Essential RNA-Based Technologies and Their Applications in Plant Functional Genomics

A high-efficiency gene silencing in plants using two-hit asymmetrical artificial MicroRNAs

MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in gene regulation. They are produced through an enzyme-guided process called dicing and have an asymmetrical structure with two nucleotide overhangs at the 3' ends. Artificial microRNAs (amiRNAs or amiRs) are designed to mimic the structure of miRNAs and can be used to silence specific genes of interest. Traditionally, amiRNAs are designed based on an endogenous miRNA precursor with certain mismatches at specific positions to increase their efficiency. In this study, the authors modified the highly expressed miR168a in Arabidopsis thaliana by replacing the single miR168 stem-loop/duplex with tandem asymmetrical amiRNA duplexes that follow the statistical rules of miRNA secondary structures. These tandem amiRNA duplexes, called "two-hit" amiRNAs, were shown to have a higher efficiency in silencing GFP and endogenous PDS reporter genes compared to traditional "one-hit" amiRNAs. The authors also demonstrated the effectiveness of "two-hit" amiRNAs in silencing genes involved in miRNA, tasiRNA, and hormone signalling pathways, individually or in families. Importantly, "two-hit" amiRNAs were also able to over-express endogenous miRNAs for their functions. The authors compare "two-hit" amiRNA technology with CRISPR/Cas9 and provide a web-based amiRNA designer for easy design and wide application in plants and even animals.

Gold nanoparticles (AuNPs) can rapidly deliver artificial microRNA (AmiRNA)-ATG6 to silence ATG6 expression in Arabidopsis

KEY MESSAGE

We establish a fast and efficient transient silencing system that facilitates functional studies of some genes, whose knockout leads to plant lethality. In plants, the generation of loss-of-function mutants is crucial for studying gene function. Artificial microRNA (AmiRNA) technology is a more targeted and effective tool for gene silencing. Gold nanoparticles (AuNPs) can bind nucleic acids and deliver them into animal cells. Here, AuNPs are used in combination with AmiRNA technology in plants. We found that AmiRNA-autophagy-related proteins (ATG6) can be delivered to cells by AuNPs to achieve the effect of ATG6 silencing. It is worth noting that on the 10th day there is still a silencing effect. Similar to the atg5 lines, silencing of ATG6 significantly reduced plant resistance to Pseudomonas syringae pv.maculicola (Psm) ES4326/AvrRpt2. Interestingly, ATG6 silencing and ATG5 mutation in NPR1-GFP (nonexpressor of pathogenesis-related genes) lines significantly reduced plant resistance to Psm ES4326/AvrRpt2, suggesting that autophagy is also involved in NPR1-regulated plant immune responses. In summary, we establish a fast and efficient transient silencing system that facilitates functional studies of some genes, whose knockout leads to plant lethality.

milR20 negatively regulates the development of fruit bodies in Pleurotus cornucopiae

The mechanism underlying the development of fruit bodies in edible mushroom is a widely studied topic. In this study, the role of milRNAs in the development of fruit bodies of Pleurotus cornucopiae was studied by comparative analyses of the mRNAs and milRNAs at different stages of development. The genes that play a crucial role in the expression and function of milRNAs were identified and subsequently expressed and silenced at different stages of development. The total number of differentially expressed genes (DEGs) and differentially expressed milRNAs (DEMs) at different stages of development was determined to be 7,934 and 20, respectively. Comparison of the DEGs and DEMs across the different development stages revealed that DEMs and its target DEGs involved in the mitogen-activated protein kinase (MAPK) signaling pathway, protein processing in endoplasmic reticulum, endocytosis, aminoacyl-tRNA biosynthesis, RNA transport, and other metabolism pathways, which may play important roles in the development of the fruit bodies of P. cornucopiae. The function of milR20, which targeted pheromone A receptor g8971 and was involved in the MAPK signaling pathway, was further verified by overexpression and silencing in P. cornucopiae. The results demonstrated that the overexpression of milR20 reduced the growth rate of mycelia and prolonged the development of the fruit bodies, while milR20 silencing had an opposite effect. These findings indicated that milR20 plays a negative role in the development of P. cornucopiae. This study provides novel insights into the molecular mechanism underlying the development of fruit bodies in P. cornucopiae.

