New insights into miR398 functions in Arabidopsis

Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective

Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.

LncRNA-mediated ceRNA regulatory network provides new insight into chlorogenic acid synthesis in sweet potato

Sweet potato (Ipomoea batatas L.) is considered a highly nutritional and economical crop due to its high contents of bioactive substances, such as anthocyanin and chlorogenic acid (CGA), especially in leaves and stems. The roles of noncoding RNAs (ncRNA), including long noncoding RNA (lncRNA) and microRNA (miRNA), in CGA synthesis, are still unknown. In this study, the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs in two leafy vegetable genotypes "FS7-6-14-7" (high CGA content) and "FS7-6" (low CGA content) were identified. The cis-regulation between lncRNA and mRNA was analyzed. Then, the CGA synthesis-related modules MEBlue and MEYellow were identified to detect trans-regulation mRNA-lncRNA pairs. The GO and KEGG annotations suggested that mRNA in these two modules was significantly enriched in the secondary metabolite synthesis biosynthesis category. A competing endogenous RNAs (ceRNA) network, including 8730 miRNA-mRNA and 444 miRNA-lncRNA pairs, was constructed by DEmiRNA target prediction. Then, a CGA synthesis-related ceRNA network was obtained with lncRNA and mRNA from MEBlue and MEYellow. Finally, one relational pair, MSTRG.47662.1/mes-miR398/itb04g00990, was selected for functional validation. Overexpression of lncRNA MSTRG.47662.1 and mRNA itb04g00990 increased CGA content in both tobacco and sweet potato callus, while overexpression of miRNA mes-miR398 decreased CGA content. Meanwhile, regression analysis of the expression patterns demonstrated that MSTRG.47662.1, acting as a ceRNA, promoted itb04g00990 expression by competitively binding mes-miR398 in CGA synthesis in sweet potato. Our results provide insights into how ncRNA-mediated ceRNA regulatory networks likely contribute to CGA synthesis in leafy sweet potato.

miR398 Attenuates Heat-Induced Leaf Cell Death via Its Target CSD1 in Chinese Cabbage

Previous research has shown that miR398 contributed to plant thermotolerance by silencing its target gene COPPER/ZINC SUPEROXIDE DISMUTASE1 (CSD1) in Arabidopsis thaliana. However, the phylogenesis of miR398 and CSD1 in Brassica crop and their role in regulating leaf cell death under heat stress remains unexplored. Here, we characterized the homologous genes of miR398a and CSD1 in Brassica rapa ssp. pekinensis (Chinese cabbage) and found miR398a abundance was accumulated under heat stress (38 °C and 46 °C for 1 h) in Chinese cabbage, while the expression level of its targets BraCSD1-1 and BraCSD2-1 were downregulated. To further explore their role in heat response, we constructed the transgenic plants overexpressing artificial miR398a (aBra-miR398a), Bra-miR398a target mimic (Bra-MIM398a), and BraCSD1-1 in Chinese cabbage for genetic study. Under high temperatures, p35S::aBra-miR398a lines reduced the areas of leaf cell death and delayed the leaf cell death. By contrast, p35S::Bra-MIM398a and p35S::BraCSD1-1 plants enlarged the areas of leaf cell death and displayed the earliness of leaf cell death. Finally, we found that the expression level of stress-responsive genes BraLEA76, BraCaM1, BraPLC, BraDREB2A, and BraP5CS increased in transgenic plants overexpressing aBra-miR398a, which may contribute to their resistance to heat-induced leaf cell death. Taken together, these results revealed the function of Bra-miR398a in attenuating leaf cell death to ensure plant thermotolerance, indicating that the miR398-CSD1 module could be potential candidates for heat-resistant crop breeding.

Global expression dynamics and miRNA evolution profile govern floral/fiber architecture in the modern cotton (Gossypium)

