NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis

The microRNA Pathway of Macroalgae: Its Similarities and Differences to the Plant and Animal microRNA Pathways

In plants and animals, the microRNA (miRNA) class of small regulatory RNA plays an essential role in controlling gene expression in all aspects of development, to respond to environmental stress, or to defend against pathogen attack. This well-established master regulatory role for miRNAs has led to each protein-mediated step of both the plant and animal miRNA pathways being thoroughly characterized. Furthermore, this degree of characterization has led to the development of a suite of miRNA-based technologies for gene expression manipulation for fundamental research or for use in industrial or medical applications. In direct contrast, molecular research on the miRNA pathway of macroalgae, specifically seaweeds (marine macroalgae), remains in its infancy. However, the molecular research conducted to date on the seaweed miRNA pathway has shown that it shares functional features specific to either the plant or animal miRNA pathway. In addition, of the small number of seaweed species where miRNA data is available, little sequence conservation of individual miRNAs exists. These preliminary findings show the pressing need for substantive research into the seaweed miRNA pathway to advance our current understanding of this essential gene expression regulatory process. Such research will also generate the knowledge required to develop novel miRNA-based technologies for use in seaweeds. In this review, we compare and contrast the seaweed miRNA pathway to those well-characterized pathways of plants and animals and outline the low degree of miRNA sequence conservation across the polyphyletic group known as the seaweeds.

Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives

ACTINs are structural proteins widely distributed in plants. They are the main components of microfilaments and participate in many crucial physiological activities, including the maintenance of cell shape and cytoplasmic streaming. Meanwhile, ACTIN, as a housekeeping gene, is widely used in qRT-PCR analyses of plants. However, ACTIN family genes have not been explored in the sweet potato. In this study, we identified 30, 39, and 44 ACTINs in the cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively, via analysis of their genome structure and by phylogenetic characterization. These ACTINs were divided into six subgroups according to their phylogenetic relationships with Arabidopsis thaliana. The physiological properties of the protein, chromosome localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction networks, and expression patterns of these 113 ACTINs were systematically investigated. The results suggested that homologous ACTINs are differentiated in the sweet potato and its two diploid relatives, and play various vital roles in plant growth, tuberous root development, hormone crosstalk, and abiotic stress responses. Some stable ACTINs that could be used as internal reference genes were found in the sweet potato and its two diploid relatives, e.g., IbACTIN18, -20, and -16.2; ItfACTIN2.2, -16, and -10; ItbACTIN18 and -19.1. This work provides a comprehensive comparison and furthers our understanding of the ACTIN genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potatoes.

Nucleotide mismatches prevent intrinsic self-silencing of hpRNA transgenes to enhance RNAi stability in plants

Hairpin RNA (hpRNA) transgenes are the most successful RNA interference (RNAi) method in plants. Here, we show that hpRNA transgenes are invariably methylated in the inverted-repeat (IR) DNA and the adjacent promoter, causing transcriptional self-silencing. Nucleotide substitutions in the sense sequence, disrupting the IR structure, prevent the intrinsic DNA methylation resulting in more uniform and persistent RNAi. Substituting all cytosine with thymine nucleotides, in a G:U hpRNA design, prevents self-silencing but still allows for the formation of hpRNA due to G:U wobble base-pairing. The G:U design induces effective RNAi in 90–96% of transgenic lines, compared to 57–65% for the traditional hpRNA design. While a traditional hpRNA transgene shows increasing self-silencing from cotyledons to true leaves, its G:U counterpart avoids this and induce RNAi throughout plant growth. Furthermore, siRNAs from G:U and traditional hpRNA show different characteristics and appear to function via different pathways to induce target DNA methylation.

Long hairpin RNA (hpRNA) transgenes are the most widely used RNAi technology in plants, but are potentially subject to self-induced transcriptional silencing. Here, the authors show nucleotide mismatches prevent intrinsic self-silencing of hpRNA transgenes in Arabidopsis and tobacco.

Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold

Background

DNA methylation is thought to influence the expression of genes, especially in response to changing environmental conditions and developmental changes. Sugar beet (Beta vulgaris ssp. vulgaris), and other biennial or perennial plants are inevitably exposed to fluctuating temperatures throughout their lifecycle and might even require such stimulus to acquire floral competence. Therefore, plants such as beets, need to fine-tune their epigenetic makeup to ensure phenotypic plasticity towards changing environmental conditions while at the same time steering essential developmental processes. Different crop species may show opposing reactions towards the same abiotic stress, or, vice versa, identical species may respond differently depending on the specific kind of stress.

Results

In this study, we investigated common effects of cold treatment on genome-wide DNA methylation and gene expression of two Beta vulgaris accessions via multi-omics data analysis. Cold exposure resulted in a pronounced reduction of DNA methylation levels, which particularly affected methylation in CHH context (and to a lesser extent CHG) and was accompanied by transcriptional downregulation of the chromomethyltransferase CMT2 and strong upregulation of several genes mediating active DNA demethylation.

Conclusion

Integration of methylomic and transcriptomic data revealed that, rather than methylation having directly influenced expression, epigenetic modifications correlated with changes in expression of known players involved in DNA (de)methylation. In particular, cold triggered upregulation of genes putatively contributing to DNA demethylation via the ROS1 pathway. Our observations suggest that these transcriptional responses precede the cold-induced global DNA-hypomethylation in non-CpG, preparing beets for additional transcriptional alterations necessary for adapting to upcoming environmental changes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08312-2.

