Hailing Jin

• University of California, Riverside

Spray-induced gene silencing (SIGS) is a powerful and eco-friendly method for crop protection. Based off the discovery of RNA uptake ability in many fungal pathogens, the application of exogenous RNAs targeting pathogen/pest genes results in gene silencing and infection inhibition. However, SIGS remains hindered by the rapid degradation of RNA in t...

Small RNAs (sRNAs) of the fungal pathogen Botrytis cinerea can enter plant cells and hijack host Argonaute protein 1 (AGO1) to silence host immunity genes. However, the mechanism by which these fungal sRNAs are secreted and enter host cells remains unclear. Here, we demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRN...

Extracellular vesicles (EVs) are membrane-enclosed nanometer-scale particles that transport biological materials such as RNAs, proteins, and metabolites. EVs have been discovered in nearly all kingdoms of life as a form of cellular communication across different cells and between interacting organisms. EV research has primarily focused on EV-mediat...

Small RNAs (sRNAs) of the fungal pathogen Botrytis cinerea can enter plant cells and hijack host Argonaute protein 1 (AGO1) to silence host immunity genes. However, the mechanism by which these fungal sRNAs are secreted and enter host cells remains unclear. Here, we demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRN...

Spray‐Induced Gene Silencing (SIGS) is an innovative and eco‐friendly technology where topical application of pathogen gene‐targeting RNAs to plant material can enable disease control. SIGS applications remain limited because of the instability of dsRNA, which can be rapidly degraded when exposed to various environmental conditions. Inspired by the...

Spray-Induced Gene Silencing (SIGS) is an innovative and eco-friendly technology where topical application of pathogen gene-targeting RNAs to plant material can enable disease control. SIGS applications remain limited because of the instability of dsRNA, which can be rapidly degraded when exposed to various environmental conditions. Inspired by the...

Cross-kingdom or cross-species RNA interference (RNAi) is broadly present in many interacting systems between microbes/parasites and their plant and animal hosts. Recent study by Qin et al. (2022) performed correlation analysis using global sRNA- and mRNA-deep sequencing data of cultured B. cinerea and B. cinerea-infected tomato leaves and claimed...

The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps...

One of the most promising tools for the control of fungal plant diseases is spray‐induced gene silencing (SIGS). In SIGS, small interfering RNA (siRNA) or double‐stranded RNA (dsRNA) targeting essential or virulence‐related pathogen genes are exogenously applied to plants and postharvest products to trigger RNA interference (RNAi) of the targeted g...

Extracellular vesicles (EVs) in plants have emerged as key players in cell‐to‐cell communication and cross‐kingdom RNAi between plants and pathogens by facilitating the exchange of RNA, proteins, and other molecules. In addition to their role in intercellular communication, plant EVs also show promise as potential therapeutics and indicators of pla...

Plants have evolved variable phenotypic plasticity to counteract different pathogens and pests during immobile life. Microbial infection invokes multiple layers of host immune responses, and plant gene expression is swiftly and precisely reprogramed at both the transcriptional level and post-transcriptional level. Recently, the importance of epigen...

Plant extracellular vesicles (EVs) play critical roles in the cross‐kingdom trafficking of molecules from hosts to interacting microbes, most notably in plant defense responses. However, the isolation of pure, intact EVs from plants remains challenging. A variety of methods have been utilized to isolate plant EVs from apoplastic washing fluid (AWF)...

Plant extracellular vesicles (EVs) have become the focus of rising interest due to their important roles in the cross-kingdom trafficking of molecules from hosts to interacting microbes to modulate pathogen virulence. However, the isolation of pure intact EVs from plants still represents a considerable challenge. Currently, plant EVs have been isol...

Small RNA (sRNA)-mediated RNA interference (RNAi) is a regulatory mechanism conserved in almost all eukaryotes. sRNAs play a critical role in host pathogen interactions either endogenously or by traveling between the interacting organisms and inducing 'cross-Kingdom RNAi' in the counterparty. Cross-kingdom RNAi is the mechanistic basis of host-indu...

Plants communicate with their interacting microorganisms through exchange of functional molecules. This communication is critical for plant immunity, for pathogen virulence and for establishing and maintain symbioses. Extracellular vesicles (EVs) are lipid bilayer‐enclosed spheres that are released by both the host and the microbe into the extracel...