Majority of differentially expressed miRNAs with functional attributes have been recruited independently and parallelly during allopolyploidy followed by the millennia of human selection of both domesticated G. hirsutum and G. barbadense. The genus Gossypium is a marvelous evolutionary model for studying allopolyploidy and morpho-evolution of long-spinnable fibers from the ancestral wild-fuzz. Many genes, transcription factors, and notably, the regulatory miRNAs essentially govern such remarkable modern fiber phenotypes. To comprehend the impact of allopolyploidy on the evolutionary selection of transcriptional dynamicity of key miRNAs, comparative transcriptome profiling of vegetative and fiber tissues of domesticated diploid G. arboreum (A₂) and allopolyploid cotton species G. hirsutum (AD₁), and G. barbadense (AD₂) identified > 300 differentially expressed miRNAs (DEmiRs) within or between corresponding tissues of A₂, AD₁ and AD₂ species. Up to 49% and 32% DEmiRs were up- and down-regulated at fiber initiation stage of AD₁ and AD₂ species, respectively, whereas 50% and 18% DEmiRs were up- and down-regulated at fiber elongation stage of both the allopolyploid species. Interestingly, A-subgenome-specific DEmiRs exhibit expression dominance in the allopolyploid genetic backgrounds. Comparative spatio-temporal expression analyses of AD₁ and AD₂ species discovered that a majority of DEmiRs were recruited independently under millennia of human selection during domestication. Functional annotations of these DEmiRs revealed selection of associated molecular functions such as hormone-signaling, calcium-signaling and reactive oxygen species (ROS) signaling during fiber initiation and elongation. To validate the functional attributes of annotated DEmiRs, we demonstrated for the first time that the target-mimicry-based constitutive diminution of auxin-signaling associated miR167 directly affected the differentiation of floral and fiber tissues of transgenic cotton. These results strongly suggested that the evolutionarily favored DEmiRs including miR167 were involved in the transcriptional regulation of numerous genes during cotton evolution for enhanced fiber-associated agronomic traits.

Phytochrome regulates cellular response plasticity and the basic molecular machinery of leaf development

Plants are plastic organisms that optimize growth in response to a changing environment. This adaptive capability is regulated by external cues, including light, which provides vital information about the habitat. Phytochrome photoreceptors detect far-red light, indicative of nearby vegetation, and elicit the adaptive shade-avoidance syndrome (SAS), which is critical for plant survival. Plants exhibiting SAS are typically more elongated, with distinctive, small, narrow leaf blades. By applying SAS-inducing end-of-day far-red (EoD FR) treatments at different times during Arabidopsis (Arabidopsis thaliana) leaf 3 development, we have shown that SAS restricts leaf blade size through two distinct cellular strategies. Early SAS induction limits cell division, while later exposure limits cell expansion. This flexible strategy enables phytochromes to maintain control of leaf size through the proliferative and expansion phases of leaf growth. mRNAseq time course data, accessible through a community resource, coupled to a bioinformatics pipeline, identified pathways that underlie these dramatic changes in leaf growth. Phytochrome regulates a suite of major development pathways that control cell division, expansion, and cell fate. Further, phytochromes control cell proliferation through synchronous regulation of the cell cycle, DNA replication, DNA repair, and cytokinesis, and play an important role in sustaining ribosome biogenesis and translation throughout leaf development.

Investigation of the effects of P1 on HC-pro-mediated gene silencing suppression through genetics and omics approaches

BACKGROUND

Posttranscriptional gene silencing (PTGS) is one of the most important mechanisms for plants during viral infection. However, viruses have also developed viral suppressors to negatively control PTGS by inhibiting microRNA (miRNA) and short-interfering RNA (siRNA) regulation in plants. The first identified viral suppressor, P1/HC-Pro, is a fusion protein that was translated from potyviral RNA. Upon infecting plants, the P1 protein itself is released from HC-Pro by the self-cleaving activity of P1. P1 has an unknown function in enhancing HC-Pro-mediated PTGS suppression. We performed proteomics to identify P1-interacting proteins. We also performed transcriptomics that were generated from Col-0 and various P1/HC-Pro-related transgenic plants to identify novel genes. The results showed several novel genes were identified through the comparative network analysis that might be involved in P1/HC-Pro-mediated PTGS suppression.

RESULTS

First, we demonstrated that P1 enhances HC-Pro function and that the mechanism might work through P1 binding to VERNALIZATION INDEPENDENCE 3/SUPERKILLER 8 (VIP3/SKI8), a subunit of the exosome, to interfere with the 5'-fragment of the PTGS-cleaved RNA degradation product. Second, the AGO1 was specifically posttranslationally degraded in transgenic Arabidopsis expressing P1/HC-Pro of turnip mosaic virus (TuMV) (P1/HC^Tu plant). Third, the comparative network highlighted potentially critical genes in PTGS, including miRNA targets, calcium signaling, hormone (JA, ET, and ABA) signaling, and defense response.