RNAi activation with homologous and heterologous sequences that induce resistance against the begomovirus Pepper golden mosaic virus (PepGMV)

This study compared the transcriptional changes in Nicotiana benthamiana plants treated with homologous sequences derived from Pepper golden mosaic virus (PepGMV) and heterologous sequences that derived from another begomovirus, Tomato chino La Paz virus (ToChLPV) prior to infection by PepGMV. The results of microarray analyses identified upregulated genes associated with RNAi such as DCL2, DCL4, AGO3, AGO7, AGO10, NRPD2B (Pol IV), DRB3, CMT3, RDR6. The components that participate in different RNAi pathways were identified, including methylation induced by both constructs, as well as the code of these genes in Arabidopsis thaliana and its counterpart in N. benthamiana through different genome assembly. The expression of these genes was validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR), where DCL3, DCL4, AGO1-1, AGO2, RDR6 and PPR1 showed increased expression during plant protection with the heterologous construct compared to those protected with the homologous construct. The results of this study confirmed the activation of the gene silencing mechanism at the transcriptional level with both constructs and established the possibility of their use as a protection system for both homologous and heterologous sequences.

A Bunyavirus-Inducible Ubiquitin Ligase Targets RNA Polymerase IV for Degradation during Viral Pathogenesis in Rice

The ubiquitin-proteasome system (UPS) is an important post-translational regulatory mechanism that controls many cellular functions in eukaryotes. Here, we show that stable expression of P3 protein encoded by Rice grassy stunt virus (RGSV), a negative-strand RNA virus in the Bunyavirales, causes developmental abnormities similar to the disease symptoms caused by RGSV, such as dwarfing and excess tillering, in transgenic rice plants. We found that both transgenic expression of P3 and RGSV infection induce ubiquitination and UPS-dependent degradation of rice NUCLEAR RNA POLYMERASE D1a (OsNRPD1a), one of two orthologs of the largest subunit of plant-specific RNA polymerase IV (Pol IV), which is required for RNA-directed DNA methylation (RdDM). Furthermore, we identified a P3-inducible U-box type E3 ubiquitin ligase, designated as P3-inducible protein 1 (P3IP1), which interacts with OsNRPD1a and mediates its ubiquitination and UPS-dependent degradation in vitro and in vivo. Notably, both knockdown of OsNRPD1 and overexpression of P3IP1 in rice plants induced developmental phenotypes similar to RGSV disease symptomss. Taken together, our findings reveal a novel virulence mechanism whereby plant pathogens target host RNA Pol IV for UPS-dependent degradation to induce disease symptoms. Our study also identified an E3 ubiquitin ligase, which targets the RdDM compotent NRPD1 for UPS-mediated degradation in rice.

Involvement of MEM1 in DNA demethylation in Arabidopsis

MEM1 participates in ROS1-mediated DNA demethylation pathway, and acts functionally as ROS3 to counteract the effects of RdDM pathway.mem1mutation leads to large numbers of hyper-DMRs inArabidopsisgenome. In higher plants, DNA methylation performs important functions in silencing transcribed genes and transposable elements (TEs). Active DNA demethylation mediated by REPRESSOR OF SILENCING 1 (ROS1) is able to antagonize the action of DNA methylation caused by RNA-directed DNA methylation (RdDM) pathway, which plays critical roles in keeping DNA methylation at a proper level. In this study, a new mutant named mem1 (for methylation elevated mutant 1) was isolated from a genetic screen of T-DNA insertional mutant population for lines with elevated DNA methylation at a particular locus through Chop-PCR method. MEM1 possesses a Zf-C3HC domain, and is localized in nucleus as well as highly expressed in cotyledons. Whole-genome bisulfite sequencing data showed that knockout mutation of MEM1 leads to 4519 CG, 1793 CHG and 12739 CHH hyper-DMRs (for differentially methylated regions). Further analysis indicated that there are 2751, 2216 and 2042 overlapped CG hyper-DMRs between mem1-1and three mutants, i.e. ros1-4, rdd and ros3-2, respectively; 797, 2514, and 6766 overlapped CHH hyper-DMRs were observed between mem1-1 and three such mutants, respectively; mem1 nrpd1-3 and mem1 rdm1 double mutants showed nearly complete or partial loss of hypermethylation at 4 tested loci, suggesting that MEM1 performs similar functions as DNA glycosylase/lyases in counteracting excessive DNA methylation, and MEM1 plays important roles as REPRESSOR OF SILENCING 3 (ROS3) in erasing CHH methylation caused by the RdDM pathway. Together, these data demonstrate the involvement of MEM1 in ROS1-mediated DNA demethylation pathway and functional connections between MEM1 and ROS3.

Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana

Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. We investigate whether positive selection is associated with genomic imprinting in the inbreeding species Arabidopsis thaliana. Our analysis of 140 genes regulated by genomic imprinting in the A. thaliana seed endosperm demonstrates they are evolving more rapidly than expected. To investigate whether positive selection drives this evolutionary acceleration, we identified orthologs of each imprinted gene across 34 plant species and elucidated their evolutionary trajectories. Increased positive selection was sought by comparing its incidence among imprinted genes with nonimprinted controls. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.

Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana

FLOWERING LOCUS T (FT) plays a major role in regulating the floral transition in response to an inductive long day photoperiod in Arabidopsis thaliana. Expression of FT in leaves is dependent on the distal transcriptional enhancer Block C, located 5-kilobases (kb) upstream of the transcriptional start site (TSS). We expressed an inverted repeat of Block C to induce local DNA methylation and heterochromatin formation, which lead to FT downregulation in an inductive photoperiod. Using targeted DNA methylation as a tool to uncover further regulatory regions at the FT locus, we identified Block E, located 1 kb downstream of the gene, as a novel enhancer of FT. As Block C, Block E is conserved across Brassicaceae and located in accessible chromatin. Block C and E act as additive transcriptional enhancers that, in combination with the proximal FT promoter, control expression of FT in response to photoperiod in the leaf phloem.

