Methods for suppressing target DNA methylation in plants

Abstract

According to the present invention, methylation of a target DNA in a plant is suppressed quickly and easily without using recombinant technology, and a plant having desired traits is thereby created.　In an RNA-directed DNA methylation mechanism, binding between scaffold RNA produced by transcription of the target DNA and an siRNA-AGO4 complex is inhibited.

Description

[Technical Field]

[0001] The present invention relates to a method for suppressing target DNA methylation in plants. [Background technology]

[0002] Gene expression in plants is regulated by DNA methylation and chemical modifications of histones, a process known as epigenetic regulation. This is a phenomenon caused by RNA silencing, which can be broadly divided into two types: post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). Plants rely on this epigenetic regulation to regulate the accumulation levels of functional compounds, and in order to accumulate these useful compounds at high levels in plants, technology to freely manipulate this epigenetics is required. However, epigenetic regulation is so complex that it was thought impossible to specifically demethylate target DNA.

[0003] To date, there have been few techniques for inducing DNA sequence-specific demethylation, and only recently has a technique been reported that uses dCAS-fused TET1 (Non-Patent Document 1). However, inducing demethylation using dCAS-fused TET1 requires recombinant technology, which poses the problem of being unable to induce demethylation simply and quickly. [Prior art documents] [Patent documents]

[0004] [Patent Document 1] International Publication No. 2014 / 129560 [Non-patent literature]

[0005] [Non-Patent Document 1] Gallego-Bartolome J et al., Proceedings of the National Academy of Sciences of the United States of America 55, E2125-E2134 (2018) [Non-patent document 2] Gallusci P et al., Trends in Plant Science 22, 610-623 (2017) [Non-patent document 3] Matzke M. A and Mosher R. A, Nature Reviews Genetics 15, 394-408 (2014) [Non-patent document 4] Philips J. G et al., PloS one, 12(2), e0171311 (2017) [Non-patent document 5] Otagaki S et al., Plant Biotechnology 23, 259-265 (2006) Summary of the Invention [Problem to be solved by the invention]

[0006] An object of the present invention is to easily and quickly suppress methylation of target DNA in plants, with or without the use of recombinant technology, thereby producing plants with desired traits. [Means for solving the problem]

[0007] In light of the above-mentioned problems, the present inventors have conducted extensive research and have made the surprising discovery that, in the RNA-directed DNA methylation mechanism, methylation of target DNA can be specifically suppressed in plants by inhibiting the binding of the scaffold RNA produced by transcription of the target DNA to the siRNA-AGO4 complex.

[0008] That is, the gist of the present invention is as follows. [1] A method for suppressing methylation of target DNA in plant cells, the method comprising inhibiting binding of a scaffold RNA produced by transcription of the target DNA to an siRNA-AGO4 complex in an RNA-directed DNA methylation mechanism. [2] The method described in 1, wherein the inhibition of binding between the scaffold RNA and the siRNA-AGO4 complex is achieved by introducing into the plant cell a short dummy RNA containing a sequence complementary to the siRNA incorporated into the siRNA-AGO4 complex. [3] The method described in 1, wherein the inhibition of binding between the scaffold RNA and the siRNA-AGO4 complex is achieved by introducing a short dummy RNA containing a sequence complementary to at least a portion of the scaffold RNA into the plant cell. [4] The method according to any one of 1 to 3, wherein the target DNA is a promoter that controls a gene that expresses a desired trait in a plant cell. [5] The method described in 4, wherein the gene that expresses the desired trait is a gene that encodes the amino acid sequence of an enzyme that controls the synthesis or accumulation of a plant-derived functional component. [6] The method according to any one of 1 to 5, wherein the short dummy RNA is introduced into the plant cell by a plant virus vector method, an agroinfiltration method, the magnICON (registered trademark) system, or a particle gun method. [7] The method according to any one of 1 to 6, wherein the plant cell is a non-isolated cell of a plant body. [8] The method according to any one of 1 to 6, wherein the plant cells are cultured cells. [9] A method for producing a plant having a desired trait, the method comprising suppressing methylation of DNA involved in the expression of the desired trait in a plant using a method according to any one of 1 to 8.

[10] A method for producing a plant-derived functional ingredient, comprising: using a method according to any one of 1 to 8 to suppress methylation of DNA involved in the synthesis or accumulation of the plant-derived functional ingredient, thereby accumulating the functional ingredient in the plant cells; and recovering the functional ingredient from the plant cells.