CONCLUSION

Through these genetic and omics approaches, we revealed an overall perspective to identify many critical genes involved in PTGS. These new findings significantly impact in our understanding of P1/HC-Pro-mediated PTGS suppression.

Evaluation of mature miR398 family, expression analysis and the post-transcriptional regulation evidence in gamma-irradiated and nitrogen-stressed Medicago sativa seedlings

BACKGROUND

The miR398 (microRNA398) posttranscriptionally regulates the superoxide dismutase (Cu/Zn-SOD).

MATERIALS AND METHODS

The miR398 level was quantitated in gamma-irradiated (20Gy and 200Gy) and nitrogen-stressed seedlings by stem-loop RT-PCR (Real Time-Polymerase chain reaction). The positional preference of nucleotide (nt) for miR398 families and new targets was done. The SOD enzyme was assayed in native PAGE (Polyacrylamide gel electrophoresis).

RESULTS

A relative increase in miR398-3p expression in the roots, and reduction in shoots for gamma-irradiated tissue and downregulation in miR398-5p in shoots is noted. The nitrogen stress shows upregulation of miR398-3p in roots and shoots, whereas the expression of miR398-5p is upregulated in roots and downregulated in shoots. Positional preference in miR398-3p for 1-14 nt is 90% conserved unlike miR398-5p where no nucleotide positional preference is seen. Targets obtained were functionally characterized.

CONCLUSIONS

The mature miR398-5p and miR398-3p levels estimated in gamma-irradiated (20 and 200Gy) and nitrogen-stressed Medicago sativa seedlings show differential levels in roots and shoots. Native PAGE of Cu/Zn-SOD suggests its negative correlation with miR398 in shoots of irradiated and nitrogen-stressed samples. The nucleotide preferences for the nucleotide for a given position and functional characterization of targets are reported herein.

Characterization of microRNAs from Arabidopsis galls highlights a role for miR159 in the plant response to the root-knot nematode Meloidogyne incognita

Root knot nematodes (RKN) are root parasites that induce the genetic reprogramming of vascular cells into giant feeding cells and the development of root galls. MicroRNAs (miRNAs) regulate gene expression during development and plant responses to various stresses. Disruption of post-transcriptional gene silencing in Arabidopsis ago1 or ago2 mutants decrease the infection rate of RKN suggesting a role for this mechanism in the plant-nematode interaction. By sequencing small RNAs from uninfected Arabidopsis roots and from galls 7 and 14 d post infection with Meloidogyne incognita, we identified 24 miRNAs differentially expressed in gall as putative regulators of gall development. Moreover, strong activity within galls was detected for five miRNA promoters. Analyses of nematode development in an Arabidopsis miR159abc mutant had a lower susceptibility to RKN, suggesting a role for the miR159 family in the plant response to M. incognita. Localization of mature miR159 within the giant and surrounding cells suggested a role in giant cell and gall. Finally, overexpression of miR159 in galls at 14 d post inoculation was associated with the repression of the miR159 target MYB33 which expression is restricted to the early stages of infection. Overall, these results implicate the miR159 in plant responses to RKN.

MicroRNA-mediated signaling and regulation of nutrient transport and utilization

MicroRNAs (miRNAs), a group of small-RNA regulators, control diverse developmental processes and stress responses. Recent studies of nutrient-responsive miRNAs have offered novel insights into how plants regulate gene expression to coordinate endogenous demand and external availability of nutrients. Here, we review the mechanisms mediated by miRNAs to facilitate nutrient transport and utilization and show that miRNAs: first, control nutrient uptake and translocation by targeting nutrient transporters or their regulators; second, adjust nutrient metabolism by redistributing nutrients for biosynthesis of more essential compounds; and third, modulate root development and microbial symbiosis to exploit soil nutrients. We also highlight the long-distance movement of miRNAs in maintaining whole-plant nutrient homeostasis and propose several directions for future research.

