression of miR172-resistant forms of SNB or OsIDS1 further delayed this process. This demonstrated that the AP2 genes function downstream of miR172. Two florigen genes -- Hd3a and RFT1 -- and their immediate upstream regulator Ehd1 were suppressed in the AP2 overexpression plants. This suggested that the AP2 genes are upstream repressors of Ehd1. In phytochrome mutants, miR172d levels were increased whereas those of SNB and OsIDS1 were decreased. Thus, it appears that phytochromes inhibit miR172d, an AP2 suppresser.

CONCLUSIONS

We revealed that miR172d developmentally induced flowering via repressing OsIDS1 and SNB, which suppressed Ehd1. We also showed that phytochromes negatively regulated miR172.

Integrated network analysis identifies fight-club nodes as a class of hubs encompassing key putative switch genes that induce major transcriptome reprogramming during grapevine development

We developed an approach that integrates different network-based methods to analyze the correlation network arising from large-scale gene expression data. By studying grapevine (Vitis vinifera) and tomato (Solanum lycopersicum) gene expression atlases and a grapevine berry transcriptomic data set during the transition from immature to mature growth, we identified a category named "fight-club hubs" characterized by a marked negative correlation with the expression profiles of neighboring genes in the network. A special subset named "switch genes" was identified, with the additional property of many significant negative correlations outside their own group in the network. Switch genes are involved in multiple processes and include transcription factors that may be considered master regulators of the previously reported transcriptome remodeling that marks the developmental shift from immature to mature growth. All switch genes, expressed at low levels in vegetative/green tissues, showed a significant increase in mature/woody organs, suggesting a potential regulatory role during the developmental transition. Finally, our analysis of tomato gene expression data sets showed that wild-type switch genes are downregulated in ripening-deficient mutants. The identification of known master regulators of tomato fruit maturation suggests our method is suitable for the detection of key regulators of organ development in different fleshy fruit crops.

The functional scope of plant microRNA-mediated silencing

Deep sequencing has identified a complex set of plant miRNAs that potentially regulates many target genes of high complementarity. Furthermore, the discovery that many plant miRNAs work through a translational repression mechanism, along with the identification of noncanonical targets, has encouraged bioinformatic searches with less stringent parameters, identifying an even wider range of potential targets. Together, these findings suggest that any given plant miRNA family may regulate a highly diverse set of mRNAs. Here we present evolutionary, genetic, and mechanistic evidence that opposes this idea but instead suggests that families of sequence-related miRNAs regulate very few functionally related targets. We propose that complexities beyond complementarity impact plant miRNA target recognition, possibly explaining the current disparity between bioinformatic prediction and functional evidence.

Identification of microRNAs and their targets in tomato infected with Cucumber mosaic virus based on deep sequencing

MicroRNAs (miRNAs) play important regulatory roles in plant development and stress responses. Tomato is an economically important vegetable crop in the world with publicly available genomic information database, but only a limited number of tomato miRNAs have been identified. In this study, two independent small RNA libraries from mock and Cucumber mosaic virus (CMV)-infected tomatoes were constructed, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 plant miRNAs and 273 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 plant miRNAs and 82 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed that 79 miRNAs (including 15 new tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries, and the expression patterns of some new tomato miRNAs and PC-miRNAs were further validated by qRT-PCR. Moreover, potential targets for some of the known and new tomato miRNAs were identified by the recently developed degradome sequencing approach, and target annotation indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that defense response- and photosynthesis-related genes were most affected in CMV-Fny-infected tomatoes. Because tomato is not only an important crop but also is a genetic model for basic biology research, our study contributes to the understanding of miRNAs in response to virus infection.

Differential profiling analysis of miRNAs reveals a regulatory role in low N stress response of Populus

Nitrogen (N) is an essential mineral element for plant growth processes, and its availability severely affects the productivity of plants, especially trees. MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nucleotides in length that play important roles in plant growth, development and stress responses. To identify Populus miRNAs and their functions in response to nutrition stress, high-throughput sequencing was performed using Populus tomentosa plantlets treated with or without low concentrations of N. We identified 160 conserved miRNAs, 15 known but non-conserved miRNAs, 2 candidate novel miRNAs and 71 corresponding miRNA*s. Differential expression analysis showed that expression of the 21 conserved miRNA families was significantly altered. Real-time quantitative PCR (qPCR) was used to further validate and analyze the dynamic expression of the identified miRNAs. A total of 218 target genes from the low-N-responsive miRNAs were predicted, and their functions were further annotated in combination with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. These results suggest that miRNAs play important roles in the response of Populus to low N stress. Furthermore, this study provides the first identification and profiles of N stress-responsive miRNAs from trees.

Deep sequencing analyses of pine wood nematode Bursaphelenchus xylophilus microRNAs reveal distinct miRNA expression patterns during the pathological process of pine wilt disease

Bursaphelenchus xylophilus is known as the causative agent of pine wilt disease with complex life cycles. In this research, four small RNA libraries derived from different infection stages of pine wilt disease were constructed and sequenced. Consequently, we obtained hundreds of evolutionarily conserved miRNAs and novel miRNA candidates. The analysis of miRNA expression patterns showed that most miRNAs were expressed at extraordinarily high levels during the middle stage of pine wilt disease. Functional analysis revealed that expression levels of miR-73 and miR-239 were mutually exclusive with their target GH45 cellulase genes. In addition, another set of atypical miRNAs, termed mirtrons, was also identified in this study. Thus, our research has provided detailed characterization of B. xylophilus miRNA expression patterns during the pathological process of pine wilt disease. These findings would contribute to more in-depth understanding of this devastating plant disease.