Perspectives on plant virus diseases in a climate change scenario of elevated temperatures

Global food production is at risk from many abiotic and biotic stresses and can be affected by multiple stresses simultaneously. Virus diseases damage cultivated plants and decrease the marketable quality of produce. Importantly, the progression of virus diseases is strongly affected by changing climate conditions. Among climate-changing variables, temperature increase is viewed as an important factor that affects virus epidemics, which may in turn require more efficient disease management. In this review, we discuss the effect of elevated temperature on virus epidemics at both macro- and micro-climatic levels. This includes the temperature effects on virus spread both within and between host plants. Furthermore, we focus on the involvement of molecular mechanisms associated with temperature effects on plant defence to viruses in both susceptible and resistant plants. Considering various mechanisms proposed in different pathosystems, we also offer a view of the possible opportunities provided by RNA -based technologies for virus control at elevated temperatures. Recently, the potential of these technologies for topical field applications has been strengthened through a combination of genetically modified (GM)-free delivery nanoplatforms. This approach represents a promising and important climate-resilient substitute to conventional strategies for managing plant virus diseases under global warming scenarios. In this context, we discuss the knowledge gaps in the research of temperature effects on plant-virus interactions and limitations of RNA-based emerging technologies, which should be addressed in future studies.

An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism

The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.

Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis

Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.

MicroRNA Techniques: Valuable Tools for Agronomic Trait Analyses and Breeding in Rice

MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. Extensive studies have revealed that miRNAs have critical functions in plant growth, development, and stress responses and may provide valuable genetic resources for plant breeding research. We herein reviewed the development, mechanisms, and characteristics of miRNA techniques while highlighting widely used approaches, namely, the short tandem target mimic (STTM) approach. We described STTM-based advances in plant science, especially in the model crop rice, and introduced the CRISPR-based transgene-free crop breeding. Finally, we discussed the challenges and unique opportunities related to combining STTM and CRISPR technology for crop improvement and agriculture.

Insights Into Genetic and Molecular Elements for Transgenic Crop Development

Climate change and the exploration of new areas of cultivation have impacted the yields of several economically important crops worldwide. Both conventional plant breeding based on planned crosses between parents with specific traits and genetic engineering to develop new biotechnological tools (NBTs) have allowed the development of elite cultivars with new features of agronomic interest. The use of these NBTs in the search for agricultural solutions has gained prominence in recent years due to their rapid generation of elite cultivars that meet the needs of crop producers, and the efficiency of these NBTs is closely related to the optimization or best use of their elements. Currently, several genetic engineering techniques are used in synthetic biotechnology to successfully improve desirable traits or remove undesirable traits in crops. However, the features, drawbacks, and advantages of each technique are still not well understood, and thus, these methods have not been fully exploited. Here, we provide a brief overview of the plant genetic engineering platforms that have been used for proof of concept and agronomic trait improvement, review the major elements and processes of synthetic biotechnology, and, finally, present the major NBTs used to improve agronomic traits in socioeconomically important crops.