Genome-wide identification of Hami melon miRNAs with putative roles during fruit development

MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages. Small RNA sequencing yielded a total of 54,553,424 raw reads from eight libraries. 113 conserved miRNAs belonging to 30 miRNA families and nine novel miRNAs comprising nine miRNA families were identified. The expression of 42 conserved miRNAs and three Hami melon-specific miRNAs significantly changed during fruit development. Furthermore, 484 and 124 melon genes were predicted as putative targets of 29 conserved and nine Hami melon-specific miRNA families, respectively. GO enrichment analysis were performed on target genes, "transcription, DNA-dependent", "rRNA processing", "oxidation reduction", "signal transduction", "regulation of transcription, DNA-dependent", and "metabolic process" were the over-represented biological process terms. Cleavage sites of six target genes were validated using 5' RACE. Our results present a comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis towards understanding the regulatory mechanisms in programmed process of normal Hami fruit development and ripening. Specific miRNAs could be selected for further research and applications in breeding practices.

Isolation of Early-Responsive MicroRNA From Diuraphis noxia (Hemiptera: Aphididae)-Resistant Wheat

The Russian wheat aphid (Diuraphis noxia Kurdjumov) is an economically important pest of small grains in many countries. The past decades have seen the deployment of resistance-carrying wheat (Triticum aestivum L.) cultivars to control D. noxia. However, the emergence of resistance-breaking biotypes is negating this strategy. The role that noncoding RNA (ncRNA) molecules play in the wheat-D. noxia interaction has not been studied to date. This study aimed to isolate differentially regulated microRNA from a resistant and susceptible near-isogenic wheat line after aphid infestation. Twenty-seven identified miRNA were mostly related to stress-linked miRNA, and their predicted targets were linked with known D. noxia-feeding regulated proteins. These included transcription factors, signaling proteins, carbohydrate metabolism, and disease resistance pathways. Gene expression of three putative miRNAs and a predicted nucleotide-binding leucine-rich repeat gene with an identified miRNA target site in the NB-ARC domain displayed differential regulation between the resistant and susceptible plants. This study marks the initial investigation into understanding the role of ncRNA in a D. noxia-resistant wheat line after infestation and reports a correlation between a miRNA and its putative target for this interaction.

Expression Profile of Stress-responsive Arabidopsis thaliana miRNAs and their Target Genes in Response to Inoculation with Pectobacterium carotovorum subsp. carotovorum

BACKGROUND

Pectobacterium carotovorum subsp. carotovorum (Pcc) is a soft rot bacterium which upon entry into the plant macerates plant tissues by producing plant cell wall degrading enzymes. It has a wide host range which includes carrot, potato, tomato, leafy greens, squash and other cucurbits, onion, green peppers and cassava. During plant-microbe interactions, one of the ways of plant response to pathogen infection is through the small RNA silencing mechanism. Under pathogen attack the plant utilizes microRNAs to regulate gene expression by means of mediating gene silencing at transcriptional and post-transcriptional level. This study aims to assess for the first time, the expression profile of some stress-responsive miRNA and differential expression pattern of their target genes in Arabidopsis thaliana inoculated with Pcc.

MATERIALS AND METHODS

Leaves of five weeks old Arabidopsis thaliana plants were infected with Pcc and the quantitative real time-PCR, was used to investigate after 0, 24, 48 and 72 h post infection, the expression profiling of the stress-responsive miRNAs which include: miR156, miR159, miR169, miR393, miR396 miR398, miR399 and miR408 along with their target genes which include: Squamosa promoter-binding-like protein, myb domain protein 101, nuclear factor Y subunit A8, concanavalin A-like lectin protein kinase, growth regulating factor 4, copper superoxide dismutase, ubiquitin-protein ligase and plantacyanin respectively.

RESULTS

The findings showed that the overexpression of 6 miRNAs at 24, 48 and 72 h after infection resulted in the repression of their target genes and the expression of 2 miRNAs didn't affect their target genes.

CONCLUSION

These results provide the first indication of the miRNAs role in response to the infection of Pcc in A. thaliana and open new vistas for a better understanding of miRNA regulation of plant response to Pcc.

The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health

Plants are colonized by a variety of bacteria, most of which are not pathogenic. Currently, the plant responses to phyllosphere commensals or to pathogen infection in the presence of commensals are not well understood. Here, we examined the transcriptional response of Arabidopsis thaliana leaves to colonization by common commensal bacteria in a gnotobiotic system using RNA sequencing and conducted plant mutant assays. Arabidopsis responded differently to the model bacteria Sphingomonas melonis Fr1 (S.Fr1) and Methylobacterium extorquens PA1 (M.PA1). Whereas M.PA1 only marginally affected the expression of plant genes (< 10), S.Fr1 colonization changed the expression of almost 400 genes. For the latter, genes related to defense responses were activated and partly overlapped with those elicited by the pathogen Pseudomonas syringae DC3000 (Pst). As S.Fr1 is able to mediate plant protective activity against Pst, we tested plant immunity mutants and found that the pattern-recognition co-receptor mutant bak1/bkk1 showed attenuated S.Fr1-dependent plant protection. The experiments demonstrate that the plant responds differently to members of its natural phyllosphere microbiota. A subset of commensals trigger expression of defense-related genes and thereby may contribute to plant health upon pathogen encounter.

