Evolutionary Footprints Reveal Insights into Plant MicroRNA Biogenesis

Elucidating the molecular basis of salt tolerance in potatoes through miRNA expression and phenotypic analysis

Potatoes are a critical staple crop worldwide, yet their yield is significantly constrained by salt stress. Understanding and enhancing salt tolerance in potatoes is crucial for ensuring food security. This study evaluated the salt tolerance of 17 diverse potato varieties using principal component analysis, membership function analysis, cluster analysis, and stepwise regression analysis. Comprehensive evaluation based on morphological, physiological, and biochemical indicators divided the varieties into three categories, identifying Z1264-1, Z700-1, Z943-1, Z1266-1, Z510-1, and Z1076-1 as having strong salt tolerance. Regression equations established stem thickness, root length, and catalase activity as rapid identification markers for salt tolerance in tetraploid potatoes. Transcriptome analysis of the highly tolerant variety Z1076-1 identified 68 differentially expressed miRNAs (DE miRNAs). qRT-PCR validation for eight randomly selected DE miRNAs confirmed consistent expression trends with transcriptome data. Predicted target genes of these miRNAs are involved in calcium channel signaling, osmotic regulation, plant hormone signaling, and reactive oxygen species clearance. Our findings provide valuable insights for the identification and screening of salt-tolerant potato germplasms. The findings also lay the foundation for studying molecular mechanisms of salt tolerance and advancing genetic breeding efforts to cultivate more resilient potato varieties.

Advantage looping: Gene regulatory circuits between microRNAs and their target transcription factors in plants

The 20 to 24 nucleotide microRNAs (miRNAs) and their target transcription factors (TF) have emerged as key regulators of diverse processes in plants, including organ development and environmental resilience. In several instances, the mature miRNAs degrade the TF-encoding transcripts, while their protein products in turn bind to the promoters of the respective miRNA-encoding genes and regulate their expression, thus forming feedback loops (FBLs) or feedforward loops (FFLs). Computational analysis suggested that such miRNA-TF loops are recurrent motifs in gene regulatory networks (GRNs) in plants as well as animals. In recent years, modeling and experimental studies have suggested that plant miRNA-TF loops in GRNs play critical roles in driving organ development and abiotic stress responses. Here, we discuss the miRNA-TF FBLs and FFLs that have been identified and studied in plants over the past decade. We then provide some insights into the possible roles of such motifs within GRNs. Lastly, we provide perspectives on future directions for dissecting the functions of miRNA-centric GRNs in plants.

Structural determinants in the miRNA/miRNA* duplex and the DCL1 PAZ domain for precise and efficient plant miRNA processing

The accessory proteins Hyponastic-like 1 (HYL1) and Serrated (SE) enhance the precise and efficient processing of miRNAs by Dicer-like 1 (DCL1), which is important for proper miRNA function. However, other factors determining the precision and efficiency of miRNA biogenesis are not well-known. Here, we found that an asymmetric bulge (AB) at the 3' end of miR-5p (produced from the 5' arm of the pre-miRNA) reduced the precision of the second cleavage, whereas an AB at other sites of miR-5p mainly affected the accumulation level of miR-5p in transient expression in Nicotiana benthamiana. In contrast, many ABs in miR-3p (produced from the 3' arm of the pre-miRNA) impose strong negative impact on the processing precision and the accumulation level of miR-5p in N. benthamiana. Arabidopsis DCL1/SE/HYL1 complex-mediated miRNA processing was reconstituted in Saccharomyces cerevisiae to further investigate AB-mediated interference with DCL1 processing. With this system, the positional effect of AB on miRNA processing was tested. The results showed that ABs on the middle of miR-5p have less of an impact on DCL1 cleavage efficiency and precision, whereas those on miR-3p or near the ends of miR-5p strongly reduce DCL1 cleavage activity, precision or both. Studies using the yeast miRNA processing system and transgenic Arabidopsis also revealed the importance of the interaction between the 2-nt 3' overhang of pre-miRNA and the 3' overhang binding pocket (3'BP) on the precision of the second cleavage reaction for many endogenous miRNAs. These findings provide new insights into the mechanism of miRNA biogenesis.

Principles of miRNA/miRNA* function in plant MIRNA processing

MicroRNAs (miRNAs) are essential regulators of gene expression, defined by their unique biogenesis, which requires the precise excision of the small RNA from an imperfect fold-back precursor. Unlike their animal counterparts, plant miRNA precursors exhibit variations in sizes and shapes. Plant MIRNAs can undergo processing in a base-to-loop or loop-to-base direction, with DICER-LIKE1 (DCL1) releasing the miRNA after two cuts (two-step MIRNAs) or more (sequential MIRNAs). In this study, we demonstrate the critical role of the miRNA/miRNA* duplex region in the processing of miRNA precursors. We observed that endogenous MIRNAs frequently experience suboptimal processing in vivo due to mismatches in the miRNA/miRNA* duplex, a key region that fine-tunes miRNA levels. Enhancing the interaction energy of the miRNA/miRNA* duplex in two-step MIRNAs results in a substantial increase in miRNA levels. Conversely, sequential MIRNAs display distinct and specific requirements for the miRNA/miRNA* duplexes along their foldback structure. Our work establishes a connection between the miRNA/miRNA* structure and precursor processing mechanisms. Furthermore, we reveal a link between the biological function of miRNAs and the processing mechanism of their precursors with the evolution of plant miRNA/miRNA* duplex structures.