MicroRNA1917-CTR1-LIKE PROTEIN KINASE 4 impacts fruit development via tuning ethylene synthesis and response

MicroRNA1917 (miR1917) is a newly identified miRNAs that regulate ethylene responses in tomato. However, evidence is still limited about its functions in fruit development and ripening. Here, we investigated the possible roles of miR1917-SlCTR4 module in tomato fruit development. We generated miR1917 knock-down mutants by expressing Short Tandem Target Mimic (STTM1917). qRT-PCR and northern-blot analyses suggested that the expression of miR1917 are down-regulated in STTM1917. Concomitantly, miR1917-targeted SlCTR4 gene was up-regulated. STTM1917 plants showed a series of developmental phenotypes, including larger biomass, longer terminal leaflet, bigger floral organ and enhanced fruit and seed size. RNA-seq and qRT-PCR analyses suggested that the expression levels of numerous miRNAs and genes in the transgenic line were significantly altered compared to the wild type. These miRNAs and genes include fruit development-related miRNAs, fruit ripening-related transcription factors and ethylene metabolism genes. Altogether, our results demonstrated that working in concert with ripening regulators, miR1917 might regulate multiple genes in ethylene pathway, thereby modulating fruit development. Our results further indicated that fine-tuning miRNAs expression via STTM can be deployed for agronomic improvement of tomato.

Overexpression of BpCUC2 Influences Leaf Shape and Internode Development in Betula pendula

The CUP-SHAPED COTYLEDON 2 (CUC2) gene, which is negatively regulated by microRNA164 (miR164), has been specifically linked to the regulation of leaf margin serration and the maintenance of phyllotaxy in model plants. However, few studies have investigated these effects in woody plants. In this study, we integrated genomic, transcriptomic, and physiology approaches to explore the function of BpCUC2 gene in Betula pendula growth and development. Our results showed that Betula pendula plants overexpressing BpCUC2, which is targeted by BpmiR164, exhibit shortened internodes and abnormal leaf shapes. Subsequent analysis indicated that the short internodes of BpCUC2 overexpressed transgenic lines and were due to decreased epidermal cell size. Moreover, transcriptome analysis, yeast one-hybrid assays, and ChIP-PCR suggested that BpCUC2 directly binds to the LTRECOREATCOR15 (CCGAC), CAREOSREP1 (CAACTC), and BIHD1OS (TGTCA) motifs of a series of IAA-related and cyclin-related genes to regulate expression. These results may be useful to our understanding of the functional role and genetic regulation of BpCUC2.

MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants

MicroRNAs (miRNAs) modulate the abundance and spatial-temporal accumulation of target mRNAs and indirectly regulate several plant processes. Transcriptional regulation of the genes encoding miRNAs (MIR genes) can be activated by numerous transcription factors, which themselves are regulated by other miRNAs. Fine-tuning of MIR genes or miRNAs is a powerful biotechnological strategy to improve tolerance to abiotic or biotic stresses in crops of economic importance. Current approaches for miRNA fine-tuning are based on the down- or up-regulation of MIR gene transcription and the use of genetic engineering tools to manipulate the final concentration of these miRNAs in the cytoplasm. Transgenesis, cisgenesis, intragenesis, artificial MIR genes, endogenous and artificial target mimicry, MIR genes editing using Meganucleases, ZNF proteins, TALENs and CRISPR/Cas9 or CRISPR/Cpf1, CRISPR/dCas9 or dCpf1, CRISPR13a, topical delivery of miRNAs and epigenetic memory have been successfully explored to MIR gene or miRNA modulation and improve agronomic traits in several model or crop plants. However, advantages and drawbacks of each of these new biotechnological tools (NBTs) are still not well understood. In this review, we provide a brief overview of the biogenesis and role of miRNAs in response to abiotic or biotic stresses, we present critically the main NBTs used for the manipulation of MIR genes and miRNAs, we show current efforts and findings with the MIR genes and miRNAs modulation in plants, and we summarize the advantages and drawbacks of these NBTs and provide some alternatives to overcome. Finally, challenges and future perspectives to miRNA modulating in important crops are also discussed.

ceRNAs in plants: computational approaches and associated challenges for target mimic research