Crosstalk between PTGS and TGS pathways in natural antiviral immunity and disease recovery

Virus-induced diseases cause severe damage to cultivated plants, resulting in crop losses. Certain plant-virus interactions allow disease recovery at later stages of infection and have the potential to reveal important molecular targets for achieving disease control. Although recovery is known to involve antiviral RNA silencing^1,2, the specific components of the many plant RNA silencing pathways ³ required for recovery are not known. We found that Arabidopsis thaliana plants infected with oilseed rape mosaic virus (ORMV) undergo symptom recovery. The recovered leaves contain infectious, replicating virus, but exhibit a loss of viral suppressor of RNA silencing (VSR) protein activity. We demonstrate that recovery depends on the 21-22 nt siRNA-mediated post-transcriptional gene silencing (PTGS) pathway and on components of a transcriptional gene silencing (TGS) pathway that is known to facilitate non-cell-autonomous silencing signalling. Collectively, our observations indicate that recovery reflects the establishment of a tolerant state in infected tissues and occurs following robust delivery of antiviral secondary siRNAs from source to sink tissues, and establishment of a dosage able to block the VSR activity involved in the formation of disease symptoms.

Efficient Generation of diRNAs Requires Components in the Posttranscriptional Gene Silencing Pathway

It has been reported that double-stranded break (DSB)-induced small RNAs (diRNAs) are generated via the RNA-directed DNA methylation pathway and function in DSB repair in Arabidposis. However, important questions remain regarding the biogenesis and function of diRNAs. Here, we used CRISPR/Cas9- or TALEN-triggered DSBs to characterize diRNAs in Arabidopsis and rice. We found that 21-nt diRNAs were generated from a 35S promoter::GU-US reporter transgene targeted by CRISPR/Cas9. Unexpectedly, Pol II transcription of the transgene was required for efficient diRNA production and the level of diRNA accumulation correlated with the expression level of the transgene. diRNAs were not detected from CRISPR/Cas9- or TALEN-induced DSBs within the examined endogenous genes in Arabidopsis or rice. We also found that DCL4 and RDR6 that are known to be involved in posttranscriptional gene silencing were required to generate diRNAs. Our results suggest that DSBs are necessary but not sufficient for efficient diRNA generation and a high level of diRNAs is not necessary for DSB repair.

Generation of different sizes and classes of small RNAs in barley is locus, chromosome and/or cultivar-dependent

Background

Various small RNA (sRNA) sizes and varieties have been identified, but their relationship as well as relationship with their origins and allocations have not been well understood or investigated.

Results

By comparing sRNAs generated from two barley cultivars, Golden Promise (GP) and Pallas, we identified that the generation of different sizes and types of sRNAs in barley was locus-, chromosome- and/or cultivar-dependent. 20-nt sRNAs mainly comprising miRNAs and chloroplast-derived sRNAs were significantly over-expressed in Pallas vs. GP on chromosomes 3H and 6H. MiRNAs-enriched 21-nt sRNAs were significantly over-expressed in Pallas vs. GP only on chromosome 4H. On chromosome 5H this size of sRNAs was significantly under-expressed in Pallas, so were 22-nt sRNAs mainly comprising miRNAs and repeat-derived sRNAs. 24-nt sRNAs mostly derived from repeats were evenly distributed in all chromosomes and expressed similarly between GP and Pallas. Unlike other sizes of sRNAs, 24-nt sRNAs were little conserved in other plant species. Abundant sRNAs were mostly generated from 3’ terminal regions of chromosome 1H and 5’ terminal regions of chromosome 5H. Over-expressed miRNAs in GP vs. Pallas primarily function in stress responses and iron-binding.

Conclusions

Our study indicates that 23−24-nt sRNAs may be linked to repressive chromatin modifications and function in genome stability while 20−21-nt sRNAs may be important for the cultivar specificity. This study provides a novel insight into the mechanism of sRNA expression and function in barley.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3023-5) contains supplementary material, which is available to authorized users.

Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana

Short interfering RNAs (siRNAs) homologous to transcriptional regulatory regions can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS) of target genes. In our system, siRNAs are produced by transcribing an inverted DNA repeat (IR) of enhancer sequences, yielding a hairpin RNA that is processed by several Dicer activities into siRNAs of 21-24 nt. Primarily 24-nt siRNAs trigger RdDM of the target enhancer in trans and TGS of a downstream GFP reporter gene. We analyzed siRNA accumulation from two different structural forms of a trans-silencer locus in which tandem repeats are embedded in the enhancer IR and distinguished distinct RNA polymerase II (Pol II)- and Pol IV-dependent pathways of siRNA biogenesis. At the original silencer locus, Pol-II transcription of the IR from a 35S promoter produces a hairpin RNA that is diced into abundant siRNAs of 21-24 nt. A silencer variant lacking the 35S promoter revealed a normally masked Pol IV-dependent pathway that produces low levels of 24-nt siRNAs from the tandem repeats. Both pathways operate concurrently at the original silencer locus. siRNAs accrue only from specific regions of the enhancer and embedded tandem repeat. Analysis of these sequences and endogenous tandem repeats producing siRNAs revealed the preferential accumulation of siRNAs at GC-rich regions containing methylated CG dinucleotides. In addition to supporting a correlation between base composition, DNA methylation and siRNA accumulation, our results highlight the complexity of siRNA biogenesis at repetitive loci and show that Pol II and Pol IV use different promoters to transcribe the same template.