Investigating the molecular genetic basis of heterosis for internode expansion in maize by microRNA transcriptomic deep sequencing

Heterosis has been used widely in the breeding of maize and other crops and plays an important role in increasing yield, improving quality, and enhancing stress resistance, but its molecular mechanism is far from clear. To determine whether microRNA (miRNA)-dependent gene regulation is responsible for heterosis of elongating internodes below the ear and ear height in maize, a deep-sequencing strategy was applied to the elite hybrid Xundan20, which is currently cultivated widely in China, and its two parents. RNA was extracted from the eighth internode because it shows clear internode length heterosis. A total of 99 conserved maize miRNAs were detected in both the hybrid and parental lines. Most of these miRNAs were expressed nonadditively in the hybrid compared with its parental lines. These results indicated that miRNAs might participate in heterosis during internode expansion in maize and exert an influence on ear and plant height via the repression of their target genes. In total, eight novel miRNAs belonging to four miRNA families were predicted in the expanding internode. Global repression of miRNAs in the hybrid, which might result in enhanced gene expression, might be one reason why the hybrid shows longer internodes and taller seedlings compared with its parental lines.

Deep sequencing identifies tissue-specific microRNAs and their target genes involving in the biosynthesis of tanshinones in Salvia miltiorrhiza

Salvia miltiorrhiza is one of the most popular traditional medicinal herbs in Asian nations. Its dried root contains a number of tanshinones, protocatechuic aldehyde, salvianolic acid B and rosmarinic, and is used for the treatment of various diseases. The finding of microRNAs (miRNAs) and their target genes will help understand their biological role on the biosynthesis of tanshinones in S. miltiorrhiza. In the present study, a total of 452 known miRNAs corresponding to 589 precursor miRNAs (pre-miRNAs), and 40 novel miRNAs corresponding to 24 pre-miRNAs were identified in different tissues of S. miltiorrhiza by high-throughput sequencing, respectively. Among them, 62 miRNAs express only in root, 95 miRNAs express only in stem, 19 miRNAs express only in leaf, and 71 miRNAs express only in flower, respectively. By the degradome analysis, 69 targets potentially cleaved by 25 miRNAs were identified. Among them, acetyl-CoA C-acetyltransferase was cleaved by miR5072, and involved in the biosynthesis of tanshinones. This study provided valuable information for understanding the tissue-specific expression patterns of miRNAs in S. miltiorrhiza, and offered a foundation for future studies of the miRNA-mediated biosynthesis of tanshinones.

Involvement of ethylene-responsive microRNAs and their targets in increased latex yield in the rubber tree in response to ethylene treatment

The rubber tree is an economically important plant that produces natural rubber for various industrial uses. The application of ethylene contributes to increased latex production in rubber trees; however, the molecular biology behind the effects of ethylene on latex yield remains to be elucidated. Recently, the intersection between microRNA (miRNA) regulation and phytohormone responses has been revealed. Insight into the regulation of miRNAs and their target genes should help to determine the functional importance of miRNAs as well as the role of miRNAs in signaling under ethylene stimulation in the rubber tree. In this study, hbr-miR159 and hbr-miR166 were down-regulated in bark under ethylene treatment. The ethylene also down-regulated ATHB15-like (Class III Homeodomain Leucine Zipper, HD-ZIP III) which have been extensively implicated in the regulation of primary and secondary vascular tissue pattern formation. The strong negative-regulation of ARF6/ARF8 caused by hbr-miR167 involved in an attenuation of vascular development and may gradually lead to bark dryness syndrome in the long term ethylene treatment. The negative correlation of hbr-miR172 and its target REF3 in the inner soft bark under ethylene treatment results in dramatic increases in latex yield in the ethylene-sensitive clone of the rubber tree. The overall results suggested that the differential expression of HD-ZIP III, miR167/ARF6, ARF8, and miR172/REF3 and related genes may play possible roles in the response to ethylene treatment, resulting in longer latex flow and increased latex yield.

Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing

MicroRNAs (miRNAs) are essential components of complex gene regulatory networks that orchestrate plant development. Although several genomic resources have been developed for the legume crop chickpea, miRNAs have not been discovered until now. For genome-wide discovery of miRNAs in chickpea (Cicer arietinum), we sequenced the small RNA content from seven major tissues/organs employing Illumina technology. About 154 million reads were generated, which represented more than 20 million distinct small RNA sequences. We identified a total of 440 conserved miRNAs in chickpea based on sequence similarity with known miRNAs in other plants. In addition, 178 novel miRNAs were identified using a miRDeep pipeline with plant-specific scoring. Some of the conserved and novel miRNAs with significant sequence similarity were grouped into families. The chickpea miRNAs targeted a wide range of mRNAs involved in diverse cellular processes, including transcriptional regulation (transcription factors), protein modification and turnover, signal transduction, and metabolism. Our analysis revealed several miRNAs with differential spatial expression. Many of the chickpea miRNAs were expressed in a tissue-specific manner. The conserved and differential expression of members of the same miRNA family in different tissues was also observed. Some of the same family members were predicted to target different chickpea mRNAs, which suggested the specificity and complexity of miRNA-mediated developmental regulation. This study, for the first time, reveals a comprehensive set of conserved and novel miRNAs along with their expression patterns and putative targets in chickpea, and provides a framework for understanding regulation of developmental processes in legumes.