Citrus psorosis virus 24K protein inhibits the processing of miRNA precursors by interacting with components of the biogenesis machinery

Sweet orange (Citrus sinensis) is one of the most important fruit crops worldwide. Virus infections in this crop can interfere with cellular processes, causing dramatic economic losses. By performing RT-qPCR analyses, we demonstrated that citrus psorosis virus (CPsV)-infected orange plants exhibited higher levels of unprocessed microRNA (miRNA) precursors than healthy plants. This result correlated with the reported reduction of mature miRNAs species. The protein 24K, the CPsV suppressor of RNA silencing (VSR), interacts with miRNA precursors in vivo. Thus, this protein becomes a candidate responsible for the increased accumulation of unprocessed miRNAs. We analyzed 24K RNA-binding and protein-protein interaction domains and described patterns of its subcellular localization. We also showed that 24K colocalizes within nuclear D-bodies with the miRNA biogenesis proteins DICER-LIKE 1 (DCL1), HYPONASTIC LEAVES 1 (HYL1), and SERRATE (SE). According to the results of bimolecular fluorescence complementation and co-immunoprecipitation assays, the 24K protein interacts with HYL1 and SE. Thus, 24K may inhibit miRNA processing in CPsV-infected citrus plants by direct interaction with the miRNA processing complex. This work contributes to the understanding of how a virus can alter the regulatory mechanisms of the host, particularly miRNA biogenesis and function.IMPORTANCESweet oranges can suffer from disease symptoms induced by virus infections, thus resulting in drastic economic losses. In sweet orange plants, CPsV alters the accumulation of some precursors from the regulatory molecules called miRNAs. This alteration leads to a decreased level of mature miRNA species. This misregulation may be due to a direct association of one of the viral proteins (24K) with miRNA precursors. On the other hand, 24K may act with components of the cell miRNA processing machinery through a series of predicted RNA-binding and protein-protein interaction domains.

Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis

MicroRNAs (miRNAs) are produced from highly structured primary transcripts (pri-miRNAs) and regulate numerous biological processes in eukaryotes. Due to the extreme heterogeneity of these structures, the initial processing sites of plant pri-miRNAs and the structural rules that determine their processing have been predicted for many miRNAs but remain elusive for others. Here we used semi-active DCL1 mutants and advanced degradome-sequencing strategies to accurately identify the initial processing sites for 147 of 326 previously annotated Arabidopsis miRNAs and to illustrate their associated pri-miRNA cleavage patterns. Elucidating the in vivo RNA secondary structures of 73 pri-miRNAs revealed that about 95% of them differ from in silico predictions, and that the revised structures offer clearer interpretation of the processing sites and patterns. Finally, DCL1 partners Serrate and HYL1 could synergistically and independently impact processing patterns and in vivo RNA secondary structures of pri-miRNAs. Together, our work sheds light on the precise processing mechanisms of plant pri-miRNAs.

Transgene-free, virus-based gene silencing in plants by artificial microRNAs derived from minimal precursors

Artificial microRNAs (amiRNAs) are highly specific, 21-nucleotide (nt) small RNAs designed to silence target transcripts. In plants, their application as biotechnological tools for functional genomics or crop improvement is limited by the need of transgenically expressing long primary miRNA (pri-miRNA) precursors to produce the amiRNAs in vivo. Here, we analyzed the minimal structural and sequence requirements for producing effective amiRNAs from the widely used, 521-nt long AtMIR390a pri-miRNA from Arabidopsis thaliana. We functionally screened in Nicotiana benthamiana a large collection of constructs transiently expressing amiRNAs against endogenous genes and from artificially shortened MIR390-based precursors and concluded that highly effective and accurately processed amiRNAs can be produced from a chimeric precursor of only 89 nt. This minimal precursor was further validated in A. thaliana transgenic plants expressing amiRNAs against endogenous genes. Remarkably, minimal but not full-length precursors produce authentic amiRNAs and induce widespread gene silencing in N. benthamiana when expressed from an RNA virus, which can be applied into leaves by spraying infectious crude extracts. Our results reveal that the length of amiRNA precursors can be shortened without affecting silencing efficacy, and that viral vectors including minimal amiRNA precursors can be applied in a transgene-free manner to induce whole-plant gene silencing.

The plant noncoding transcriptome: a versatile environmental sensor

Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.

Dose-dependent long-distance movement of microRNA399 duplex regulates phosphate homeostasis in Arabidopsis

MicroRNA399 (miR399), a phosphate (Pi) starvation-induced long-distance signal, is first produced in shoots and moves to roots to suppress PHO2 encoding a ubiquitin conjugase, leading to enhanced Pi uptake and root-to-shoot translocation. However, the molecular mechanism underlying miR399 long-distance movement remains elusive. Hypocotyl grafting with various Arabidopsis mutants or transgenic lines expressing artificial miR399f was employed. The movement of miR399 across graft junction and the rootstock PHO2 transcript and scion Pi levels were analyzed to elucidate the potential factors involved. Our results showed that miR399f precursors are cell-autonomous and mature miR399f movement is independent of its biogenesis, sequence context, and length (21 or 22 nucleotides). Expressing viral silencing suppressor P19 in the root stele or blocking unloading in the root phloem pore pericycle (PPP) antagonized its silencing effect, suggesting that the miR399f/miR399f* duplex is a mobile entity unloaded through PPP. Notably, the scion miR399f level positively correlates with its amount translocated to rootstocks, implying dose-dependent movement. This study uncovers the molecular basis underlying the miR399-mediated long-distance silencing in coordinating shoot Pi demand with Pi acquisition and translocation activities in the roots.