Pleiotropic phenotypes of the salt-tolerant and cytosine hypomethylated leafless inflorescence, evergreen dwarf and irregular leaf lamina mutants of Catharanthus roseus possessing Mendelian inheritance

In Catharanthus roseus, three morphological cum salt-tolerant chemically induced mutants of Mendelian inheritance and their wild-type parent cv Nirmal were characterized for overall cytosine methylation at DNA repeats, expression of 119 protein coding and seven miRNA-coding genes and 50 quantitative traits. The mutants, named after their principal morphological feature(s), were leafless inflorescence (lli), evergreen dwarf (egd) and irregular leaf lamina (ill). The Southern-blot analysis of MspI digested DNAs of mutants probed with centromeric and 5S and 18S rDNA probes indicated that, in comparison to wild type, the mutants were extensively demethylated at cytosine sites. Among the 126 genes investigated for transcriptional expression, 85 were upregulated and 41 were downregulated in mutants. All of the five genes known to be stress responsive had increased expression in mutants. Several miRNA genes showed either increased or decreased expression in mutants. The C. roseus counterparts of CMT3, DRM2 and RDR2 were downregulated in mutants. Among the cell, organ and plant size, photosynthesis and metabolism related traits studied, 28 traits were similarly affected in mutants as compared to wild type. Each of the mutants also expressed some traits distinctively. The egd mutant possessed superior photosynthesis and water retention abilities. Biomass was hyperaccumulated in roots, stems, leaves and seeds of the lli mutant. The ill mutant was richest in the pharmaceutical alkaloids catharanthine, vindoline, vincristine and vinblastine. The nature of mutations, origins of mutant phenotypes and evolutionary importance of these mutants are discussed.

Transient down-regulation of the RNA silencing machinery increases efficiency of Agrobacterium-mediated transformation of Arabidopsis

Agrobacterium tumefaciens is a plant pathogen that is widely used in plant transformation. As the process of transgenesis includes the delivery of single-stranded T-DNA molecule, we hypothesized that transformation rate may negatively correlate with the efficiency of the RNA-silencing machinery. Using mutants compromised in either the transcriptional or post-transcriptional gene-silencing pathways, two inhibitors of stable transformation were revealed-AGO2 and NRPD1a. Furthermore, an immunoprecipitation experiment has shown that NRPD1, a subunit of Pol IV, directly interacts with Agrobacterium T-DNA in planta. Using the Tobacco rattle virus (TRV)--based virus-induced gene silencing (VIGS) technique, we demonstrated that the transient down-regulation of the expression of either AGO2 or NRPD1a genes in reproductive organs of Arabidopsis, leads to an increase in transformation rate. We observed a 6.0- and 3.5-fold increase in transformation rate upon transient downregulation of either AGO2 or NRPD1a genes, respectively. This is the first report demonstrating the increase in the plant transformation rate via VIGS-mediated transient down-regulation of the components of epigenetic machinery in reproductive tissue.

Small RNAs and heritable epigenetic variation in plants

Recent studies suggest that inheritance of phenotypes in plants is more likely to involve epigenetics than in mammals. There are two reasons for this difference. First, there is a RNA-based system in plants involving small (s)RNAs that influences de novo establishment and maintenance of DNA methylation at many sites in plant genomes. These regions of methylated DNA are epigenetic marks with the potential to affect gene expression that are transmitted between dividing cells of the same generation. Second, unlike mammals, DNA methyltransferases in plants are active during gametogenesis and embryogenesis so that patterns of DNA methylation can persist from parent to progeny and do not need to be reset. We discuss how the effects of stress and genome interactions in hybrid plants are two systems that illustrate how RNA-based mechanisms can influence heritable phenotypes in plants.

The stochastic silencing phenotype of Arabidopsis morc6 mutants reveals a role in efficient RNA-directed DNA methylation

The RNA-directed DNA methylation (RdDM) pathway is of central importance to the initiation and maintenance of transcriptional gene silencing in plants. DNA methylation is directed to target sequences by a mechanism that involves production of small RNAs by RNA polymerase IV and long non-coding RNAs by RNA polymerase V. DNA methylation then leads to recruitment of histone-modifying enzymes, followed by establishment of a silenced chromatin state. Recently MORC6, a member of the microrchidia (MORC) family of adenosine triphosphatases (ATPases), has been shown to be involved in transcriptional gene silencing. However, reports differ regarding whether MORC6 is involved in RdDM itself or acts downstream of DNA methylation to enable formation of higher-order chromatin structure. Here we demonstrate that MORC6 is required for efficient RdDM at some target loci, and, using a GFP reporter system, we found that morc6 mutants show a stochastic silencing phenotype. By using cell sorting to separate silenced and unsilenced cells, we show that release of silencing at this locus is associated with a loss of DNA methylation. Thus our data support a view that MORC6 influences RdDM and that it is not acting downstream of DNA methylation. For some loci, efficient initiation or maintenance of DNA methylation may depend on the ability to form higher-order chromatin structure.