Engineered plant virus resistance

Virus diseases are among the key limiting factors that cause significant yield loss and continuously threaten crop production. Resistant cultivars coupled with pesticide application are commonly used to circumvent these threats. One of the limitations of the reliance on resistant cultivars is the inevitable breakdown of resistance due to the multitude of variable virus populations. Similarly, chemical applications to control virus transmitting insect vectors are costly to the farmers, cause adverse health and environmental consequences, and often result in the emergence of resistant vector strains. Thus, exploiting strategies that provide durable and broad-spectrum resistance over diverse environments are of paramount importance. The development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Genetic engineering offers various options for introducing transgenic virus resistance into crop plants to provide a wide range of resistance to viral pathogens. This review examines the current strategies of developing virus resistant transgenic plants.

Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes

Verticillium longisporum, a soil-borne pathogenic fungus, causes vascular disease in oilseed rape (Brassica napus). We proposed that plant microRNAs (miRNAs) are involved in the plant-V. longisporum interaction. To identify oilseed rape miRNAs, we deep-sequenced two small RNA libraries made from V. longisporum infected/noninfected roots and employed Brassica rapa and Brassica oleracea genomes as references for miRNA prediction and characterization. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to the AA and CC genomes, respectively. Microsynteny analysis with the conserved miRNAs and their flanking protein coding sequences revealed 137 AA-CC genome syntenic miRNA pairs and 61 AA and 42 CC genome-unique miRNAs. Sixty-two miRNAs were responsive to the V. longisporum infection. We present data for specific interactions and simultaneously reciprocal changes in the expression levels of the miRNAs and their targets in the infected roots. We demonstrate that miRNAs are involved in the plant-fungus interaction and that miRNA168-Argonaute 1 (AGO1) expression modulation might act as a key regulatory module in a compatible plant-V. longisporum interaction. Our results suggest that V. longisporum may have evolved a virulence mechanism by interference with plant miRNAs to reprogram plant gene expression and achieve infection.

Novel miRNA and phasiRNA biogenesis networks in soybean roots from two sister lines that are resistant and susceptible to SCN race 4

The soybean cyst nematode (SCN), Heterodera glycines, is the most devastating pathogen of soybean worldwide. SiRNAs (small interfere RNAs) have been proven to induce the silencing of cyst nematode genes. However, whether small RNAs from soybean root have evolved a similar mechanism against SCN is unknown. Two genetically related soybean sister lines (ZP03-5373 and ZP03-5413), which are resistant and susceptible, respectively, to SCN race 4 infection were selected for small RNA deep sequencing to identify small RNAs targeted to SCN. We identified 71 less-conserved miRNAs-miRNAs* counterparts belonging to 32 families derived from 91 loci, and 88 novel soybean-specific miRNAs with distinct expression patterns. The identified miRNAs targeted 42 genes representing a wide range of enzymatic and regulatory activities. Roots of soybean conserved one TAS (Trans-acting siRNA) gene family with a similar but unique trans-acting small interfering RNA (tasiRNA) biogenesis profile. In addition, we found that six miRNAs (gma-miR393, 1507, 1510, 1515, 171, 2118) guide targets to produce secondary phasiRNAs (phased, secondary, small interfering RNAs) in soybean root. Multiple targets of these phasiRNAs were predicted and detected. Importantly, we also found that the expression of 34 miRNAs differed significantly between the two lines. Seven ZP03-5373-specific miRNAs were differentially expressed after SCN infection. Forty-four transcripts from SCN were predicted to be potential targets of ZP03-5373-specific differential miRNAs. These findings suggest that miRNAs play an important role in the soybean response to SCN.

Identification of conserved and novel microRNAs in Catharanthus roseus by deep sequencing and computational prediction of their potential targets

MicroRNAs are small endogenous non-coding RNAs of ~19-24 nucleotides and perform regulatory roles in many plant processes. To identify miRNAs involved in regulatory networks controlling diverse biological processes including secondary metabolism in Catharanthus roseus, an important medicinal plant, we employed deep sequencing of small RNA from leaf tissue. A total of 88 potential miRNAs comprising of 81 conserved miRNAs belonging to 35 families and seven novel miRNAs were identified. Precursors for 16 conserved and seven novel cro-miRNAs were identified, and their stem-loop hairpin structures were predicted. Selected cro-miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in different vegetative tissues of C. roseus. Targets were predicted for conserved and novel cro-miRNAs, which were found to be involved in diverse biological role(s) including secondary metabolism. Our study enriches available resources and information regarding miRNAs and their potential targets for better understanding of miRNA-mediated gene regulation in plants.

Identification of miR159s and their target genes and expression analysis under drought stress in potato

The MYB proteins comprise one of the largest families of plant transcription factors (TFs) and many of MYB families, which play essential roles in plant growth, development and respond to environmental stresses, and have yet been identified in plant. Previous research has shown that miR159 family members repressed the conserved plant R2R3 MYB domain TFs in model plants. In the present research, we identified three potato novel miR159 family members named as stu-miR159a, stu-miR159b and stu-miR159c based on bioinformatics analysis. Target prediction showed that they have a bite sit on the three GAMyb-like genes (StGAMyb-like1, StGAMyb-like2.1 and StGAMyb-like2.2) of potato. Those GAMyb-like genes also have been selected and cloned from potato, which belong to R2R3 MYB domain TFs. We further measured expressional levels of stu-miR159s and potato GAMyb-like genes during the different periods of drought treated samples using quantitative real-time PCR (qRT-PCR). The results showed that they had a opposite expression pattern, briefly, three stu-miR159 members showed similar expressional trends which were significantly decreased expression after experiencing 25 days of drought stress treatment, while the potato GAMyb-like family members were greatly increased. Therefore, we suggested that stu-miR159s negatively regulated the expression of potato GAMyb-like genes which responsible for drought stress. The findings can facilitate functional studies of miRNAs in plants and provide molecular evidence for involvement process of drought tolerance in potato.