A conserved SNP variation in the pre-miR396c flanking region in Oryza sativa indica landraces correlates with mature miRNA abundance

Plant precursor miRNAs (pre-miRNA) have conserved evolutionary footprints that correlate with mode of miRNA biogenesis. In plants, base to loop and loop to base modes of biogenesis have been reported. Conserved structural element(s) in pre-miRNA play a major role in turn over and abundance of mature miRNA. Pre-miR396c sequences and secondary structural characteristics across Oryza species are presented. Based on secondary structure, twelve Oryza pre-miR396c sequences are divided into three groups, with the precursor from halophytic Oryza coarctata forming a distinct group. The miRNA-miRNA* duplex region is completely conserved across eleven Oryza species as are other structural elements in the pre-miRNA, suggestive of an evolutionarily conserved base-to-loop mode of miRNA biogenesis. SNPs within O. coarctata mature miR396c sequence and miRNA* region have the potential to alter target specificity and association with the RNA-induced silencing complex. A conserved SNP variation, rs10234287911 (G/A), identified in O. sativa pre-miR396c sequences alters base pairing above the miRNA-miRNA* duplex. The more stable structure conferred by the 'A_10234287911' allele may promote better processing vis-à-vis the structure conferred by 'G_10234287911' allele. We also examine pri- and pre-miR396c expression in cultivated rice under heat and salinity and their correlation with miR396c expression.

Transcriptional Regulation of zma-MIR528a by Action of Nitrate and Auxin in Maize

In recent years, miR528, a monocot-specific miRNA, has been assigned multifaceted roles during development and stress response in several plant species. However, the transcription regulation and the molecular mechanisms controlling MIR528 expression in maize are still poorly explored. Here we analyzed the zma-MIR528a promoter region and found conserved transcription factor binding sites related to diverse signaling pathways, including the nitrate (TGA1/4) and auxin (AuxRE) response networks. Accumulation of both pre-miR528a and mature miR528 was up-regulated by exogenous nitrate and auxin treatments during imbibition, germination, and maize seedling establishment. Functional promoter analyses demonstrated that TGA1/4 and AuxRE sites are required for transcriptional induction by both stimuli. Overall, our findings of the nitrogen- and auxin-induced zma-MIR528a expression through cis-regulatory elements in its promoter contribute to the knowledge of miR528 regulome.

Investigation and Expression Analysis of R2R3-MYBs and Anthocyanin Biosynthesis-Related Genes during Seed Color Development of Common Bean (Phaseolus vulgaris)

Anthocyanins are responsible for the coloration of common bean seeds, and their accumulation is positively correlated with the expression level of anthocyanin biosynthetic genes. The MBW (MYB-bHLH-WD40) complex is thought to regulate the expression of these genes, and MYB proteins, which are a key factor in activating anthocyanin pathway genes, have been identified in several plants. This study demonstrated gene structures, chromosomal placements, gene duplications of R2R3-MYBs, miRNAs associated with R2R3-MYBs, and the interaction of these genes with other flavonoid regulatory genes. qRT-PCR was used to investigate the role of specific R2R3-MYBs and flavonoid genes in common bean seed color development. As a result of a comprehensive analysis with the help of in silico tools, we identified 160 R2R3-MYB genes in the common bean genome. We divided these genes into 16 classes on the basis of their intron-exon and motif structures. Except for three, the rest of the common bean R2R3-MYB members were distributed to all chromosomes with different densities, primarily located on chromosomes 3 and 8. We identified a total of 44 duplicated gene pairs dispersed across 11 chromosomes and evolved under purifying selection (Ka/Ks  <  1), 19 of which were derived from a whole-genome duplication. Our research uncovered 25 putative repressor PvMYB proteins that contain the EAR motif. Additionally, fifty different cis-regulatory elements regulated by light, stress, and hormone were identified. Within the genome of the common bean, we discovered a total of 36 microRNAs that target a total of 72 R2R3-MYB transcripts. The effect of 16 R2R3-MYB genes and 16 phenylpropanoid pathway genes, selected on the basis of their interaction in the protein-protein interaction map, playing role in the regulation of seed coat color development was evaluated using qRT-PCR in 5 different tissues at different developmental stages. The results revealed that these specific genes have different expression levels during different developmental periods, with higher levels in the pod filling and early pod stages than in the rest of the developmental periods. Furthermore, it was shown that PvTT8 (bHLH), PvTT2 (PvMYB42), PvMYB113, PvTTG1, and PvWD68 genes have effects on the regulation of seed coat color. The findings of this study, which is the first to use whole-genome analysis to identify and characterize the R2R3-MYB genes in common bean, may serve as a reference for future functional research in the legume.

MicroRNAs Mediated Plant Responses to Salt Stress

One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.

Evolutionary conservation of nested MIR159 structural microRNA genes and their promoter characterization in Arabidopsis thaliana

MicroRNAs (miRNAs) are endogenous small RNAs, that are vital for gene expression regulation in eukaryotes. Whenever a pri-miRNA precursor includes another miRNA precursor, and both of these precursors may generate independent, non-overlapping mature miRNAs, we named them nested miRNAs. However, the extent of nested miR159 structural evolutionary conservation and its promoter characterization remains unknown. In this study, the sequence alignment and phylogenetic analysis reveal that the MIR159 family is ancient, and its nested miR159 structures are evolutionary conserved in different plant species. The overexpression of ath-MIR159a, including the 1.2 kb downstream region, has no effect on rescuing the mir159ab phenotype. The promoter truncation results revealed that the 1.0 kb promoter of ath-MIR159a is sufficient for rescuing the mir159ab phenotype. The cis-regulatory elements in the ath-miR159a promoters indicated functions related to different phytohormones, abiotic stresses, and transcriptional activation. While the MybSt1 motif-containing region is not responsible for activating the regulation of the miR159a promoter. The qRT-PCR results showed that overexpression of ath-MIR159a led to high expression levels of miR159a.1-5 and miR159a.1-3 and complemented the growth defect of mir159ab via downregulation of MYB33 and MYB65. Furthermore, continuously higher expression of the miR159a.2 duplex in transgenic lines with the curly leaf phenotype indicates that miR159a.2 is functional in Arabidopsis and suggests that it is possible for a miRNA precursor to encode several regulatory small RNAs in plants. Taken together, our study demonstrates that the nested miR159 structure is evolutionary conserved and miRNA-mediated gene regulation is more complex than previously thought.

MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development

MicroRNAs (miRNAs) are a class of 21-24 nucleotides (nt) noncoding small RNAs ubiquitously distributed across the plant kingdom. miR482/2118, one of the conserved miRNA superfamilies originating from gymnosperms, has divergent main functions in core-angiosperms. It mainly regulates NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT (NBS-LRR) genes in eudicots, functioning as an essential component in plant disease resistance; in contrast, it predominantly targets numerous long noncoding RNAs (lncRNAs) in monocot grasses, which are vital for plant reproduction. Usually, miR482/2118 is 22-nt in length, which can trigger the production of phased small interfering RNAs (phasiRNAs) after directed cleavage. PhasiRNAs instigated from target genes of miR482/2118 enhance their roles in corresponding biological processes by cis-regulation on cognate genes and expands their function to other pathways via trans activity on different genes. This review summarizes the origin, biogenesis, conservation, and evolutionary characteristics of the miR482/2118 superfamily and delineates its diverse functions in disease resistance, plant development, stress responses, etc.

Significance of miRNA in enhancement of flavonoid biosynthesis

Flavonoid metabolism shows very strong plasticity in plant development and coping with the changing environment. Flavonoid biosynthesis is regulated by many metabolic pathways, including transcriptional regulation, post-transcriptional control, post-translational regulationand epigenetic regulation. miRNA is a form of endogenous noncoding single-strand small molecule RNA that primarily regulates the expression of target genes horizontally after transcription through splicing and translational suppression. It also plays an important role in regulating plant growth and development, secondary metabolism and biotic and abiotic stress. miRNA can regulate the formation of flavonoids by acting on structural genes or indirectly by using an MBW transcription complex comprising MYB-bHLH-WD40. This study summarizes the biosynthesis and mechanisms of miRNA, and provides a summary of the mechanisms of miRNAs involved in production of flavonoids, in order to elucidate the biosynthesis pathway and complex regulatory network of plant flavonoids. We aim to provide new insights into improving the content of flavonoid active ingredients in plants.

Systematic Characterization of MicroRNA Processing Modes in Plants With Parallel Amplification of RNA Ends

In plants, the RNase III-type enzyme Dicer-like 1 (DCL1) processes most microRNAs (miRNAs) from their primary transcripts called pri-miRNAs. Four distinct processing modes (i.e., short base to loop, sequential base to loop, short loop to base, and sequential loop to base) have been characterized in Arabidopsis, mainly by the Specific Parallel Amplification of RNA Ends (SPARE) approach. However, SPARE is a targeted cloning method which requires optimization of cloning efficiency and specificity for each target. PARE (Parallel Amplification of RNA Ends) is an untargeted method per se and is widely used to identify miRNA mediated target slicing events. A major concern with PARE in characterizing miRNA processing modes is the potential contamination of mature miRNAs. Here, we provide a method to estimate miRNA contamination levels and showed that most publicly available PARE libraries have negligible miRNA contamination. Both the numbers and processing modes detected by PARE were similar to those identified by SPARE in Arabidopsis. PARE also determined the processing modes of 36 Arabidopsis miRNAs that were unexplored by SPARE, suggesting that it can complement the SPARE approach. Using publicly available PARE datasets, we identified the processing modes of 36, 91, 90, and 54 miRNAs in maize, rice, soybean, and tomato, respectively, and demonstrated that the processing mode was conserved overall within each miRNA family. Through its power of tracking miRNA processing remnants, PARE also facilitated miRNA characterization and annotation.

Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants

MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.

Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions

Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.

Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants

In plants, miRNA production is orchestrated by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. Post-transcriptional processing of miRNAs is controlled by a pair of physically interacting proteins, hyponastic leaves 1 (HYL1) and Dicer-like 1 (DCL1). However, the evolutionary history and structural basis of the HYL1–DCL1 interaction is unknown. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 in vitro and in Arabidopsis thaliana to better understand the origin and evolution of the HYL1–DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner before the divergence of mosses from seed plants (∼500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two dsRNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1–DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in A. thaliana was sufficient to rescue many key aspects of plant development disrupted by HYL1⁻ knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1–DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant “developmental toolkit.”

Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant

miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.

Nuclear RNA purification by flow cytometry to study nuclear processes in plants

The nature of plant tissues has continuously hampered understanding of the spatio-temporal and subcellular distribution of RNA-guided processes. Here, we describe a universal protocol based on Arabidopsis to investigate subcellular RNA distribution from virtually any plant species using flow cytometry sorting. This protocol includes all necessary control steps to assess the quality of the nuclear RNA purification. Moreover, it can be easily applied to different plant developmental stages, tissues, cell cycle phases, experimental growth conditions, and specific cell type(s). For complete information on the use and execution of this protocol, please refer to Bologna et al. (2018) and de Leone et al. (2020).