The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions. We divided this article in three main contributions. First, a general overview of research on TMs in plants is presented with practical descriptions of the available literature, tools, data, databases and computational reports. Second, we describe a common protocol for the computational and experimental analyses of TM. Third, we provide a bioinformatics approach for the prediction of TM motifs potentially cross-targeting both members within the same or from different miRNA families, based on the identification of consensus miRNA-binding sites from known TMs across sequenced genomes, transcriptomes and known miRNAs. This computational approach is promising because, in contrast to animals, miRNA families in plants are large with identical or similar members, several of which are also highly conserved. From the three consensus TM motifs found with our approach: MIM166, MIM171 and MIM159/319, the last one has found strong support on the recent experimental work by Reichel and Millar [Specificity of plant microRNA TMs: cross-targeting of mir159 and mir319. J Plant Physiol 2015;180:45-8]. Finally, we stress the discussion on the major computational and associated experimental challenges that have to be faced in future ceRNA studies.

Solanum lycopersicum microRNA1916 targets multiple target genes and negatively regulates the immune response in tomato

MicroRNA1916 (miR1916) is one of the nonconserved miRNAs that respond to various stresses in plants, but little has been known at present about its mechanisms in biotic stresses. In this study, the expression of Solanum lycopersicum (sly)-miR1916 in tomato was found to be down-regulated after infection with Phytophthora infestans or Botrytis cinerea. Tomato plants that overexpressed sly-miR1916 displayed significant enhancement in susceptibility to P. infestans and B. cinerea infection, as well as increased tendency to produce reactive oxygen species. Silencing of sly-miR1916 by short tandem target mimic and artificial microRNA strategies caused the tomato plants to become more tolerant to adverse conditions. In addition, lower sly-miR1916 expression could up-regulate the expression of strictosidine synthase (STR-2), UDP-glycosyltransferases (UGTs), late blight resistance protein homolog R1B-16, disease resistance protein RPP13-like, and MYB transcription factor (MYB12), which ultimately resulted in the accumulation of α-tomatine and anthocyanins via STR-2, UGT, and MYB12. Furthermore, ectopic expression of sly-miR1916/STR-2 significantly changed the tolerance of tobacco to B. cinerea. Taken together, the results demonstrated that sly-miR1916 might regulate the expression of STR-2, UGT, and MYB12 in tomato plant, conferring sensitivity to biotic stress via modulating α-tomatine and anthocyanins.

The interaction between miR160 and miR165/166 in the control of leaf development and drought tolerance in Arabidopsis

MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in plant development and abiotic stresses. To date, studies have mainly focused on the roles of individual miRNAs, however, a few have addressed the interactions among multiple miRNAs. In this study, we investigated the interplay and regulatory circuit between miR160 and miR165/166 and its effect on leaf development and drought tolerance in Arabidopsis using Short Tandem Target Mimic (STTM). By crossing STTM160 Arabidopsis with STTM165/166, we successfully generated a double mutant of miR160 and miR165/166. The double mutant plants exhibited a series of compromised phenotypes in leaf development and drought tolerance in comparison to phenotypic alterations in the single STTM lines. RNA-seq and qRT-PCR analyses suggested that the expression levels of auxin and ABA signaling genes in the STTM-directed double mutant were compromised compared to the two single mutants. Our results also suggested that miR160-directed regulation of auxin response factors (ARFs) contribute to leaf development via auxin signaling genes, whereas miR165/166- mediated HD-ZIP IIIs regulation confers drought tolerance through ABA signaling. Our studies further indicated that ARFs and HD-ZIP IIIs may play opposite roles in the regulation of leaf development and drought tolerance that can be further applied to other crops for agronomic traits improvement.

A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants

microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression, leading to gene silencing. We previously developed short tandem target mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice, and maize, providing a resource for the functional interrogation of miRNAs. We not only revealed the functions of several miRNAs in plant development, but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, and ion-channel activity-associated electrophysiology, demonstrating that STTM technology is an effective approach for studying miRNA functions. To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks, we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants.