Small RNAs as positional signal for pattern formation

Pattern formation in plant relies on intimate cell-cell communication exchanging positional information. While ligand-receptor interaction is commonly used by plants and animals as a means to transmit positional information, plant cells can directly exchange regulatory molecules such as transcription factors through a cytoplasmic continuum called the plasmodesmata. Recently endogenous small RNAs (sRNAs) of various biogenetic origins have been shown to function non-cell-autonomously. To date, non-cell-autonomous sRNAs have been shown to regulate leaf polarity, root vascular patterning, meristem formation in embryos, shoot meristem maintenance and female gametogenesis. All these developmental processes are fundamental to the life cycle and architecture of flowering plants, suggesting that sRNA-mediated cell-to-cell signaling has been adopted to achieve novel morphology in the course of plant evolution.

MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis

Plant laccase (LAC) enzymes belong to the blue copper oxidase family and polymerize monolignols into lignin. Recent studies have established the involvement of microRNAs in this process; however, physiological functions and regulation of plant laccases remain poorly understood. Here, we show that a laccase gene, LAC4, regulated by a microRNA, miR397b, controls both lignin biosynthesis and seed yield in Arabidopsis. In transgenic plants, overexpression of miR397b (OXmiR397b) reduced lignin deposition. The secondary wall thickness of vessels and the fibres was reduced in the OXmiR397b line, and both syringyl and guaiacyl subunits are decreased, leading to weakening of vascular tissues. In contrast, overexpression of miR397b-resistant laccase mRNA results in an opposite phenotype. Plants overexpressing miR397b develop more than two inflorescence shoots and have an increased silique number and silique length, resulting in higher seed numbers. In addition, enlarged seeds and more seeds are formed in these miR397b overexpression plants. The study suggests that miR397-mediated development via regulating laccase genes might be a common mechanism in flowering plants and that the modulation of laccase by miR397 may be potential for engineering plant biomass production with less lignin.

System analysis of microRNAs in the development and aluminium stress responses of the maize root system

MicroRNAs (miRNAs) are a class of regulatory small RNAs (sRNAs) that down-regulate target genes through mRNA cleavage or translational inhibition. miRNA is known to play an important role in the root development and environmental responses in both the Arabidopsis and rice. However, little information is available to form a complete view of miRNAs in the development of the maize root system and Al stress responses in maize. Four sRNA libraries were generated and sequenced from the early developmental stage of primary roots (PRY), the later developmental stage of maize primary roots (PRO), seminal roots (SR) and crown roots (CR). Through integrative analysis, we identified 278 miRNAs (246 conserved and 32 novel ones) and found that the expression patterns of miRNAs differed dramatically in different maize roots. The potential targets of the identified conserved and novel miRNAs were also predicted. In addition, our data showed that CR is more resistant to Al stress compared with PR and SR, and the differentially expressed miRNAs are likely to play significant roles in different roots in response to environmental stress such as Al stress. Here, we demonstrate that the expression patterns of miRNAs are highly diversified in different maize roots. The differentially expressed miRNAs are correlated with both the development and environmental responses in the maize root. This study not only improves our knowledge about the roles of miRNAs in maize root development but also reveals the potential role of miRNAs in the environmental responses of different maize roots.

Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression

MicroRNAs (miRNAs) were discovered two decades ago, yet there is still a great need for further studies elucidating their genesis and targeting in different phyla. Since experimental discovery and validation of miRNAs is difficult, computational predictions are indispensable and today most computational approaches employ machine learning. Toxoplasma gondii, a parasite residing within the cells of its hosts like human, uses miRNAs for its post-transcriptional gene regulation. It may also regulate its hosts’ gene expression, which has been shown in brain cancer. Since previous studies have shown that overexpressed miRNAs within the host are causal for disease onset, we hypothesized that T. gondii could export miRNAs into its host cell. We computationally predicted all hairpins from the genome of T. gondii and used mouse and human models to filter possible candidates. These were then further compared to known miRNAs in human and rodents and their expression was examined for T. gondii grown in mouse and human hosts, respectively. We found that among the millions of potential hairpins in T. gondii, only a few thousand pass filtering using a human or mouse model and that even fewer of those are expressed. Since they are expressed and differentially expressed in rodents and human, we suggest that there is a chance that T. gondii may export miRNAs into its hosts for direct regulation.

The characteristics of the porcine (Sus scrofa) liver miRNAome with the use of next generation sequencing

MicroRNAs (miRNAs) are a class of small, noncoding RNAs, which play a vital role in the regulation of gene expression by binding to the 3' untranslated region (3'UTR) of a target mRNA. Despite a significant improvement in the identification of miRNAs in a variety of species, the coverage of the porcine miRNAome is still scarce. To identify porcine miRNAs potentially regulating processes taking place in the liver, we applied next generation sequencing. As a result, we detected 206 distinct miRNAs, of which 68 represented potential novel miRNAs. Among these new miRNAs, there were miRNAs deriving from the opposite arm of a hairpin precursor of already known miRNAs. Moreover, we observed 3' and 5' length and sequence variants, probably constituting so called isomiRs, as well as differentially mapped precursor loci, alternative precursor sequences and clustering of miRNA encoding genes. On the basis of expression levels, reflected by the number of sequence reads, we identified the most abundant miRNAs followed by gene target prediction and pathway analysis. The enriched pathways were connected with cellular and metabolic processes, growth factors as well as enzymatic activity. The obtained results are the first ones to concern the porcine liver miRNAome. Consequently, they will increase the number of known porcine miRNAs and facilitate further research on gene regulation mechanisms as well as biological processes associated with the liver functioning in pigs.