From immunity to susceptibility: virus resistance induced in tomato by a silenced transgene is lost as TGS overcomes PTGS

Tomato line 30.4 was obtained engineering the nucleocapsid (N) gene of tomato spotted wilt virus into plant genome, and immunity to tomato spotted wilt virus infection of its self-pollinated homozygous progeny was observed. Despite the presence of a high amount of transgenic transcripts, transgenic proteins have not been detected, suggesting a mechanism of resistance mediated by RNA. In the present study, we identify post-transcriptional gene silencing as the main mechanism of resistance, which is able to spread systemically through grafting, and show that the line 30.4 resistant plants produce both 24 and 21-22 nt N-gene specific siRNA classes. The transgenic locus in chromosome 4 shows complex multiple insertions of four T-DNA copies in various orientations, all with 3' end deletions in the terminator and part of the N gene. However, for three of them, polyadenylated transcripts are produced, due to flanking tomato genome sequences acting as alternative terminators. Interestingly, starting at the fifth generation after the transformation event, some individual plants show a tomato spotted wilt virus-susceptible phenotype. The change is associated with the disappearance of transgene-specific transcripts and siRNAs, and with hyper-methylation of the transgene, which proceeds gradually through the generations. Once it reaches a critical threshold, the shift from post-transcriptional gene silencing to transcriptional silencing of the transgene eliminates the previously well established virus resistance.

Transitive RNA silencing signals induce cytosine methylation of a transgenic but not an endogenous target

Post-transcriptional gene silencing of a primary target gene in plants can coincide with the production of secondary small interfering RNAs (siRNAs) of coding sequences adjacent to the target region and with de novo RNA-directed DNA methylation (RdDM) thereof. Here, we analyzed the susceptibility of transgenic and endogenous targets to RdDM induced by primary and secondary silencing signals. In three different configurations, primary silencing signals were able to direct in trans methylation of chimeric transgenes and the CATALASE2 (CAT2) endogene; however, extensive spreading of methylation occurred only in the transgene, resulting in the methylation of the flanking CAT2 sequence, whereas methylation of the CAT2 endogene was restricted to the target region and the enclosed introns. The secondary silencing signals arising from this transgenic primary target simultaneously silenced a secondary transgene target and the CAT2 endogene, but were only capable of directing RdDM to the transgene. Our data indicate that RdDM is correlated with the in situ generation of secondary siRNAs, occurring in P35S-driven transgenes but not in most endogenes. We conclude that although both endogenes and transgenes are equally sensitive to transitive silencing, differences exist in their susceptibility to undergo secondary RdDM.

The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs

Transposable elements (TEs) are mobile fragments of DNA that are repressed in both plant and animal genomes through the epigenetic inheritance of repressed chromatin and expression states. The epigenetic silencing of TEs in plants is mediated by a process of RNA-directed DNA methylation (RdDM). Two pathways of RdDM have been identified: RNA Polymerase IV (Pol IV)-RdDM, which has been shown to be responsible for the de novo initiation, corrective reestablishment, and epigenetic maintenance of TE and/or transgene silencing; and RNA-dependent RNA Polymerase6 (RDR6)-RdDM, which was recently identified as necessary for maintaining repression for a few TEs. We have further characterized RDR6-RdDM using a genome-wide search to identify TEs that generate RDR6-dependent small interfering RNAs. We have determined that TEs only produce RDR6-dependent small interfering RNAs when transcriptionally active, and we have experimentally identified two TE subfamilies as direct targets of RDR6-RdDM. We used these TEs to test the function of RDR6-RdDM in assays for the de novo initiation, corrective reestablishment, and maintenance of TE silencing. We found that RDR6-RdDM plays no role in maintaining TE silencing. Rather, we found that RDR6 and Pol IV are two independent entry points into RdDM and epigenetic silencing that perform distinct functions in the silencing of TEs: Pol IV-RdDM functions to maintain TE silencing and to initiate silencing in an RNA Polymerase II expression-independent manner, while RDR6-RdDM functions to recognize active Polymerase II-derived TE mRNA transcripts to both trigger and correctively reestablish TE methylation and epigenetic silencing.

Interplay among RNA polymerases II, IV and V in RNA-directed DNA methylation at a low copy transgene locus in Arabidopsis thaliana

RNA-directed DNA methylation (RdDM) is an epigenetic process whereby small interfering RNAs (siRNAs) guide cytosine methylation of homologous DNA sequences. RdDM requires two specialized RNA polymerases: Pol IV transcribes the siRNA precursor whereas Pol V generates scaffold RNAs that interact with siRNAs and attract the methylation machinery. Recent evidence also suggests the involvement of RNA polymerase II (Pol II) in recruiting Pol IV and Pol V to low copy, intergenic loci. We demonstrated previously that Pol V-mediated methylation at a transgene locus in Arabidopsis spreads downstream of the originally targeted region by means of Pol IV/RNA-DEPENDENT RNA POLYMERASE2 (RDR2)-dependent 24-nt secondary siRNAs. Here we show that these secondary siRNAs can not only induce methylation in cis but also in trans at an unlinked target site, provided this sequence is transcribed by Pol II to produce a non-coding RNA. The Pol II transcript appears to be important for amplification of siRNAs at the unlinked target site because its presence correlates not only with methylation but also with elevated levels of 24-nt siRNAs. Potential target sites that lack an overlapping Pol II transcript and remain unmethylated in the presence of trans-acting 24-nt siRNAs can nevertheless acquire methylation in the presence of 21-24-nt hairpin-derived siRNAs, suggesting that RdDM of non-transcribed target sequences requires multiple size classes of siRNA. Our findings demonstrate that Pol II transcripts are not always needed for RdDM at low copy loci but they may intensify RdDM by facilitating amplification of Pol IV-dependent siRNAs at the DNA target site.