[11] An expression system for accumulating a plant-derived functional component, comprising: (A) A plant or plant cell that produces a scaffold RNA and an siRNA-AGO4 complex produced by transcription of DNA involved in the synthesis or accumulation of a plant-derived functional component in an RNA-directed DNA methylation mechanism; and (B) a short dummy RNA having a sequence complementary to the siRNA incorporated into the siRNA-AGO4 complex or a sequence complementary to at least a portion of the scaffold RNA; An expression system comprising: [Effects of the Invention]

[0009] The present invention enables specific regulation of TGS of target DNA in plants simply and quickly by suppressing methylation of the target DNA, which makes it possible to obtain plants with desired traits and significantly contributes to, for example, the production of useful proteins and the improvement of the accumulation levels of functional components in plants. [Brief explanation of the drawings]

[0010] [Figure 1] Figure 1 shows a model of DNA methylation in the RdDM pathway. [Figure 2] Figure 2 shows a model of DNA demethylation based on the capture of siRNA-AGO4 complexes by short dummy RNAs. [Figure 3] Figure 3 shows a model of DNA demethylation based on blocking the binding of scaffold RNA to siRNA-AGO4 by short dummy RNA. [Figure 4]Figure 4 shows the sequence of the 35S promoter targeted by the short dummy RNA and the sequence of the short dummy RNA construct (SD-51) created to target the region (-51 to -76) where scaffold RNA is abundantly detected. [Figure 5] FIG. 5 shows fluorescence images of GFP-expressing revertants in the current generation of N. benthamiana (labeled SD-51 in the figure) in which SD-51 was expressed by the CMV-A1 vector, compared with the controls (16c and 208RED). [Figure 6] FIG. 6 shows a fluorescence image of a GFP-expressing revertant plant (35 days after sowing) in the next generation of N. benthamiana in which SD-51 was expressed by a CMV-A1 vector. [Figure 7] FIG. 7 shows a schematic diagram classifying the phenotype of GFP expression in N. benthamiana in which SD-51 is expressed using a CMV-A1 vector. DETAILED DESCRIPTION OF THE INVENTION

[0011] [1. Miscellaneous] Gene expression in plants is regulated by epigenetic control. "Epigenetics" refers to changes in gene function that are transmitted through cell division without causing changes in DNA sequence, and the mechanisms by which they occur. One type of epigenetic control is DNA methylation (Non-Patent Document 2). This reaction involves the addition of a methyl group to the carbon atom at position 5 of the pyrimidine ring of cytosine or the nitrogen atom at position 6 of the purine ring of adenine. Gene expression in plants is thought to be primarily controlled by cytosine methylation. In other words, methylation and demethylation of cytosine in DNA switches gene expression on and off without changing the base sequence information itself. This suppression of gene expression by DNA methylation is called transcriptional gene silencing (TGS). The present invention is based on the basic idea that by artificially controlling epigenetic regulation in plants, it is possible to change the phenotype of a desired plant without genetic modification.

[0012] Significant progress has been made in understanding DNA methylation in the model plant Arabidopsis thaliana. In plants, the major DNA methyltransferase enzymes responsible for methylation at CpG, CpHpG, and CpHpH sites (where H represents a nucleotide other than guanine) are known to transfer methyl groups to DNA and covalently bond them. These include DRM2, MET1, CMT3, and CMT2. Currently, DNA methyltransferases are classified into two types: de novo enzymes that create new methyl marks on DNA, and maintenance enzymes that recognize methylated sites on the parent strand of DNA and transfer the new methylation to the daughter strand after DNA replication. Of these, only DRM2 is considered a de novo DNA methyltransferase. It is unclear how cells determine the locations of de novo DNA methylation, but evidence suggests that an RNA-directed DNA methylation (RdDM) mechanism is involved at many sites.

[0013] As described above, the present invention is based on the finding that target DNA methylation can be specifically suppressed in plants by inhibiting the binding of the scaffold RNA produced by transcription of the target DNA to the siRNA-AGO4 complex in the RNA-directed DNA methylation system. Therefore, we first explain the RNA-directed DNA methylation system that is the premise of the present invention.

[0014] [RdDM mechanism] The RdDM mechanism refers to a mechanism by which methylation is induced in target DNA via small double-stranded RNA (siRNA) that has at least a partial base sequence identical to the DNA region targeted for methylation (target DNA). As shown in Figure 1, the RdDM mechanism involves first recruiting PolIV to a methylated target genomic region and transcribing the RNA of the target region. The PolIV transcript is then converted in situ into double-stranded RNA by RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and cleaved into 24-nucleotide siRNAs by the RNase III-like enzyme DICER-LIKE 3 (DCL3) (Non-Patent Document 3). This siRNA undergoes 3'-end methylation by HUA ENHANCER 1 (HEN1) and is then incorporated into ARGONAUT 4 (AGO4) to form a silencing effector complex (hereafter referred to as the "siRNA-AGO4 complex"). The complementary siRNA incorporated into the siRNA-AGO4 complex recruits the RNA (hereafter referred to as the "scaffold RNA") transcribed by DNA-dependent RNA polymerase V (PolV) by base pairing with the complex. Next, the de novo methyltransferase Domains Rearranged Methyltransferase (DRM2) is recruited to the DNA region corresponding to the siRNA via the siRNA-AGO4 complex, where it methylates the DNA. AGO4, DRM2, and the three enzymes RNA-Directed DNA Methylation 1 (RDM1), Defective-in RNA-Directed DNA Methylation 1 (DRD1), and Defective-in Meristem Silencing 3 (DMS3), which bind to methylated DNA, are thought to play an important role in this recruitment.