Genome-wide identification of microRNA and siRNA responsive to endophytic beneficial diazotrophic bacteria in maize

Background

Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays – hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we analyzed the sRNA regulated by its association with two diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense.

Results

Deep sequencing analysis was done with RNA extracted from plants inoculated with H. seropedicae, allowing the identification of miRNA and siRNA. A total of 25 conserved miRNA families and 15 novel miRNAs were identified. A dynamic regulation in response to inoculation was also observed. A hypothetical model involving copper-miRNA is proposed, emphasizing the fact that the up-regulation of miR397, miR398, miR408 and miR528, which is followed by inhibition of their targets, can facilitate association with diazotrophic bacteria. Similar expression patterns were observed in samples inoculated with A. brasilense. Moreover, novel miRNA and siRNA were classified in the Transposable Elements (TE) database, and an enrichment of siRNA aligned with TE was observed in the inoculated samples. In addition, an increase in 24-nt siRNA mapping to genes was observed, which was correlated with an increase in methylation of the coding regions and a subsequent reduction in transcription.

Conclusion

Our results show that maize has RNA-based silencing mechanisms that can trigger specific responses when plants interact with beneficial endophytic diazotrophic bacteria. Our findings suggest important roles for sRNA regulation in maize, and probably in other plants, during association with diazotrophic bacteria, emphasizing the up-regulation of Cu-miRNA.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-766) contains supplementary material, which is available to authorized users.

MicroRNAs in fruit trees: discovery, diversity and future research directions

Since the first description of microRNAs (miRNAs) 20 years ago, the number of miRNAs identified in different eukaryotic organisms has exploded, largely due to the recent advances in DNA sequencing technologies. Functional studies, mostly from model species, have revealed that miRNAs are major post-transcriptional regulators of gene expression in eukaryotes. In plants, they are implicated in fundamental biological processes, from plant development and morphogenesis, to regulation of plant pathogen and abiotic stress responses. Although a substantial number of miRNAs have been identified in fruit trees to date, their functions remain largely uncharacterised. The present review aims to summarise the progress made in miRNA research in fruit trees, focusing specifically on the economically important species Prunus persica, Malus domestica, Citrus spp, and Vitis vinifera. We also discuss future miRNA research prospects in these plants and highlight potential applications of miRNAs in the on-going improvement of fruit trees.

'Movers and shakers' in the regulation of fruit ripening: a cross-dissection of climacteric versus non-climacteric fruit

Fruit ripening is a complex and highly coordinated developmental process involving the expression of many ripening-related genes under the control of a network of signalling pathways. The hormonal control of climacteric fruit ripening, especially ethylene perception and signalling transduction in tomato has been well characterized. Additionally, great strides have been made in understanding some of the major regulatory switches (transcription factors such as RIPENING-INHIBITOR and other transcriptional regulators such as COLOURLESS NON-RIPENING, TOMATO AGAMOUS-LIKE1 and ETHYLENE RESPONSE FACTORs), that are involved in tomato fruit ripening. In contrast, the regulatory network related to non-climacteric fruit ripening remains poorly understood. However, some of the most recent breakthrough research data have provided several lines of evidences for abscisic acid- and sucrose-mediated ripening of strawberry, a non-climacteric fruit model. In this review, we discuss the most recent research findings concerning the hormonal regulation of fleshy fruit ripening and their cross-talk and the future challenges taking tomato as a climacteric fruit model and strawberry as a non-climacteric fruit model. We also highlight the possible contribution of epigenetic changes including the role of plant microRNAs, which is opening new avenues and great possibilities in the fields of fruit-ripening research and postharvest biology.

Transcellular chaperone signaling: an organismal strategy for integrated cell stress responses

The ability of each cell within a metazoan to adapt to and survive environmental and physiological stress requires cellular stress-response mechanisms, such as the heat shock response (HSR). Recent advances reveal that cellular proteostasis and stress responses in metazoans are regulated by multiple layers of intercellular communication. This ensures that an imbalance of proteostasis that occurs within any single tissue 'at risk' is protected by a compensatory activation of a stress response in adjacent tissues that confers a community protective response. While each cell expresses the machinery for heat shock (HS) gene expression, the HSR is regulated cell non-autonomously in multicellular organisms, by neuronal signaling to the somatic tissues, and by transcellular chaperone signaling between somatic tissues and from somatic tissues to neurons. These cell non-autonomous processes ensure that the organismal HSR is orchestrated across multiple tissues and that transmission of stress signals between tissues can also override the neuronal control to reset cell- and tissue-specific proteostasis. Here, we discuss emerging concepts and insights into the complex cell non-autonomous mechanisms that control stress responses in metazoans and highlight the importance of intercellular communication for proteostasis maintenance in multicellular organisms.