CRISPR RNA Array-Guided Multisite Cleavage for Gene Disruption by Cas9 and Cpf1

To achieve multisite-targeting-based DNA cleavage simultaneously, we designed two kinds of CRISPR RNA arrays by fusing four single guide RNAs (sgRNAs for Cas9 or crRNAs for Cpf1) with uncleavable RNA linkers (CRISPRay). The CRISPRay could operate on four adjacent target sites to cleave target DNA in a collaborative manner. Two CRISPR RNA arrays demonstrated robust inactivation of the firefly luciferase gene in living cells. In vitro DNA cleavage and DNA sequencing also verified that sgRNA arrays directed SpCas9 nuclease to cut target DNA at four cleavage sites simultaneously whereas crRNA-array-guided FnCpf1 nuclease showed target-activated, nonspecific DNase activity on both target DNA and nontarget DNA at random sites. Through optimization of the ratio of nuclease and CRIPSR RNAs, CRISPRay should further enhance gene interference in cells. This work presents a simple approach through which to improve multisite-directed gene disruption by fusing four guide RNAs (sgRNAs or crRNAs) into a CRISPR RNA string.

Role of Helicity in DNA Hairpin Folding Dynamics

We study hairpin folding dynamics by means of extensive molecular dynamics simulations, with particular attention paid to the influence of helicity on the folding time. We find that the dynamical exponent α in the anomalous scaling n(t)∼t^{1/α} of the hairpin length n with time changes from 1.6 (≃1+ν, where ν is the Flory exponent) to 1.2 (≃2ν) in three dimensions, when duplex helicity is removed. The relation α=2ν in rotationless hairpin folding is further verified in two dimensions (ν=0.75) and for a ghost chain (ν=0.5). Our findings suggest that the folding dynamics in long helical chains is governed by the duplex dynamics, contrasting the earlier understanding based on the stem-flower picture of unpaired segments. We propose a scaling argument for α=1+ν in helical chains, assuming that duplex relaxation required for orientational positioning of the next pair of bases is the rate-limiting process.

RNA Interference Mechanisms and Applications in Plant Pathology

The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor ( 138 ). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.

Elucidating the role of highly homologous Nicotiana benthamiana ubiquitin E2 gene family members in plant immunity through an improved virus-induced gene silencing approach

BACKGROUND

Virus-induced gene silencing (VIGS) has been used in many plant species as an attractive post transcriptional gene silencing (PTGS) method for studying gene function either individually or at large-scale in a high-throughput manner. However, the specificity and efficiency for knocking down members of a highly homologous gene family have remained to date a significant challenge in VIGS due to silencing of off-targets.

RESULTS

Here we present an improved method for the selection and evaluation of gene fragments used for VIGS to specifically and efficiently knock down members of a highly homologous gene family. Using this method, we knocked down twelve and four members, respectively of group III of the gene family encoding ubiquitin-conjugating enzymes (E2) in Nicotiana benthamiana. Assays using these VIGS-treated plants revealed that the group III E2s are essential for plant development, plant immunity-associated reactive oxygen species (ROS) production, expression of the gene NbRbohB that is required for ROS production, and suppression of immunity-associated programmed cell death (PCD) by AvrPtoB, an effector protein of the bacterial pathogen Pseudomons syringae. Moreover, functional redundancy for plant development and ROS production was found to exist among members of group III E2s.

CONCLUSIONS

We have found that employment of a gene fragment as short as approximately 70 base pairs (bp) that contains at least three mismatched nucleotides to other genes within any 21-bp sequences prevents silencing of off-target(s) in VIGS. This improved approach in the selection and evaluation of gene fragments allows for specific and efficient knocking down of highly homologous members of a gene family. Using this approach, we implicated N. benthamiana group III E2s in plant development, immunity-associated ROS production, and suppression of multiple immunity-associated PCD by AvrPtoB. We also unraveled functional redundancy among group III members in their requirement for plant development and plant immunity-associated ROS production.