Recent advances in the regulation of plant miRNA biogenesis

MicroRNAs (miRNAs) are essential non-coding riboregulators of gene expression in plants and animals. In plants, miRNAs guide their effector protein named ARGONAUTE (AGO) to find target RNAs for gene silencing through target RNA cleavage or translational inhibition. miRNAs are derived from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by the DNA-dependent RNA polymerase II. In plants, an RNase III enzyme DICER-LIKE1-containing complex processes pri-miRNAs in the nucleus into miRNAs. To ensure proper function of miRNAs, plants use multiple mechanisms to control miRNA accumulation. On one hand, pri-miRNA levels are controlled through transcription and stability. On the other hand, the activities of the DCL1 complex are regulated by many protein factors at transcriptional, post-transcriptional and post-translational levels. Notably, recent studies reveal that pri-miRNA structure/sequence features and modifications also play important roles in miRNA biogenesis. In this review, we summarize recent progresses on the mechanisms regulating miRNA biogenesis.

MicroRNA-mediated regulation of agronomically important seed traits: a treasure trove with shades of grey!

Seed development is an intricate process with multiple levels of regulation. MicroRNAs (miRNAs) have emerged as one of the crucial components of molecular networks underlying agronomically important seed traits in diverse plant species. In fact, loss of function of the genes regulating miRNA biogenesis also exhibits defects in seed development. A total of 21 different miRNAs have experimentally been shown to regulate seed size, nutritional content, vigor, and shattering, and have been reviewed here. The mechanism details of the associated regulatory cascades mediated through transcriptional regulators, phytohormones, basic metabolic machinery, and secondary siRNAs are elaborated. Co-localization of miRNAs and their target regions with seed-related QTLs provides new avenues for engineering these traits using conventional breeding programs or biotechnological interventions. While global analysis of miRNAs using small RNA sequencing studies are expanding the repertoire of candidate miRNAs, recent revelations on their inheritance, transport, and mechanism of action would be instrumental in designing better strategies for optimizing agronomically relevant seed traits.

Systematic analyses of the MIR172 family members of Arabidopsis define their distinct roles in regulation of APETALA2 during floral transition

MicroRNAs (miRNAs) play important roles in regulating flowering and reproduction of angiosperms. Mature miRNAs are encoded by multiple MIRNA genes that can differ in their spatiotemporal activities and their contributions to gene regulatory networks, but the functions of individual MIRNA genes are poorly defined. We functionally analyzed the activity of all 5 Arabidopsis thaliana MIR172 genes, which encode miR172 and promote the floral transition by inhibiting the accumulation of APETALA2 (AP2) and APETALA2-LIKE (AP2-LIKE) transcription factors (TFs). Through genome editing and detailed confocal microscopy, we show that the activity of miR172 at the shoot apex is encoded by 3 MIR172 genes, is critical for floral transition of the shoot meristem under noninductive photoperiods, and reduces accumulation of AP2 and TARGET OF EAT2 (TOE2), an AP2-LIKE TF, at the shoot meristem. Utilizing the genetic resources generated here, we show that the promotion of flowering by miR172 is enhanced by the MADS-domain TF FRUITFULL, which may facilitate long-term silencing of AP2-LIKE transcription, and that their activities are partially coordinated by the TF SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN 15. Thus, we present a genetic framework for the depletion of AP2 and AP2-LIKE TFs at the shoot apex during floral transition and demonstrate that this plays a central role in floral induction.

Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases

Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.

Identification of key sequence features required for microRNA biogenesis in plants

MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop structure. In plants, the ribonuclease type III DICER-LIKE1 assisted by accessory proteins cleaves the precursor to release the mature miRNA. Numerous studies highlight the role of the precursor secondary structure during plant miRNA biogenesis; however, little is known about the relevance of the precursor sequence. Here, we analyzed the sequence composition of plant miRNA primary transcripts and found specifically located sequence biases. We show that changes in the identity of specific nucleotides can increase or abolish miRNA biogenesis. Most conspicuously, our analysis revealed that the identity of the nucleotides at unpaired positions of the precursor plays a crucial role during miRNA biogenesis in Arabidopsis.

The secondary structure of miRNA precursor sequences is known to affect processing by DICER-like proteins. Here Rojas et al. show that additional sequence features also play a regulatory role in plants with nucleotide identity at unpaired positions substantially impacting processing efficiency.

Origin and Evolutionary Dynamics of the miR2119 and ADH1 Regulatory Module in Legumes

MicroRNAs are important regulators of gene expression in eukaryotes. Previously, we reported that in Phaseolus vulgaris, the precursor for miR2119 is located in the same gene as miR398a, conceiving a dicistronic MIR gene. Both miRNA precursors are transcribed and processed from a single transcript resulting in two mature microRNAs that regulate the mRNAs encoding ALCOHOL DEHYDROGENASE 1 (ADH1) and COPPER-ZINC SUPEROXIDE DISMUTASE 1 (CSD1). Genes for miR398 are distributed throughout the spermatophytes; however, miR2119 is only found in Leguminosae species, indicating its recent emergence. Here, we used public databases to explore the presence of the miR2119 sequence in several plant species. We found that miR2119 is present only in specific clades within the Papilionoideae subfamily, including important crops used for human consumption and forage. Within this subfamily, MIR2119 and MIR398a are found together as a single gene in the genomes of the Millettioids and Hologalegina. In contrast, in the Dalbergioids MIR2119 is located in a different locus from MIR398a, suggesting this as the ancestral genomic organization. To our knowledge, this is a unique example where two separate MIRNA genes have merged to generate a single polycistronic gene. Phylogenetic analysis of ADH1 gene sequences in the Papilionoideae subfamily revealed duplication events resulting in up to four ADH1 genes in certain species. Notably, the presence of MIR2119 correlates with the conservation of target sites in particular ADH1 genes in each clade. Our results suggest that post-transcriptional regulation of ADH1 genes by miR2119 has contributed to shaping the expansion and divergence of this gene family in the Papilionoideae. Future experimental work on ADH1 regulation by miR2119 in more legume species will help to further understand the evolutionary history of the ADH1 gene family and the relevance of miRNA regulation in this process.