Communication between plant cells and interacting microorganisms requires the secretion and uptake of functional molecules to and from the extracellular environment and is essential for the survival of both plants and their pathogens. Extracellular vesicles (EVs) are lipid bilayer–enclosed spheres that deliver RNA, protein, and metabolite cargos fr...

Recent discoveries show that fungi can take up environmental RNA, which can then silence fungal genes through environmental RNA interference. This discovery prompted the development of Spray‐Induced Gene Silencing (SIGS) for plant disease management. In this study, we aimed to determine the efficacy of SIGS across a variety of eukaryotic microbes....

A Correction to this paper has been published: https://doi.org/10.1038/s41477-021-00901-5.

Plants utilize extracellular vesicles (EVs) to transport small RNAs (sRNAs) into their fungal pathogens and silence fungal virulence-related genes through a phenomenon called “cross-kingdom RNAi.” It remains unknown, however, how sRNAs are selectively loaded into EVs. Here, we identified several RNA-binding proteins (RBPs) in Arabidopsis, including...

Citrus Huanglongbing (HLB), caused by a vector-transmitted phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease worldwide. Currently, there are no effective strategies to prevent infection or to cure HLB-positive trees. Here, using comparative analysis between HLB-sensitive citrus culti-vars and...

Recent discoveries show that fungi can take up environmental RNA, which can then silence fungal genes through environmental RNA interference. This discovery prompted the development of Spray-Induced Gene Silencing (SIGS) for plant disease management. In this study, we aimed to determine the efficacy of SIGS across a variety of eukaryotic microbes....

In both plant and animal innate immune responses, surveillance of pathogen infection is mediated by membrane-associated receptors and intracellular nucleotide-binding domain and leucine-rich-repeat receptors (NLRs). Homeostasis of NLRs is under tight multilayered regulation to avoid over-accumulation or over-activation, which often leads to autoimm...

Small RNA (sRNA)-mediated RNA interference (RNAi) is critical for regulating both host immunity and pathogen virulence. Recent studies have revealed that RNA-silencing signals travel between different organisms and trigger gene silencing in trans, termed cross-kingdom RNAi. To investigate cross-kingdom RNAi, it is necessary to purify the fungal cel...

Huanglongbing (HLB) is the most devastating citrus disease in the world. Almost all commercial citrus varieties are susceptible to the causal bacterium, Candidatus Liberibacter asiaticus (CLas), which is transmitted by the Asian citrus psyllid (ACP). Currently, there are no effective management strategies to control HLB. HLB‐tolerant traits have be...

Fungal pathogens are responsible for severe crop losses worldwide. Defending crops against fungal disease is critical for global food security; however, most current disease management approaches rely on chemical fungicides that can leave dangerous residues in the environment. RNA interference (RNAi) is an important process through which RNA molecu...

Small RNAs play an important role in plant innate immunity. However, their regulatory function in induced systemic resistance (ISR) triggered by plant growth‐promoting rhizobacteria remains unclear. Here, using Arabidopsis as a model system, one plant endogenous small RNA, miR472, was identified as an important regulator involved in the process of...

Plant small RNA (sRNA)-mediated gene expression has a conserved role in regulating plant growth, development, and immunity. Heterologous expression of sRNA contributes to determining whether the function of sRNA is conservative or independent. We recently characterized the Tourist-miniature inverted-repeat transposable element (MITE)-derived siR109...

Plant small RNAs (sRNAs) play significant roles in regulating various developmental processes and hormone signalling pathways involved in plant responses to a wide range of biotic and abiotic stresses. However, the functions of sRNAs in response to rice sheath blight remain unclear. We screened rice (Oryza sativa) sRNA expression patterns against R...

Defense cargo shuttles in vesicles Plants can use small RNAs (sRNAs) to interfere with virulence factor gene expression in pathogens. Cai et al. show that the small mustard plant Arabidopsis shuttles defensive sRNAs into the necrotrophic fungus Botrytis cinerea via extracellular vesicles (see the Perspective by Thomma and Cook). The vesicles are as...

Exploring the regulatory mechanism played by endogenous rice miRNAs in defense responses against the blast disease is of great significance in both resistant variety breeding and disease control management. We identified rice defense‐related miRNAs by comparing rice miRNA expression patterns before and after Magnaporthe oryzae strain Guy11 infectio...