SINAT E3 Ligases Control the Light-Mediated Stability of the Brassinosteroid-Activated Transcription Factor BES1 in Arabidopsis

The plant hormones brassinosteroids (BRs) participate in light-mediated regulation of plant growth, although the underlying mechanisms are far from being fully understood. In addition, the function of the core transcription factor in the BR signaling pathway, BRI1-EMS-SUPPRESSOR 1 (BES1), largely depends on its phosphorylation status and its protein stability, but the regulation of BES1 is not well understood. Here, we report that SINA of Arabidopsis thaliana (SINATs) specifically interact with dephosphorylated BES1 and mediate its ubiquitination and degradation. Our genetic data demonstrated that SINATs inhibit BR signaling in a BES1-dependent manner. Interestingly, we found that the protein levels of SINATs were decreased in the dark and increased in the light, which changed BES1 protein levels accordingly. Thus, our study not only uncovered a new mechanism of BES1 degradation but also provides significant insights into how light conditionally regulates plant growth through controlling accumulation of different forms of BES1.

Knockdown of Rice microRNA166 by Short Tandem Target Mimic (STTM)

Small RNAs, including microRNAs (miRNAs), are abundant in plants and play key roles in controlling plant development and physiology. miRNAs regulate the expression of the target genes involved in key plant processes. Due to functional redundancy among miRNA family members in plants, an ideal approach to silence the expression of all members simultaneously, for their functional characterization, is desirable. Target mimic (TM) was the first approach to achieve this goal. Short tandem target mimic (STTM) is a potent approach complementing TM for silencing miRNAs in plants. STTMs have been successfully used in dicots to block miRNA functions. Here, we describe in detail the protocol for designing STTM construct to block miRNA functions in rice. Such approach can be applied to silence miRNAs in other monocots as well.

Silencing of Stress-Regulated miRNAs in Plants by Short Tandem Target Mimic (STTM) Approach

In plants, microRNAs (miRNAs) regulate more than hundred target genes comprising largely transcription factors that control growth and development as well as stress responses. However, the exact functions of miRNA families could not be deciphered because each miRNA family has multiple loci in the genome, thus are functionally redundant. Therefore, an ideal approach to study the function of a miRNA family is to silence the expression of all members simultaneously, which is a daunting task. However, this can be partly overcome by Target Mimic (TM) approach that can knockdown an entire miRNA family. STTM is a modification of TM approach and complements it. STTMs have been successfully used in monocots and dicots to block miRNA functions. miR159 has been shown to be differentially regulated by various abiotic stresses including ABA in various plant species. Here, we describe in detail the protocol for designing STTM construct to block miR159 functions in Arabidopsis, with the potential to apply this technique on a number of other stress-regulated miRNAs in plants.

GUIDE-Seq to Detect Genome-wide Double-Stranded Breaks in Plants

Animal and plant cells have repair capabilities to combat DNA damage. DNA damage and repair dynamics can be determined by technologies such as IDLV capture, BLESS, HTGTS, digenome-seq, and GUIDE-seq. Here we highlight GUIDE-seq, a technology used in therapeutics, and envision its application in plants.

Novel Functional Genomics Approaches: A Promising Future in the Combat Against Plant Viruses

Advances in functional genomics and genome editing approaches have provided new opportunities and potential to accelerate plant virus control efforts through modification of host and viral genomes in a precise and predictable manner. Here, we discuss application of RNA-based technologies, including artificial micro RNA, transacting small interfering RNA, and Cas9 (clustered regularly interspaced short palindromic repeat-associated protein 9), which are currently being successfully deployed in generating virus-resistant plants. We further discuss the reverse genetics approach, targeting induced local lesions in genomes (TILLING) and its variant, known as EcoTILLING, that are used in the identification of plant virus recessive resistance gene alleles. In addition to describing specific applications of these technologies in plant virus control, this review discusses their advantages and limitations.