Identification of microRNAs and their corresponding targets involved in the susceptibility interaction of wheat response to Puccinia striiformis f. sp. tritici

MicroRNAs (miRNAs) play very important roles in plant defense responses. However, little is known about their roles in the susceptibility interaction between wheat and Puccinia striiformis f. sp. tritici (Pst). In this study, two miRNA libraries were constructed from the leaves of the cultivar Xingzi 9104 inoculated with the virulent Pst race CYR32 and sterile water, respectively. A total of 1316 miRNA candidates, including 173 known miRNAs that were generated from 98 pre-miRNAs, were obtained. The remaining 1143 miRNA candidates included 145 conserved and 998 wheat-specific miRNAs that were generated from 87 and 1088 pre-miRNAs, respectively. The 173 known and 145 conserved miRNAs were sub-classified into 63 miRNA families. The target genes of wheat miRNAs were also confirmed using degradome sequencing technology. Most of the annotated target genes were related to signal transduction or energy metabolism. Additionally, we found that miRNAs and their target genes form complicated regulation networks. The expression profiles of miRNAs and their corresponding target genes were further analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and the results indicate that some miRNAs are involved in the compatible wheat-Pst susceptibility interaction. Importantly, tae-miR1432 was highly expressed when wheat was challenged with CYR32, and the corresponding target gene, predicted to be a calcium ion-binding protein, also exhibited upregulated expression but a divergent expression trend. PC-3P-7484, a specific wheat miRNA, was highly expressed in the wheat response to Pst infection, while the expression of the corresponding target gene ubiquillin was dramatically downregulated. These data provide the foundation for evaluating the important regulatory roles of miRNAs in wheat-Pst susceptibility interaction.

Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods

To survive under abiotic stresses in the environment, plants trigger a reprogramming of gene expression, by transcriptional regulation or translational regulation, to turn on protective mechanisms. The current focus of research on how plants cope with abiotic stresses has transitioned from transcriptomic analyses to small RNA investigations. In this review, we have summarized and evaluated the current methodologies used in the identification and validation of small RNAs and their targets, in the context of plant responses to abiotic stresses.

Lipopolysaccharide perception leads to dynamic alterations in the microtranscriptome of Arabidopsis thaliana cells and leaf tissues

BACKGROUND

MicroRNAs (miRNAs) are non-coding RNA molecules which have recently emerged as important gene regulators in plants and their gene expression analysis is becoming increasingly important. miRNAs regulate gene expression at the post-transcriptional level by translational repression or target degradation of specific mRNAs and gene silencing. In order to profile the microtranscriptome of Arabidopsis thaliana leaf and callus tissues in response to bacterial lipopolysaccharide (LPS), small RNA libraries were constructed at 0 and 3 h post induction with LPS and sequenced by Illumina sequencing technology.

RESULTS

Differential regulation of subset of miRNAs in response to LPS treament was observed. Small RNA reads were mapped to the miRNA database and 358 miRNAs belonging to 49 miRNA families in the callus tissues and 272 miRNAs belonging to 40 miRNA families in the leaf tissues were identified. Moreover, target genes for all the identified miRNAs families in the leaf tissues and 44 of the 49 miRNAs families in the callus tissues were predicted. The sequencing analysis showed that in both callus and leaf tissues, various stress regulated-miRNAs were differentially expressed and real time PCR validated the expression profile of miR156, miR158, miR159, miR169, miR393, miR398, miR399 and miR408 along with their target genes.

CONCLUSION

A. thaliana callus and leaf callus tissues respond to LPS as a microbe-associated molecular pattern molecule through dynamic changes to the microtranscriptome associated with differential transcriptional regulation in support of immunity and basal resistance.