Computational Methods for MicroRNA Target Prediction

MicroRNAs (miRNAs) have been identified as one of the most important molecules that regulate gene expression in various organisms. miRNAs are short, 21–23 nucleotide-long, single stranded RNA molecules that bind to 3' untranslated regions (3' UTRs) of their target mRNAs. In general, they silence the expression of their target genes via degradation of the mRNA or by translational repression. The expression of miRNAs, on the other hand, also varies in different tissues based on their functions. It is significantly important to predict the targets of miRNAs by computational approaches to understand their effects on the regulation of gene expression. Various computational methods have been generated for miRNA target prediction but the resulting lists of candidate target genes from different algorithms often do not overlap. It is crucial to adjust the bioinformatics tools for more accurate predictions as it is equally important to validate the predicted target genes experimentally.

Computational identification of novel microRNAs and targets in Glycine max

Plant miRNAs, the endogenous non-coding small RNAs of about 20-24 nucleotides, play important roles in multiple biological processes by acting as negative regulators of their targeted mRNAs. Soybean (Glycine max (L.) Merr.) is one of the important oil crops of the world, in which many miRNAs have been obtained through the computational prediction or experiments. However, the miRNA genes identified for soybean are still far from saturation, and their biological functions are largely unknown. Here, a total of 48 candidates of miRNAs were identified following a range of strict filtering criteria. Detailed sequence analysis showed that G. max pre-miRNAs vary in length from 47 to 380 nt, embody mature miRNAs that differ in their physical location within the pre-miRNAs. In this study, twenty miRNAs were confirmed by microarray and three miRNAs were further validated by poly(A)-tailed RT-PCR. Comparative sequence analysis of soybean miRNA sequences showed that uracil is the dominant base in the first position at the 5' end of the mature miRNAs, and the base may have an important functional role in miRNA biogenesis and/or miRNA-mediated gene regulation. Finally, we predicted potential targets of these miRNAs. These target genes were predicted to encode transcription factors, resistance protein, heat shock protein, protein kinase, transporter, zinc finger protein and others, which might play important roles in soybean development and stress response.

Genome-wide analysis of salt-responsive and novel microRNAs in Populus euphratica by deep sequencing

BACKGROUND

Populus euphratica is a representative model woody plant species for studying resistance to abiotic stresses such as drought and salt. Salt stress is one of the most common environmental factors that affect plant growth and development. MicroRNAs (miRNAs) are small, noncoding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress.

RESULTS

To investigate the miRNAs involved in the salt-stress response, we constructed four small cDNA libraries from P. euphratica plantlets treated with or without salt (300 mM NaCl, 3 days) in either the root or leaf. Using high-throughput sequencing to identify miRNAs, we found 164 conserved miRNAs belonging to 44 families. Of these, 136 novel miRNAs were from the leaf, and 128 novel miRNAs were from the root. In response to salt stress, 95 miRNAs belonging to 46 conserved miRNAs families changed significantly, with 56 miRNAs upregulated and 39 miRNAs downregulated in the leaf. A comparison of the leaf and root tissues revealed 155 miRNAs belonging to 63 families with significantly altered expression, including 84 upregulated and 71 downregulated miRNAs. Furthermore, 479 target genes in the root and 541 targets of novel miRNAs in the leaf were predicted, and functional information was annotated using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases.

CONCLUSIONS

This study provides a novel visual field for understanding the regulatory roles of miRNAs in response to salt stress in Populus.

Carica papaya microRNAs are responsive to Papaya meleira virus infection

MicroRNAs are implicated in the response to biotic stresses. Papaya meleira virus (PMeV) is the causal agent of sticky disease, a commercially important pathology in papaya for which there are currently no resistant varieties. PMeV has a number of unusual features, such as residence in the laticifers of infected plants, and the response of the papaya to PMeV infection is not well understood. The protein levels of 20S proteasome subunits increase during PMeV infection, suggesting that proteolysis could be an important aspect of the plant defense response mechanism. To date, 10,598 plant microRNAs have been identified in the Plant miRNAs Database, but only two, miR162 and miR403, are from papaya. In this study, known plant microRNA sequences were used to search for potential microRNAs in the papaya genome. A total of 462 microRNAs, representing 72 microRNA families, were identified. The expression of 11 microRNAs, whose targets are involved in 20S and 26S proteasomal degradation and in other stress response pathways, was compared by real-time PCR in healthy and infected papaya leaf tissue. We found that the expression of miRNAs involved in proteasomal degradation increased in response to very low levels of PMeV titre and decreased as the viral titre increased. In contrast, miRNAs implicated in the plant response to biotic stress decreased their expression at very low level of PMeV and increased at high PMeV levels. Corroborating with this results, analysed target genes for this miRNAs had their expression modulated in a dependent manner. This study represents a comprehensive identification of conserved miRNAs inpapaya. The data presented here might help to complement the available molecular and genomic tools for the study of papaya. The differential expression of some miRNAs and identifying their target genes will be helpful for understanding the regulation and interaction of PMeV and papaya.

Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava

BACKGROUND

Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs.

RESULTS

In order to understand sncRNAs' roles in plant chilling response and stress acclimation, we performed a comprehensive study of miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate chilling stresses, that underwent further severe chilling stress after chilling acclimation at moderate stress, and that grew under the normal condition. We also included castor bean (Ricinus communis) in our study to understand conservation of sncRNAs. In addition to known miRNAs, we identified 32 (22 and 10) novel miRNAs as well as 47 (26 and 21) putative secondary siRNA-yielding and 8 (7 and 1) nat-siRNA-yielding candidate loci in Cassava and castor bean, respectively. Among the expressed sncRNAs, 114 miRNAs, 12 ta-siRNAs and 2 nat-siRNAs showed significant expression changes under chilling stresses.