MicroRNAs (miRNAs) play crucial roles in plant responses to pathogen infections. Rice is the major staple food worldwide, and the rice blast disease is the most important disease of rice. To explore the miRNA species participating in rice immunity against the rice blast disease, we compared small RNA expression between mock- and Magnaporthe oryzae-...

In plants, small RNA (sRNA)-mediated RNA interference (RNAi) is critical for regulating host immunity against bacteria, fungi, oomycetes, viruses, and pests. Similarly, sRNAs from pathogens and pests also play an important role in modulating their virulence. Strikingly, recent evidence supports that some sRNAs can travel between interacting organis...

Small RNA (sRNA) induces RNA interference (RNAi) in almost all eukaryotes. While sRNAs can move within an organism, they can also move between interacting organisms to induce gene silencing, a phenomenon called ‘cross-kingdom RNAi’. Some sRNAs from pathogens or pests move into host cells and suppress host immunity in both plants and animals; wherea...

Plants fine‐tune their sophisticated immunity systems in response to pathogen infections. We previously showed that Atlsi RNA ‐1, a bacteria‐induced plant endogenous small interfering RNA , silences the At RAP gene, which encodes a putative RNA binding protein. In this study, we demonstrate that At RAP functions as a negative regulator in plant imm...

Pathogens secrete effector proteins to suppress host immune responses. Recently, we showed that an aggressive plant fungal pathogen Botrytis cinerea can also deliver small RNA effectors into host cells to suppress host immunity. B. cinerea sRNAs (Bc-sRNAs) translocate into host plants and hijack the plant RNAi machinery to induce cross-kingdom RNAi...

Plant pathogens cause serious crop losses worldwide. Recent new studies demonstrate that spraying double-stranded RNAs (dsRNAs) and small RNAs (sRNAs) that target essential pathogen genes on plant surfaces confer efficient crop protection. This so-called spray-induced gene silencing (SIGS) strategy of disease control is potentially sustainable and...

Aggressive fungal pathogens such as Botrytis and Verticillium spp. cause severe crop losses worldwide. We recently discovered that Botrytis cinerea delivers small RNAs (Bc-sRNAs) into plant cells to silence host immunity genes. Such sRNA effectors are mostly produced by Botrytis cinerea Dicer-like protein 1 (Bc-DCL1) and Bc-DCL2. Here we show that...

Plant small RNAs play important roles in gene regulation during pathogen infection. Here we show that miR863-3p is induced by the bacterial pathogen Pseudomonas syringae carrying various effectors. Early during infection, miR863-3p silences two negative regulators of plant defence, atypical receptor-like pseudokinase1 (ARLPK1) and ARLPK2, both lack...

Supplementary Figures 1-11, Supplementary Table 1 and Supplementary References

Plants are constantly under attack by pathogens, pests, and parasites, resulting in severe consequences on global food production and human health. While pathogens and pests find their ways to invade and communicate with their hosts, plants have evolved sophisticated immune systems fight infections. In the field of plant-microbial interactions, alt...

In both animals and plants, mRNA export has been shown to contribute to immune response regulation. The Arabidopsis nuclear protein MOS11 along with the nucleoporins MOS3/Nup96/SAR3 and Nup160/SAR1 are components of the mRNA export machinery and contribute to immunity mediated by nucleotide binding leucine-rich repeat immune receptors (NLRs). The h...

Small RNAs play an important role in plant immune responses. However, their regulatory function in induced systemic resistance (ISR) is nascent. Bacillus cereus AR156 is a plant growth-promoting rhizobacterium that induces ISR in Arabidopsis against bacterial infection. Here, by comparing small RNA profiles of Pseudomonas syringae pv. tomato (Pst)...

Small RNAs (sRNAs) are loaded into ARGONAUTE (AGO) proteins to induce gene silencing. In plants, the 5'-terminal nucleotide is important for sRNA sorting into different AGOs. Here we show that microRNA (miRNA) duplex structure also contributes to miRNA sorting. Base pairing at the 15th nucleotide of a miRNA duplex is important for miRNA sorting in...

RNA silencing is a mechanism of gene expression regulation mediated by short noncoding RNAs called small RNAs. Small RNAs can suppress gene expression transcriptionally or posttranscriptionally by base pairing to their targets. In plants, they are involved in a diverse range of pathways and processes. Forward genetic screens have led to the identif...