A conserved sequence signature is essential for robust plant miRNA biogenesis

Micro (mi)RNAs are 20–22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise processing and abundance of miRNAs was confirmed through detailed molecular and functional analysis. Consistent with the presence of the miRNA-specific GC signature, target RNAs of miRNAs also possess conserved complementary sequence signatures in their miRNA binding motifs. The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1. Finally, we demonstrate a direct application of this discovery for enhancing the abundance and efficiency of artificial miRNAs that are popular in plant functional genomic studies.

Novel insights into expansion and functional diversification of MIR169 family in tomato

MAIN CONCLUSION

Expansion of MIR169 members by duplication and new mature forms, acquisition of new promoters, differential precursor-miRNA processivity and engaging novel targets increase the functional diversification of MIR169 in tomato. MIR169 family is an evolutionarily conserved miRNA family in plants. A systematic in-depth analysis of MIR169 family in tomato is lacking. We report 18 miR169 precursors, annotating new loci for MIR169a, b and d, as well as 3 novel mature isoforms (MIR169f/g/h). The family has expanded by both tandem- and segmental-duplication events during evolution. A tandem-pair MIR169b/b-1 and MIR169b-2/h is polycistronic in nature coding for three MIR169b isoforms and a new variant miR169h, that is evidently absent in the wild relatives S. pennellii and S. pimpinellifolium. Seven novel miR169 targets including RNA-binding protein, protein-phosphatase, aminotransferase, chaperone, tetratricopeptide-repeat-protein, and transcription factors ARF-9B and SEPELLATA-3 were established by efficient target cleavage in the presence of specific precursors as well as increased target abundance upon miR169 chelation by short-tandem-target-mimic construct in transient assays. Comparative antagonistic expression profiles of MIR169:target pairs suggest MIR169 family as ubiquitous regulator of various abiotic stresses (heat, cold, dehydration and salt) and developmental pathways. This regulation is partly brought about by acquisition of new promoters as demonstrated by promoter MIR169:GUS reporter assays as well as differential processivity of different precursors and miRNA cleavage efficiencies. Thus, the current study augments the functional horizon of MIR169 family with applications for stress tolerance in crops.

MicroRNA528, a hub regulator modulating ROS homeostasis via targeting of a diverse set of genes encoding copper-containing proteins in monocots

Plant microRNAs (miRNAs) regulate vital cellular processes, including responses to extreme temperatures with which reactive oxygen species (ROS) are often closely associated. In the present study, it was found that aberrant temperatures caused extensive changes in abundance to numerous miRNAs in banana fruit, especially the copper (Cu)-associated miRNAs. Among them, miR528 was significantly downregulated under cold stress and it was found to target genes encoding polyphenol oxidase (PPO), different from those identified in rice and maize. Expression of PPO genes was upregulated by > 100-fold in cold conditions, leading to ROS surge and subsequent peel browning of banana fruit. Extensive comparative genomic analyses revealed that the monocot-specific miR528 can potentially target a large collection of genes encoding Cu-containing proteins. Most of them are actively involved in cellular ROS metabolism, including not only ROS generating oxidases, but also ROS scavenging enzymes. It also was demonstrated that miR528 has evolved a distinct preference of target genes in different monocots, with its target site varying in position among/within gene families, implying a highly dynamic process of target gene diversification. Its broad capacity to target genes encoding Cu-containing protein implicates miR528 as a key regulator for modulating the cellular ROS homeostasis in monocots.

Keep calm and carry on: miRNA biogenesis under stress

MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression. Their biogenesis relies on the cleavage of longer precursors by a nuclear localized processing machinery. The evolutionary preference of plant miRNAs to silence transcription factors turned these small molecules into key actors during growth and adaptive responses. Furthermore, during their life cycle plants are subject to changes in the environmental conditions surrounding them. In order to face these changes, plants display unique adaptive capacities based on an enormous developmental plasticity, where miRNAs play central roles. Many individual miRNAs have been shown to modulate the plant response to different environmental cues and stresses. In the last few years, increasing evidence has shown that not only individual genes encoding miRNAs but also the miRNA pathway as a whole is subject to regulation in response to external stimulus. In this review, we discuss the current knowledge about the miRNA pathway. We dissect the pathway to analyze the events leading to the generation of these small RNAs and emphasize the regulation of core components of the miRNA biogenesis machinery.

Efficiency and precision of microRNA biogenesis modes in plants

Many evolutionarily conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized an approach to detect processing intermediates during miRNA biogenesis. We characterized a miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15–17 bp. Interestingly, precision and efficiency vary with the processing modes. Despite the various potential structural determinants present in a single a miRNA precursor, DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, our studies in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative processing determinants. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.

Novel and Conserved miRNAs Among Brazilian Pine and Other Gymnosperms

The knowledge about plant miRNAs has increased exponentially, with thousands of miRNAs been reported in different plant taxa using high throughput sequencing technologies and bioinformatic tools. Nevertheless, several groups of plants remain unexplored, and the gap of knowledge about conifer miRNAs is considerable. There is no sequence or functional information available on miRNAs in Araucariaceae. This group is represented in Brazil by only one species, Araucaria angustifolia, an endangered species known as Brazilian pine. In the present study, Brazilian pine has its transcriptome explored with respect to small RNAs, representing the first description in a member of the Araucariaceae family. The screening for conserved miRNAs in Brazilian pine revealed 115 sequences of 30 miRNA families. A total of 106 precursors sequences were predicted. Forty one comprised conserved miRNAs from 16 families, whereas 65 were annotated as novel miRNAs. The comparison of Brazilian pine precursors with sRNA libraries of other five conifer species indicates that 9 out 65 novel miRNAs are conserved among gymnosperms, while 56 seems to be specific for Brazilian pine or restricted to Araucariaceae family. Analysis comparing novel Brazilian pine miRNAs precursors and Araucaria cunninghamii RNA-seq data identified seven orthologs between both species. Mature miRNA identified by bioinformatics predictions were validated using stem-loop RT-qPCR assays. The expression pattern of conserved and novel miRNAs was analyzed in five different tissues of 3-month-old Araucaria seedlings. The present study provides insights about the nature and composition of miRNAs in an Araucariaceae species, with valuable information on miRNAs diversity and conservation in this taxon.