CONCLUSION

Systematic and computational analysis of microRNAome and experimental validation collectively showed that miRNAs, ta-siRNAs, and possibly nat-siRNAs play important roles in chilling response and chilling acclimation in Cassava by regulating stress-related pathways, e.g. Auxin signal transduction. The conservation of these sncRNA might shed lights on the role of sncRNA-mediated pathways affected by chilling stress and stress acclimation in Euphorbiaceous plants.

Identification of 23 novel conserved microRNAs in three rice cultivars

Plant microRNAs (miRNAs) play important roles as modulators of gene expression at the post-transcriptional level. Previous studies have shown that high-throughput sequencing is a powerful tool for the identification of miRNAs, and it is believed that many more miRNAs remain to be discovered. Here, we found 23 novel conserved miRNAs from three rice cultivars by high-throughput sequencing and further identified these through subsequent cloning and quantitative real-time polymerase chain reaction (qPCR). Eight of these novel miRNAs were detected with significant signals in the three rice cultivars by northern blotting assays. The quantitative analysis of their expression profiles showed that most of these miRNAs were perfectly or imperfectly negatively correlated with their target genes, which suggests that these miRNAs may play important roles during rice development. This is the first genome-wide investigation of miRNAs from different rice cultivars, and the data obtained expand the known rice miRNA inventory and provide further information about the regulatory roles played by miRNAs in rice development.

Autophagy and microRNA dysregulation in liver diseases

Autophagy is a catabolic process through which organelles and cellular components are sequestered into autophagosomes and degraded via fusion with lysosomes. Autophagy plays a role in many physiological processes, including stress responses, energy homeostasis, elimination of cellular organelles, and tissue remodeling. In addition, autophagy capacity changes in various disease states. A series of studies have shown that autophagy is strictly controlled to maintain homeostatic balance of energy metabolism and cellular organelle and protein turnover. These studies have also shown that this process is post-transcriptionally controlled by small noncoding microRNAs that regulate gene expression through complementary base pairing with mRNAs. Conversely, autophagy regulates the expression of microRNAs. Therefore, dysregulation of the link between autophagy and microRNA expression exacerbates the pathogenesis of various diseases. In this review, we summarize the roles of autophagy and microRNA dysregulation in the course of liver diseases, with the aim of understanding how microRNAs modify key autophagic effector molecules, and we discuss how this dysregulation affects both physiological and pathological conditions. This article may advance our understanding of the cellular and molecular bases of liver disease progression and promote the development of strategies for pharmacological intervention.

High-throughput sequence analysis of small RNAs in skotomorphogenic seedlings of Brassica rapa ssp. rapa

Skotomorphogenic development is the process by which seedlings adapt to a stressful dark environment. Such metabolic responses to abiotic stresses in plants are known to be regulated in part by microRNAs (miRNAs); however, little is known about the involvement of miRNAs in the regulation of skotomorphogenesis. To identify miRNAs at the genome-wide level in skotomorphogenic seedlings of turnip (Brassica rapa subsp. rapa), an important worldwide root vegetable, we used Solexa sequencing to sequence a small RNA library from seedlings grown in the dark for 4 days. Deep sequencing showed that the small RNAs (sRNAs) were predominantly 21 to 24 nucleotides long. Specifically, 13,319,035 reads produced 359,531 unique sRNAs including rRNA, tRNA, miRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and unannotated sRNAs. Sequence analysis identified 96 conserved miRNAs belonging to 36 miRNA families and 576 novel miRNAs. qRT-PCR confirmed that the miRNAs were expressed during skotomorphogenesis similar to the trends shown by the Solexa sequencing results. A total of 2013 potential targets were predicted, and the targets of BrmiR157, BrmiR159 and BrmiR160 were proved to be regulated by miRNA-guided cleavage. These results show that specific regulatory miRNAs are present in skotomorphogenic seedlings of turnip and may play important roles in growth, development, and response to dark environment.

Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks

Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling pathways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and protein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network.

miR396a-Mediated basic helix-loop-helix transcription factor bHLH74 repression acts as a regulator for root growth in Arabidopsis seedlings

miR396 targets seven GROWTH-REGULATING FACTOR (GRF) genes and the BASIC HELIX-LOOP-HELIX (bHLH) TRANSCRIPTION FACTOR 74 gene (bHLH74) in Arabidopsis. Previous research revealed that the miR396 target module regulates cell proliferation and plays a critical role in leaf development. However, no additional biological functions of miR396 have been investigated in detail. In this study, T-DNA insertion mutants and transgenic plants with altered levels of miR396 or its target genes were used to characterize the regulatory role of miR396 in root development. We found that AtMIR396a was the predominant source for miR396 accumulation in the roots of seedlings, and that the mir396a-1 mutant had longer roots than wild-type seedlings. Overexpression of AtMIR396a decreased the transcript levels of target genes such as GRF genes and bHLH74, and resulted in a shorter root phenotype. Furthermore, the bhlh74-1 mutant had shorter roots, whereas overexpression of an miR396-resistant form of bHLH74 (mbHLH74) had an enhanced root growth phenotype. Moreover, MIR396a regulated root growth by affecting the elongation zone. Taken together, these data indicate that miR396a-mediated bHLH74 repression helps regulate root growth in Arabidopsis seedlings.

Genome-wide analysis of salt-responsive and novel microRNAs in Populus euphratica by deep sequencing

Background

Populus euphratica is a representative model woody plant species for studying resistance to abiotic stresses such as drought and salt. Salt stress is one of the most common environmental factors that affect plant growth and development. MicroRNAs (miRNAs) are small, noncoding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress.