A never-ending arms race drives coevolution between pathogens and hosts. In plants, pathogen attacks invoke multiple layers of host immune responses. Many pathogens deliver effector proteins into host cells to suppress host immunity, and many plants have evolved resistance proteins to recognize effectors and trigger robust resistance. Here, we disc...

A report on the Plant and Animal Genome XXII meeting held in San Diego, California, USA, January 11-15, 2014.

Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argo...

A large proportion of eukaryotic genomes is transcribed from both the positive and negative strands of the DNA and thus may generate overlapping sense and antisense transcripts. Some of these so-called natural antisense transcripts are possibly co-regulated. When the overlapping sense and antisense transcripts are expressed at the same time in the...

Small RNAs regulate a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity, in a sequence-specific manner. Accumulating evidence reveals that host endogenous small RNAs and small RNA pathway components play important roles in plant immune responses against various pathogens, inclu...

Despite a general repression of translation under hypoxia, cells selectively upregulate a set of hypoxia-inducible genes. Results from deep sequencing revealed that Let-7 and miR-103/107 are hypoxia-responsive microRNAs (HRMs) that are strongly induced in vascular endothelial cells. In silico bioinformatics and in vitro validation showed that these...

Huanglongbing (HLB) is a devastating citrus disease that is associated with bacteria of the genus "Candidatus Liberibacter" (Ca. L.). Powerful diagnostic tools and management strategies are desired to control HLB. Host small RNAs (sRNA) play a vital role in regulating host responses to pathogen infection and are used as early diagnosis markers for...

MicroRNAs (miRNAs) are small RNA molecules that play important regulatory roles in plant development and stress responses. Identification of stress-regulated miRNAs is crucial for understanding how plants respond to environmental stimuli. Abiotic stresses are one of the major factors that limit crop growth and yield. Whereas abiotic stress-regulate...

Small RNAs are short noncoding RNAs with important regulatory roles in many cellular processes. Small RNAs are generated by DICER or DICER-like proteins and then incorporated into RNAi effector -proteins ARGONAUTEs (AGOs) for silencing of their targets. In plants, small RNAs regulate host innate immunity against various pathogens, but their mode of...

Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain...

Distributions of the sequencing reads from small RNA libraries of abiotic and biotic treated Arabidopsis and abiotic challenged rice. Shown in the table are the total number of raw sequencing reads (total), the number of qualified reads that can map perfectly to the corresponding Arabidopsis or rice genome (mapped), intergenic regions (intergenic),...

Normalized reads of siRNAs mapped to the overlapping regions of Arabidopsis and rice cis-NAT pairs, respectively (a) siRNAs mapped to the overlapping regions of 84 Arabidopsis cis-NAT pairs. (b) siRNAs mapped to the overlapping regions of 119 rice cis-NAT pairs. Each small RNA library was normalized to one million reads with 100% matching to the ge...

Classification of cis-NAT pairs. We analyzed 84 Arabidopsis and 119 rice cis-NAT pairs that have more than 10 raw siRNAs mapped to the overlap region. The reads analyzed here are the raw sequencing reads mapped to the whole region from the combination of all libraries. (a) Arabidopsis cis-NAT pairs display different distribution patterns. (b) Rice...

Oligos used in this study. A plus sign ('+') before the nucleotide depicts LNA residues.

Expression analysis of NAT transcripts in the fwf2 single mutant. The expression of NAT transcripts was analyzed by quantitative RT-PCR. Total RNA (5 μg) was used for DNase treatment and reverse transcription. Error bars indicate the technical replicates and similar results were obtained from two biological repeats.

(a-d) Distributions of the lengths (a, b) and the first nucleotides (c, d) of total siRNAs and nat-siRNAs in stress-challenged Arabidopsis and rice. (a) Length distributions of unique sequencing reads in Arabidopsis. The blue and red bars represent total siRNAs and nat-siRNAs, respectively. (b) Length distributions of unique sequencing reads in ric...

(a) Distributions of the number of small RNA clusters in 84 Arabidopsis cis-NATs. The red line represents the separation between site-specific (left) and distributed (right) patterns. (b) The plot of two metrics of 84 cis-NATs in Arabidopsis. Each dot represents the number of clusters within the cis-NAT whole region and the percentage of small RNA...