Exploration of microRNAs and their targets engaging in the resistance interaction between wheat and stripe rust

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. miRNAs are important regulators, they play very central roles in plant organ development, vegetable phase change and defense responses. In this study, two miRNA libraries from wheat cultivar Xingzi 9104 (XZ) challenged with the avirulent Pst race CYR32 and sterile water were constructed, respectively. A total of 596 miRNA candidates were obtained. 420 wheat-specific candidate miRNAs were screened in adult plants challenged with Pst using microarray-based analyses. We analyzed the abundance of candidate miRNAs, and the levels of a subset of candidate miRNAs were determined by quantitative real time PCR (qRT-PCR). The qRT-PCR results indicated that some miRNAs were involved in the incompatible interaction between wheat and Pst. In addition, we identified some miRNAs differentially expressed in different leaves. Additionally, the target genes of wheat miRNAs were confirmed by using degradome sequencing technology. Most of the annotated target genes are related to signal transduction, energy metabolism, and other functions. We selected some target genes for relative expression analysis using qRT-PCR, and found that RabGAP/TBC domain-containing protein, zinc finger protein and Cysteine-rich receptor-like protein kinase 41 may play important role in the incompatible interaction between XZ and CYR32. Intriguingly, miRNAs and target gene seem to form a complicated regulation network that regulates the wheat-Pst interaction. Our data provide the foundation for evaluating the important regulatory roles of miRNAs in the wheat-Pst interaction.

RACK1 scaffold proteins influence miRNA abundance in Arabidopsis

MicroRNAs (miRNAs) regulate plant development by post-transcriptional regulation of target genes. In Arabidopsis thaliana, DCL1 processes precursors (pri-miRNAs) to miRNA duplexes, which associate with AGO1. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) or AGO1 to facilitate efficient and precise pri-miRNA processing and miRNA loading, respectively. In this study, we show that the accumulation of plant microRNAs depends on RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), a scaffold protein that is found in all higher eukaryotes. miRNA levels are reduced in rack1 mutants, and our data suggest that RACK1 affects the microRNA pathway via several distinct mechanisms involving direct interactions with known microRNA factors: RACK1 ensures the accumulation and processing of some pri-miRNAs, directly interacts with SERRATE and is part of an AGO1 complex. As a result, mutations in RACK1 lead to over-accumulation of miRNA target mRNAs, which are important for ABA responses and phyllotaxy, for example. In conclusion, our study identified complex functioning of RACK1 proteins in the Arabidopsis miRNA pathway; these proteins are important for miRNA production and therefore plant development.

Manipulation of microRNA expression to improve nitrogen use efficiency

Nitrogen is the key limiting nutrient required for plant growth. The application of nitrogen-based fertilizers to crops has risen dramatically in recent years, resulting in significant yield increases. However, increased production has come at the cost of substantial negative environmental consequences. Higher crop production costs, increased consumption of food and fertilizer, and a growing global population have led to calls for a "second green revolution" using modern genetic manipulation techniques to improve the production, yield, and quality of crops. Considerable research is being directed toward the study and engineering of nitrogen use efficiency in crop plants. The end goal is to reduce the amount of nitrogen-based fertilizer used and thereby reduce production costs and environmental damage while increasing yields. In this review, we present an overview of recent advances in understanding the regulation of nitrogen metabolism by the action of microRNAs with a view toward engineering crops with increased nitrogen use efficiency.

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

The Ago2 component of the RNA-induced silencing complex (RISC) is an endonuclease that cleaves mRNAs that base pair with high complementarity to RISC-bound microRNAs. Many examples of such direct cleavage have been identified in plants, but not in vertebrates, despite the conservation of catalytic capacity in vertebrate Ago2. We performed parallel analysis of RNA ends (PAREs), a deep sequencing approach that identifies 5'-phosphorylated, polyadenylated RNAs, to detect potential microRNA-directed mRNA cleavages in mouse embryo and adult tissues. We found that numerous mRNAs are potentially targeted for cleavage by endogenous microRNAs, but at very low levels relative to the mRNA abundance, apart from miR-151-5p-guided cleavage of the N4BP1 mRNA. We also find numerous examples of non-miRNA-directed cleavage, including cleavage of a group of mRNAs within a CA-repeat consensus sequence. The PARE analysis also identified many examples of adenylated small non-coding RNAs, including microRNAs, tRNA processing intermediates and various other small RNAs, consistent with adenylation being part of a widespread proof-reading and/or degradation pathway for small RNAs.