Results

To investigate the miRNAs involved in the salt-stress response, we constructed four small cDNA libraries from P. euphratica plantlets treated with or without salt (300 mM NaCl, 3 days) in either the root or leaf. Using high-throughput sequencing to identify miRNAs, we found 164 conserved miRNAs belonging to 44 families. Of these, 136 novel miRNAs were from the leaf, and 128 novel miRNAs were from the root. In response to salt stress, 95 miRNAs belonging to 46 conserved miRNAs families changed significantly, with 56 miRNAs upregulated and 39 miRNAs downregulated in the leaf. A comparison of the leaf and root tissues revealed 155 miRNAs belonging to 63 families with significantly altered expression, including 84 upregulated and 71 downregulated miRNAs. Furthermore, 479 target genes in the root and 541 targets of novel miRNAs in the leaf were predicted, and functional information was annotated using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases.

Conclusions

This study provides a novel visual field for understanding the regulatory roles of miRNAs in response to salt stress in Populus.

Virus versus host plant microRNAs: who determines the outcome of the interaction?

Considering the importance of microRNAs (miRNAs) in the regulation of essential processes in plant pathogen interactions, it is not surprising that, while plant miRNA sequences counteract viral attack via antiviral RNA silencing, viruses in turn have developed antihost defense mechanisms blocking these RNA silencing pathways and establish a counter-defense. In the current study, computational and stem-loop Reverse Transcription – Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5′/3′ harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. Different viral pre-miRNA hairpin sequences and viral miR/miR* length variants occurring as isomiRs were predicted in both viruses. These miRNAs were located in three Open Reading Frames (ORFs) and in the Intergenic Region (IR). Moreover, various target genes for miRNAs from both viruses were predicted and annotated in the host plant genomes indicating that they are involved in biotic response, metabolic pathways and transcription factors. Plant miRs/miRs* from conserved and highly expressed families were identified, which were shown to have potential targets in the genome of both begomoviruses, representing potential plant miRNAs mediating antiviral defense. This is the first assessment of predicted viral miRs/miRs* of ACMV and EACMV-UG and host plant miRNAs, providing a reference point for miRNA identification in pathogens and their hosts. These findings will improve the understanding of host- pathogen interaction pathways and the function of viral miRNAs in Euphorbiaceous crop plants.

Undesired small RNAs originate from an artificial microRNA precursor in transgenic petunia (Petunia hybrida)

Although artificial microRNA (amiRNA) technology has been used frequently in gene silencing in plants, little research has been devoted to investigating the accuracy of amiRNA precursor processing. In this work, amiRNAchs1 (amiRchs1), based on the Arabidopsis miR319a precursor, was expressed in order to suppress the expression of CHS genes in petunia. The transgenic plants showed the CHS gene-silencing phenotype. A modified 5′ RACE technique was used to map small-RNA-directed cleavage sites and to detect processing intermediates of the amiRchs1 precursor. The results showed that the target CHS mRNAs were cut at the expected sites and that the amiRchs1 precursor was processed from loop to base. The accumulation of small RNAs in amiRchs1 transgenic petunia petals was analyzed using the deep-sequencing technique. The results showed that, alongside the accumulation of the desired artificial microRNAs, additional small RNAs that originated from other regions of the amiRNA precursor were also accumulated at high frequency. Some of these had previously been found to be accumulated at low frequency in the products of ath-miR319a precursor processing and some of them were accompanied by 3′-tailing variant. Potential targets of the undesired small RNAs were discovered in petunia and other Solanaceae plants. The findings draw attention to the potential occurrence of undesired target silencing induced by such additional small RNAs when amiRNA technology is used. No appreciable production of secondary small RNAs occurred, despite the fact that amiRchs1 was designed to have perfect complementarity to its CHS-J target. This confirmed that perfect pairing between an amiRNA and its targets is not the trigger for secondary small RNA production. In conjunction with the observation that amiRNAs with perfect complementarity to their target genes show high efficiency and specificity in gene silencing, this finding has an important bearing on future applications of amiRNAs in gene silencing in plants.

Identification of maize long non-coding RNAs responsive to drought stress

Long non-coding RNAs (lncRNAs) represent a class of riboregulators that either directly act in long form or are processed to shorter miRNAs and siRNAs. Emerging evidence shows that lncRNAs participate in stress responsive regulation. In this study, to identify the putative maize lncRNAs responsive to drought stress, 8449 drought responsive transcripts were first uploaded to the Coding Potential Calculator website for classification as protein coding or non-coding RNAs, and 1724 RNAs were identified as potential non-coding RNAs. A Perl script was written to screen these 1724 ncRNAs and 664 transcripts were ultimately identified as drought-responsive lncRNAs. Of these 664 transcripts, 126 drought-responsive lncRNAs were highly similar to known maize lncRNAs; the remaining 538 transcripts were considered as novel lncRNAs. Among the 664 lncRNAs identified as drought responsive, 567 were upregulated and 97 were downregulated in drought-stressed leaves of maize. 8 lncRNAs were identified as miRNA precursor lncRNAs, 62 were classified as both shRNA and siRNA precursors, and 279 were classified as siRNA precursors. The remaining 315 lncRNAs were classified as other lncRNAs that are likely to function as longer molecules. Among these 315 lncRNAs, 10 are identified as antisense lncRNAs and 7 could pair with 17 CDS sequences with near-perfect matches. Finally, RT-qPCR results confirmed that all selected lncRNAs could respond to drought stress. These findings extend the current view on lncRNAs as ubiquitous regulators under stress conditions.