Alternative use of miRNA-biogenesis co-factors in plants at low temperatures

Plants use molecular mechanisms to sense temperatures, trigger quick adaptive responses and thereby cope with environmental changes. MicroRNAs (miRNAs) are key regulators of plant development under such conditions. The catalytic action of DICER LIKE 1 (DCL1), in conjunction with HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE), produces miRNAs from double-stranded RNAs. As plants lack a stable internal temperature to which enzymatic reactions could be optimized during evolution, reactions such as miRNA processing have to be adjusted to fluctuating environmental temperatures. Here, we report that with decreasing ambient temperature, the plant miRNA biogenesis machinery becomes more robust, producing miRNAs even in the absence of the key DCL1 co-factors HYL1 and SE. This reduces the morphological and reproductive defects of se and hyl1 mutants, restoring seed production. Using small RNA-sequencing and bioinformatics analyses, we have identified specific miRNAs that become HYL1/SE independent for their production in response to temperature decrease. We found that the secondary structure of primary miRNAs is key for this temperature recovery. This finding may have evolutionary implications as a potential adaptation-driving mechanism to a changing climate.

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

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

Detection of MicroRNA Processing Intermediates Through RNA Ligation Approaches

MicroRNAs (miRNA) are small RNAs of 20-22 nt that regulate diverse biological pathways through the modulation of gene expression. miRNAs recognize target RNAs by base complementarity and guide them to degradation or translational arrest. They are transcribed as longer precursors with extensive secondary structures. In plants, these precursors are processed by a complex harboring DICER-LIKE1 (DCL1), which cuts on the precursor stem region to release the mature miRNA together with the miRNA*. In both plants and animals, the miRNA precursors contain spatial clues that determine the position of the miRNA along their sequences. DCL1 is assisted by several proteins, such as the double-stranded RNA binding protein, HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). The precise biogenesis of miRNAs is of utter importance since it determines the exact nucleotide sequence of the mature small RNAs and therefore the identity of the target genes. miRNA processing itself can be regulated and therefore can determine the final small RNA levels and activity. Here, we describe methods to analyze miRNA processing intermediates in plants. These approaches can be used in wild-type or mutant plants, as well as in plants grown under different conditions, allowing a molecular characterization of the miRNA biogenesis from the RNA precursor perspective.

An Overview of miRNA and miRNA Target Analysis Tools

microRNA molecules have been shown to play various significant roles in many physiological and pathophysiological processes in living organisms. The tremendous interest in these molecules has led to the significant development and constant release of a number of computational tools useful for basic as well as advanced miRNA-related analyses. These approaches have various constantly evolving utilities, such as detection, target prediction, functional annotation, and many others. In this chapter, we provide an overview of several computational tools useful for broadly defined plant miRNA analysis.

Identification and expression profiles of putative leaf growth related microRNAs in maize (Zea mays L.) hybrid ADA313

Throughout the plant life cycle, growth of new leaves is governed by cell division and cell expansion. During steady-state growth of the maize leaf, these processes are spatially separated between the meristem zone, consisting of dividing cells at the leaf base, the elongation zone, consisting of expanding cells moving upwards from the meristem, and the mature zone containing differentiated mature cells. Increased leaf size can be achieved through increasing cell number or cell size, for example by manipulating the genes controlling the transition between those zones. In this study, microRNA (miRNA) genes, which are a class of endogenous small, non-coding gene regulatory RNAs, were investigated in the growth zones, to gain insight into their role in the transition between cell division and cell expansion. A genome-wide survey was conducted using a miRNA-microarray and 59 miRNA genes were detected to be differentially expressed between the growth zones. miR160, miR166, miR168, miR172, miR319 and miR390 families were significantly up-regulated in the meristem relative to the elongation and mature zones. In contrast, expression of the miR167 and miR396 families was lower in the meristem and higher in the mature zone. Therefore, these were considered to be candidate growth-regulated miRNAs that control cell division processes indirectly by repressing target genes. The miR156, miR166, miR167, miR399, miR408 and miR2275 families were expressed most highly in the elongation zone, and so were classified as elongation-specific, with possible roles in switching from cell division to cell elongation during leaf differentiation. In silico target prediction analysis showed that these miRNAs target several transcription factors and metabolic genes, and a reciprocal relationship between the expression levels of miR319 and miR396 and their targets was confirmed by qRT-PCR. Furthermore, 12 candidate novel miRNAs were identified from the microarray data and computationally verified. Three out of twelve were also validated by qRT-PCR. These findings provide important information regarding the regulatory functions of miRNAs in controlling progression of growth mechanisms.