Co-expression of soybean Dicer-like genes in response to stress and development

Regulation of gene transcription and post-transcriptional processes is critical for proper development, genome integrity, and stress responses in plants. Many genes involved in the key processes of transcriptional and post-transcriptional regulation have been well studied in model diploid organisms. However, gene and genome duplication may alter the function of the genes involved in these processes. To address this question, we assayed the stress-induced transcription patterns of duplicated gene pairs involved in RNAi and DNA methylation processes in the paleopolyploid soybean. Real-time quantitative PCR and Sequenom MassARRAY expression assays were used to profile the relative expression ratios of eight gene pairs across eight different biotic and abiotic stress conditions. The transcriptional responses to stress for genes involved in DNA methylation, RNAi processing, and miRNA processing were compared. The strongest evidence for pairwise co-expression in response to stresses was exhibited by non-paralogous Dicer-like (DCL) genes GmDCL2a-GmDCL3a and GmDCL1b-GmDCL2b, most profoundly in root tissues. Among homoeologous or paralogous DCL genes, the Dicer-like 2 (DCL2) gene pair exhibited the strongest response to stress and most conserved co-expression pattern. This was surprising because the DCL2 duplication event is more ancient than the other DCL duplications. Possible mechanisms that may be driving the DCL2 co-expression are discussed.

NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis

In Arabidopsis, transcriptional gene silencing (TGS) can be triggered by 24 nt small-interfering RNAs (siRNAs) through the RNA-directed DNA methylation (RdDM) pathway. By functional analysis of NERD, a GW repeat- and PHD finger-containing protein, we demonstrate that Arabidopsis harbors a second siRNA-dependent DNA methylation pathway targeting a subset of nonconserved genomic loci. The activity of the NERD-dependent pathway differs from RdDM by the fact that it relies both on silencing-related factors previously implicated only in posttranscriptional gene silencing (PTGS), including RNA-DEPENDENT RNA POLYMERASE1/6 and ARGONAUTE2, and most likely on 21 nt siRNAs. A central role for NERD in integrating RNA silencing and chromatin signals in transcriptional silencing is supported by data showing that it binds both to histone H3 and AGO2 proteins and contributes to siRNA accumulation at a NERD-targeted locus. Our results unravel the existence of a conserved chromatin-based RNA silencing pathway encompassing both PTGS and TGS components in plants.

Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions

In Arabidopsis thaliana, the putative RNA-helicase SDE3 assists posttranscriptional-gene-silencing (PTGS) amplification by RNA-dependent-RNA-polymerase-6 (RDR6). SDE3 homologs in Drosophila, worm and human contribute to silence viruses, transposons or recently duplicated genes but the underlying mechanisms remain largely unknown. Here, we demonstrate that SDE3 is present with the PTGS effectors AGO1 and AGO2 in higher-order protein complexes owing to a specialized GW-repeat-containing C-terminal domain. We uncover an essential contribution of the RNA-helicase activity and a facilitating role for AGO binding in SDE3 action, which occurs downstream of RDR6. We show that these biochemical properties underpin dual roles for SDE3 in antiviral defense and, unexpectedly, in transposon silencing via a hitherto unanticipated pathway that correlates with DNA methylation, suggesting a continuum of action between PTGS and chromatin-level silencing. We identified endogenous SDE3 targets corresponding to nonconserved intergenic regions, transposons and recently evolved pseudogenes, unraveling striking functional convergences among plant and metazoan SDE3 pathways.

Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development

Environmental cues influence the development of stomata on the leaf epidermis, and allow plants to exert plasticity in leaf stomatal abundance in response to the prevailing growing conditions. It is reported that Arabidopsis thaliana 'Landsberg erecta' plants grown under low relative humidity have a reduced stomatal index and that two genes in the stomatal development pathway, SPEECHLESS and FAMA, become de novo cytosine methylated and transcriptionally repressed. These environmentally-induced epigenetic responses were abolished in mutants lacking the capacity for de novo DNA methylation, for the maintenance of CG methylation, and in mutants for the production of short-interfering non-coding RNAs (siRNAs) in the RNA-directed DNA methylation pathway. Induction of methylation was quantitatively related to the induction of local siRNAs under low relative humidity. Our results indicate the involvement of both transcriptional and post-transcriptional gene suppression at these loci in response to environmental stress. Thus, in a physiologically important pathway, a targeted epigenetic response to a specific environmental stress is reported and several of its molecular, mechanistic components are described, providing a tractable platform for future epigenetics experiments. Our findings suggest epigenetic regulation of stomatal development that allows for anatomical and phenotypic plasticity, and may help to explain at least some of the plant's resilience to fluctuating relative humidity.

Isolation and detection of small RNAs from plant tissues

In plants, several classes of non-coding small RNA (sRNA) have been shown to be important regulators of gene expression in a wide variety of biological processes. The two main classes of sRNA, the small-interfering RNA (siRNA) and microRNA (miRNA) classes, are well documented and several experimental approaches have been developed to allow for their routine isolation and detection from plant tissues. Here, we describe the current methods used for the isolation of total RNA and the subsequent enrichment of low-molecular-weight (LMW) RNA species, as well as to outline how sRNAs are detected from such nucleic acid preparations.

DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene

In plants, the exogenous transgene transcribing inverted-repeat (exo-IR) sequences produces double-stranded RNAs that are processed by DCL4. The 21-nt small interfering RNAs generated function as mobile signals to trigger non-cell autonomous silencing of target endogenes in the neighboring 10-15 cells. The potential involvement of nuclear silencing pathway components in signal spreading or sensing in target cells is not clear. Here, we demonstrate that the exo-IR silencer (exo-Pdsi) is negatively autoregulated through methylation spreading, which acts in cis to reinforce the self-silencing of the silencer. Mutations affecting nuclear proteins DRD1 and Pol V (NRPE1 or NRPD2) relieved exo-Pdsi self-silencing, resulting in higher levels of Pdsi transcripts, which increased the non-cell autonomous silencing of endo-PDS. Our results suggest that in an experimental silencing pathway, methylation spreading on a silencer transgene may not have a direct endogenous plant counterpart when the protein-encoding gene is the target. DRD1-Pol V-dependent de novo methylation, by acting in cis to reinforce self-silencing of exo-IR, may play a role in restraining the inappropriate silencing of active protein-coding genes in plants.