Small RNAs mapped to the introns or intron-exon junction regions of rice cis-NATs. Raw reads from all the libraries were analyzed. (a) siRNAs mapping to introns in the overlapping region of cis-NATs in rice. (b) siRNAs mapping to introns in the whole region of cis-NATs in rice

Normalized reads of siRNAs mapped to 84 Arabidopsis NATs under different conditions. Each library was normalized to a million reads that perfectly mapped to the genome. The fold change with maximum absolute value between treated sample and corresponding control is listed as a supplemental value. The pairs with more than two-fold change were annotat...

Normalized reads of siRNAs mapped to 119 rice NATs under different conditions. siRNAs matching 100% to the genome were analyzed and each library was normalized to a million reads before analyzing. The fold change with maximum absolute value between treated and untreated libraries is listed. The pairs with more than a two-fold change are displayed i...

Arabidopsis cis-NATs that are up-regulated in the dcl1-7 mutant. (a) List of probes of the 93 genes of the 84 cis-NAT pairs. Annotations of the Affymetrix ATH1-121501 chip were used and no probes were found for the rest of the cis-NAT genes. (b) The 23 cis-NAT genes up-regulated in dcl1-7.

Arabidopsis cis-NATs with two classes of small RNAs mapped to the overlapping regions. 'gene1' and 'gene2' represent the first and second transcript in each cis-NAT pair. Listed are 84 Arabidopsis cis-NATs with siRNAs mapped to the overlapping region. Raw reads of 20- to 22-nucleotide and 23- to 28-nucleotide classes of siRNAs matching 100% to the...

Small RNAs mapped to the introns or intron-exon junction regions of Arabidopsis cis-NATs. Copy number indicates the number of raw reads in the combination of all libraries. (a) siRNAs mapping to introns in the overlapping region of cis-NATs in Arabidopsis. (b) siRNAs mapping to introns in the whole region of cis-NATs in Arabidopsis.

Association of 20- to 22-nucleotide and 23- to 26-nucleotide classes of nat-siRNAs with different AGOs in Arabidopsis. Unique reads of nat-siRNAs associated with AGO1, AGO2, AGO4 and AGO7 were analyzed. Loaded reads represent unique reads of nat-siRNAs that were loaded into distinct AGOs. The percentage in total nat-siRNA-AGO libraries indicates th...

SRO5-P5CDH siRNAs derived from salt and cold stress challenged Arabidopsis. The siRNAs were identified from GEO database accession number GSE33642. (a) Reads of siRNAs positively/negatively match to At5G62520 (SRO5) in the overlap/non-overlap region. The '+ strand' and '- strand' indicate positively or negatively matching. (b) Distribution pattern...

The accumulation of a number of small RNAs in plants is affected by abscisic acid (ABA) and abiotic stresses, but the underlying mechanisms are poorly understood. The miR168-mediated feedback regulatory loop regulates ARGONAUTE1 (AGO1) homeostasis, which is crucial for gene expression modulation and plant development. Here, we reveal a transcriptio...

Argonaute (AGO) proteins are critical components of RNA silencing pathways that bind small RNAs and mediate gene silencing at their target sites. We found that Arabidopsis AGO2 is highly induced by the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Further genetic analysis demonstrated that AGO2 functions in antibacterial immunity. One a...

Bacillus cereus AR156 is a plant growth-promoting rhizobacterium that induces resistance against a broad spectrum of pathogens including Pseudomonas syringae pv. tomato DC3000. This study analyzed AR156-induced systemic resistance (ISR) to DC3000 in Arabidopsis ecotype Col-0 plants. Compared with mock-treated plants, AR156-treated ones showed an in...

Plant- and animal-pathogenic bacteria deploy a variable arsenal of type III effector proteins (T3EP) to manipulate host defense. Specific biochemical functions and molecular or subcellular targets have been demonstrated or proposed for a growing number of T3EP but remain unknown for the majority of them. Here, we show that transient expression of g...

MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses in most eukaryotes. We globally profiled plant miRNAs in response to infection of bacterial pathogen Pseudomonas syringae pv. tomato (Pst). We sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 and 14 h post infection of non-pathogenic, viru...

MicroRNAs (miRNAs) are key regulators of gene expression in development and stress responses in most eukaryotes. We globally profiled plant miRNAs in response to infection of bacterial pathogen Pseudomonas syringae pv. tomato (Pst). We sequenced 13 small-RNA libraries constructed from Arabidopsis at 6 and 14 h post infection of non-pathogenic, viru...