A novel miRNA, miR-13664, targets CpCYP314A1 to regulate deltamethrin resistance in Culex pipiens pallens

Extensive insecticide use has led to the resistance of mosquitoes to these insecticides, posing a major barrier to mosquito control. Previous Solexa high-throughput sequencing of Culex pipiens pallens in the laboratory has revealed that the abundance of a novel microRNA (miRNA), miR-13664, was higher in a deltamethrin-sensitive (DS) strain than a deltamethrin-resistant (DR) strain. Real-time quantitative PCR revealed that the miR-13664 transcript level was lower in the DR strain than in the DS strain. MiR-13664 oversupply in the DR strain increased the susceptibility of these mosquitoes to deltamethrin, whereas inhibition of miR-13664 made the DS strain more resistant to deltamethrin. Results of bioinformatic analysis, quantitative reverse-transcriptase polymerase chain reaction, luciferase assay and miR mimic/inhibitor microinjection revealed CpCYP314A1 to be a target of miR-13664. In addition, downregulation of CpCYP314A1 expression in the DR strain reduced the resistance of mosquitoes to deltamethrin. Taken together, our results indicate that miR-13664 could regulate deltamethrin resistance by interacting with CpCYP314A1, providing new insights into mosquito resistance mechanisms.

TAS3 miR390-dependent loci in non-vascular land plants: towards a comprehensive reconstruction of the gene evolutionary history

Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic TAS loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms, ferns and mosses. In this study, bioinformatic and experimental PCR-based approaches were used as tools to analyze TAS3 and TAS6 loci in transcriptomes and genomic DNAs from representatives of evolutionary distant non-vascular plant taxa such as Bryophyta, Marchantiophyta and Anthocerotophyta. We revealed previously undiscovered TAS3 loci in plant classes Sphagnopsida and Anthocerotopsida, as well as TAS6 loci in Bryophyta classes Tetraphidiopsida, Polytrichopsida, Andreaeopsida and Takakiopsida. These data further unveil the evolutionary pathway of the miR390-dependent TAS3 loci in land plants. We also identified charophyte alga sequences coding for SUPPRESSOR OF GENE SILENCING 3 (SGS3), which is required for generation of ta-siRNAs in plants, and hypothesized that the appearance of TAS3-related sequences could take place at a very early step in evolutionary transition from charophyte algae to an earliest common ancestor of land plants.

Despacito: the slow evolutionary changes in plant microRNAs

MicroRNAs (miRNAs) are key regulators of gene expression. A handful of miRNAs are broadly conserved in land plants, while the majority are lineage specific; this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution. Additional factors guiding miRNA evolution include functional constraints on their length and the importance of precursor conservation that is observed in regions above or below the mature miRNA duplex; these regions represent recognition sites for components of biogenesis machinery and direct precursor processing. Insights into the mechanisms of miRNA emergence and divergence are important for understanding plant genome evolution and the impact of miRNA regulatory networks.

Evolution of microRNA827 targeting in the plant kingdom

Unlike most ancient microRNAs, which conservatively target homologous genes across species, microRNA827 (miR827) targets two different types of SPX (SYG1/PHO81/XPR1)-domain-containing genes, NITROGEN LIMITATION ADAPTATION (NLA) and PHOSPHATE TRANSPORTER 5 (PHT5), in Arabidopsis thaliana and Oryza sativa to regulate phosphate (Pi) transport and storage, respectively. However, how miR827 shifted its target preference and its evolutionary history are unknown. Based on target prediction analysis, we found that in most angiosperms, miR827 conservatively targets PHT5 homologs, but in Brassicaceae and Cleomaceae it preferentially targets NLA homologs, and we provide evidence for the transition of target preference during Brassicales evolution. Intriguingly, we found a lineage-specific loss of the miR827-regulatory module in legumes. Analysis of miR827-mediated cleavage efficiency and the expression of PHT5 in A. thaliana indicated that accumulation of mutations in the target site and the exclusion of the target site by alternative transcriptional initiation eliminated PHT5 targeting by miR827. Here, we identified a transition of miR827 target preference during plant evolution and revealed the uniqueness of miR827-mediated regulation among conserved plant miRNAs. Despite the change in its target preference, upregulation of miR827 by Pi starvation and its role in regulating cellular Pi homeostasis were retained.

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

MicroRNAs (miRNAs) are ∼21-nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential posttranscriptional regulators of target mRNAs and long noncoding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of posttranscriptional regulation). Next-generation DNA sequencing methods have yielded extensive data sets of plant small RNAs, resulting in many miRNA annotations. However, it has become clear that many miRNA annotations are questionable. The sheer number of endogenous siRNAs compared with miRNAs has been a major factor in the erroneous annotation of siRNAs as miRNAs. Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of "big data" from DNA sequencing. The updated criteria emphasize replication and the minimization of false positives, and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.

The Emergence, Evolution, and Diversification of the miR390-TAS3-ARF Pathway in Land Plants

In plants, miR390 directs the production of tasiRNAs from TRANS-ACTING SIRNA3 (TAS3) transcripts to regulate AUXIN RESPONSIVE FACTOR (ARF) genes, critical for auxin signaling; these tasiRNAs are known as tasiARFs. To understand the evolution of this miR390-TAS3-ARF pathway, we characterized homologs of these three genes from thousands of plant species, from bryophytes to angiosperms. We found the lower-stem region of MIR390 genes, critical for accurate DICER-LIKE1 processing, is conserved in sequence in seed plants. We propose a model for the transition of functional tasiRNA sequences in TAS3 genes occurred at the emergence of vascular plants, in which the two miR390 target sites of TAS3 genes showed distinct pairing patterns. Based on the cleavability of miR390 target sites and the distance between target site and tasiARF, we inferred a potential bidirectional processing mechanism exists for some TAS3 genes. We also demonstrated a tight mutual selection between tasiARF and its target genes and that ARGONAUTE7, the partner of miR390, was specified later than other factors in the pathway. All these data illuminate the evolutionary path of the miR390-TAS3-ARF pathway in land plants and demonstrate the significant variation that occurs in this functionally important and archetypal regulatory circuit.