Cell-to-cell and long-distance siRNA movement in plants: mechanisms and biological implications

In plants, once triggered within a single-cell type, transgene-mediated RNA-silencing can move from cell-to-cell and over long distances through the vasculature to alter gene expression in tissues remote form the primary sites of its initiation. Although, transgenic approaches have been instrumental to genetically decipher the components and channels required for mobile silencing, the possible existence and biological significance of comparable endogenous mobile silencing pathways has remained an open question. Here, we summarize the results from recent studies that shed light on the molecular nature of the nucleic acids involved and on existing endogenous mechanisms that allow long-distance gene regulation and epigenetic modifications. We further elaborate on these and other results to propose a unified view of various non-cell autonomous RNA silencing processes that appear to differ in their genetic requirement and modes of perpetuation in plants.

Diverse spontaneous silencing of a transgene among two Nicotiana species

In plants, transgenes frequently become spontaneously silenced for unknown reasons. Typically, transgene silencing involves the generation of small interfering RNAs (siRNAs) that directly or indirectly target cognate DNA and mRNA sequences for methylation and degradation, respectively. In this report, we compared spontaneous silencing of a transgene in Nicotiana benthamiana and Nicotiana tabacum. In both species, abundant siRNAs were produced. In N. benthamiana, the self-silencing process involved mRNA degradation and dense DNA methylation of the homologous coding region. In N. tabacum, self-silencing occurred without complete mRNA degradation and with low methylation of the cognate coding region. Our data indicated that in plants, siRNA-mediated spontaneous silencing is, in addition to mRNA degradation, based on translational inhibition. Differences in the initiation and establishment of self-silencing together with marked differences in the degree of de novo DNA methylation showed that the mechanistic details of RNA silencing, although largely conserved, may vary also in genetically close plant species.

Small RNA-mediated epigenetic modifications in plants

Epigenetic modifications in plants can be directed and mediated by small RNAs (sRNAs). This regulation is composed of a highly interactive network of sRNA-directed DNA methylation, histone, and chromatin modifications, all of which control transcription. Identification and functional characterization of components of the siRNA-directed DNA methylation pathway have provided insights into epigenetic pathways that form heterochromatin and into chromatin-based pathways for gene silencing, paramutation, genetic imprinting, and epigenetic reprogramming. Next-generation sequencing technologies have facilitated new discoveries and have helped create a basic blueprint of the plant epigenome. As the multiple layers of epigenetic regulation in plants are dissected, a more comprehensive understanding of the biological importance of epigenetic marks and states has been developed.

Genome reprogramming and small interfering RNA in the Arabidopsis germline

The movement of mobile small RNA signals between cells has garnered much interest over the last few years, and has recently been extended to germ cells during gamete development. Focusing on plants, we review mobile RNA signals that arise following reprogramming in the germline, and their effect on transposable element silencing on the one hand and on meiotic and apomictic germ cell fate on the other. A potential role for reprogramming and small RNA in hybrid formation and speciation is proposed.

A chimeric satellite transgene sequence is inefficiently targeted by viroid-induced DNA methylation in tobacco

In plants, transgenes containing Potato spindle tuber viroid (PSTVd) cDNA sequences were efficient targets of PSTVd infection-mediated RNA-directed DNA methylation. Here, we demonstrate that in PSTVd-infected tobacco plants, a 134 bp PSTVd fragment (PSTVd-134) did not become densely methylated when it was inserted into a chimeric Satellite tobacco mosaic virus (STMV) construct. Only about 4-5% of all cytosines (Cs) of the PSTVd-134 were methylated when flanked by satellite sequences. In the same plants, C methylation was approximately 92% when the PSTVd-134 was in a PSTVd full length sequence context and roughly 33% when flanked at its 3' end by a 19 bp PSTVd and at its 5' end by a short viroid-unrelated sequence. In addition, PSTVd small interfering RNAs (siRNAs) produced from the replicating viroid failed to target PSTVd-134-containing chimeric STMV RNA for degradation. Satellite RNAs appear to have adopted secondary structures that protect them against RNA interference (RNAi)-mediated degradation. Protection can be extended to short non-satellite sequences residing in satellite RNAs, rendering them poor targets for nuclear and cytoplasmic RNAi induced in trans.

Suppression of microRNA accumulation via RNA interference in Arabidopsis thaliana

MicroRNAs (miRNAs) are key regulatory molecules in plants. These small RNAs are processed in the nucleus from longer precursor transcripts that form distinct secondary structures. The miRNAs target specific messenger RNAs (mRNAs) and consequently down-regulate gene expression. The importance of these regulatory molecules is wide-ranging, however, few loss-of-function mutants have been identified in miRNA genes and understanding the biology of miRNA-target pairings has largely depended upon creating alterations in the sequences of the target genes. Here we demonstrate using Arabidopsis thaliana, that it is possible to use RNA interference (RNAi) to suppress accumulation of miRNAs. Significantly reduced accumulation of miR163 and miR171a was achieved using hairpin RNAi constructs that were designed to target both the primary miRNA transcripts and their promoters. The presence of DNA methylation in the targeted promoter regions suggests that inhibition of transcription of the miRNA precursors is responsible. Reduction of miRNA accumulation resulted in an increase in accumulation of the mRNA targets of these miRNAs. This demonstrates that knock-down of miRNA expression can be achieved, thereby providing a straightforward approach for disrupting miRNA-target pairings and studying miRNA functions.

Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis

In many plants, including Arabidopsis, hybrids between species and subspecies encounter postfertilization barriers in which hybrid seed fail to develop, or else give rise to infertile progeny. In Arabidopsis, some of these barriers are sensitive to ploidy and to the epigenetic status of donor and recipient genomes. Recently, a role has been proposed for heterochromatin in reprogramming events that occur in reproductive cells, as well as in the embryo and endosperm after fertilization. 21 nt small interfering RNA (siRNA) from activated transposable elements accumulate in pollen, and are translocated from companion vegetative cells into the sperm, while in the maturing seed 24 nt siRNA are primarily maternal in origin. Thus maternal and paternal genomes likely contribute differing small RNA to the zygote and to the endosperm. As heterochromatic sequences also differ radically between, and within, species, small RNA sequences will diverge in hybrids. If transposable elements in the seed are not targeted by small RNA from the pollen, or vice versa, this could lead to hybrid seed failure, in a mechanism reminiscent of hybrid dysgenesis in Drosophila. Heterochromatin also plays a role in apomixis and nucleolar dominance, and may utilize a similar mechanism.

NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation

RNA-directed DNA methylation (RdDM) is an RNAi-based mechanism for establishing transcriptional gene silencing in plants. The plant-specific RNA polymerases IV and V are required for the generation of 24-nucleotide (nt) siRNAs and for guiding sequence-specific DNA methylation by the siRNAs, respectively. However, unlike the extensively studied multisubunit Pol II, our current knowledge about Pol IV and Pol V is restricted to only the two largest subunits NRPD1a/NRPD1 and NRPD1b/NRPE1 and the one second-largest subunit NRPD2a. It is unclear whether other subunits may be required for the functioning of Pol IV and Pol V in RdDM. From a genetic screen for second-site suppressors of the DNA demethylase mutant ros1, we identified a new component (referred to as RDM2) as well as seven known components (NRPD1, NRPE1, NRPD2a, AGO4, HEN1, DRD1, and HDA6) of the RdDM pathway. The differential effects of the mutations on two mechanistically distinct transcriptional silencing reporters suggest that RDM2, NRPD1, NRPE1, NRPD2a, HEN1, and DRD1 function only in the siRNA-dependent pathway of transcriptional silencing, whereas HDA6 and AGO4 have roles in both siRNA-dependent and -independent pathways of transcriptional silencing. In the rdm2 mutants, DNA methylation and siRNA accumulation were reduced substantially at loci previously identified as endogenous targets of Pol IV and Pol V, including 5S rDNA, MEA-ISR, AtSN1, AtGP1, and AtMU1. The amino acid sequence of RDM2 is similar to that of RPB4 subunit of Pol II, but we show evidence that RDM2 has diverged significantly from RPB4 and cannot function in Pol II. An association of RDM2 with both NRPD1 and NRPE1 was observed by coimmunoprecipitation and coimmunolocalization assays. Our results show that RDM2/NRPD4/NRPE4 is a new component of the RdDM pathway in Arabidopsis and that it functions as part of Pol IV and Pol V.

RNA-mediated chromatin-based silencing in plants

Plants have evolved an elaborate transcriptional machinery dedicated to eliciting sequence-specific, chromatin-based gene silencing. Two Pol II-related, plant-specific RNA polymerases, named Pol IV and Pol V, collaborate with proteins of the RNA interference machinery to generate long and short noncoding RNAs involved in epigenetic regulation. As revealed by a variety of genetic, molecular, and genomic technologies, these RNAs are used extensively in plants to direct the establishment, spread, and removal of DNA cytosine methylation throughout their genomes. RNA-mediated chromatin-level silencing is increasingly implicated in development, stress responses, and natural epigenetic variation that may promote phenotypic diversity, physiological plasticity, and evolutionary change.

A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation

We used a transgene system to study spreading of RNA-directed DNA methylation (RdDM) during transcriptional gene silencing in Arabidopsis thaliana. Forward and reverse genetics approaches using this system delineated a stepwise pathway for the biogenesis of secondary siRNAs and unidirectional spreading of methylation from an upstream enhancer element into downstream sequences. Trans-acting, hairpin-derived primary siRNAs induce primary RdDM, independently of an enhancer-associated 'nascent' RNA, at the target enhancer region. Primary RdDM is a key step in the pathway because it attracts the secondary siRNA-generating machinery, including RNA polymerase IV, RNA-dependent RNA polymerase2 and Dicer-like3 (DCL3). These factors act in a turnover pathway involving a nascent RNA, which normally accumulates stably in non-silenced plants, to produce cis-acting secondary siRNAs that induce methylation in the downstream region. The identification of DCL3 in a forward genetic screen for silencing-defective mutants demonstrated a strict requirement for 24-nt siRNAs to direct methylation. A similar stepwise process for spreading of DNA methylation may occur in mammalian genomes, which are extensively transcribed in upstream regulatory regions.

Use, tolerance and avoidance of amplified RNA silencing by plants

In plants and several other organisms, the effects of RNA silencing can be amplified by the action of cellular RNA-DEPENDENT RNA POLYMERASES (RDRs). These enzymes were primarily studied for their role in antiviral defense in plants, but it is becoming increasingly apparent that they also have important endogenous functions, including the control of chromatin structure and the regulation of cellular gene expression. Recent evidence suggests that endogenous RDR activities intercept several RNA quality control pathways that normally prevent or restrain widespread amplification of silencing, which is likely to be detrimental. Plants appear, however, to have evolved sophisticated measures to tolerate or exploit amplified silencing under specific biological circumstances.