[0015] RNAs transcribed from target DNA by PolIV or PolV (they have nearly identical sequences because they are transcribed from the same region, but the RNA transcribed by PolV is specifically called scaffold RNA) recruit the methyltransferase DRM2 to target DNA via binding to the siRNA-AGO4 complex. Therefore, we can either capture the siRNA-AGO4 complex with a short RNA (hereafter referred to as "short dummy RNA") that contains a sequence complementary to the siRNA incorporated into the siRNA-AGO4 complex, which recruits DRM2 to the target sequence (Figure 2), or we can first bind the short dummy RNA to the scaffold RNA to block the binding of siRNA-AGO4 (Figure 3), thereby preventing DRM2 recruitment to the target sequence and thereby inhibiting DNA methylation.

[0016] 2. Methods for suppressing target DNA methylation in plant cells According to a first aspect of the present invention, there is provided a method for suppressing methylation of target DNA in plant cells, the method comprising inhibiting binding of a scaffold RNA produced by transcription of the target DNA to an siRNA-AGO4 complex in an RNA-directed DNA methylation mechanism.

[0017] Inhibiting the binding of the scaffold RNA, which is responsible for DNA methylation that suppresses the expression of desired traits in plants, to the siRNA-AGO4 complex inhibits the recruitment of DRM2 to the DNA region corresponding to the siRNA, thereby enabling specific suppression of target DNA methylation in plants. Inhibition of the binding of the scaffold RNA to the siRNA-AGO4 complex can be achieved, for example, by introducing into the plant cell a short dummy RNA containing a sequence complementary to the siRNA incorporated into the siRNA-AGO4 complex, or by introducing into the plant cell a short dummy RNA containing a sequence complementary to at least a portion of the scaffold RNA.

[0018] The term "short dummy RNA" as used herein refers to an RNA that is short enough not to induce RdDM and can bind to at least a portion of the siRNA and / or scaffold RNA incorporated into the siRNA-AGO4 complex. The short dummy RNA preferably has a base sequence identity of at least 80%, 85%, 90%, 92%, 94%, 95%, 96%, 97%, 98%, or 99% to the target DNA. Because such sequences are complementary to at least a portion of the siRNA and / or scaffold RNA incorporated into the siRNA-AGO4 complex, short dummy RNAs prevent DRM2 from being recruited to the target sequence, thereby inhibiting target DNA methylation in the DNA demethylation model based on the capture of the siRNA-AGO4 complex (Figure 2) and / or the DNA demethylation model based on the blocking of scaffold RNA binding to siRNA-AGO4 by short dummy RNA (Figure 3). As mentioned above, the RNAs transcribed from target DNA by PolIV and those transcribed by PolV are transcribed from the same region and therefore have nearly identical sequences. Therefore, short dummy RNAs with identical sequences can be used in both DNA demethylation models. Short dummy RNAs are typically supplied by viral vectors. However, if viral vectors are not used, they can be supplied by generating recombinant plants in which the RNA is transcribed from a sequence inserted downstream of the promoter of a plant expression vector. However, it is believed that the amount of short dummy RNA supplied by viral vectors is far superior.

[0019] The upper limit of the length of the short dummy RNA may be, for example, 200 bp or less, 190 bp or less, 180 bp or less, 170 bp or less, 160 bp or less, 150 bp or less, 140 bp or less, 130 bp or less, 120 bp or less, 110 bp or less, 100 bp or less, 90 bp or less, 80 bp or less, 70 bp or less, 60 bp or less, or 50 bp or less, and the lower limit of the length of the short dummy RNA may be, for example, 19 bp or more, 20 bp or more, 21 bp or more, 22 bp or more, 23 bp or more, 24 bp or more, 25 bp or more, 30 bp or more, 35 bp or more, 40 bp or more, or 45 bp or more. The length of the short dummy RNA is typically 19 bp to 200 bp, preferably 20 bp to 80 bp, and most preferably 20 bp to 50 bp.

[0020] The target DNA is not particularly limited as long as it is DNA involved in the expression of a desired trait in a plant and is repressed by methylation, and examples thereof include promoters that control genes that express the desired trait in plant cells. Desired traits include, for example, properties that can be observed as appearance (morphology) such as shape, color, and size, physiological properties that can be observed such as flowering time, and physiological properties such as resistance to pathogens and temperature, but preferably properties related to the accumulation of functional components (metabolic components) in plants. Therefore, the gene that expresses the desired trait is preferably a gene encoding the amino acid sequence of an enzyme that controls the synthesis or accumulation of a plant-derived functional component.

[0021] Examples of plant-derived functional components include acetylene, thiophene, glycoside, glucosinate, purine, pyrimidine, alkaloid, phenolics (e.g., quinone), essential oils, vitamins, terpenoids (e.g., iridoid, sesquiterpenes, diterpenoids, and triterpenoids), lignans, and flavonoids.

[0022] Short dummy RNAs can be introduced into plant cells using recombinant techniques, or, for ease and speed, using transient expression systems, such as the plant virus vector method, agroinfiltration, the magnICON® system, particle gun technology, or a combination of these.

[0023] The plant virus vector method involves in vitro transcription of cDNA from a plant virus genome into which the target DNA has been inserted, and then inoculating the resulting RNA into plants as a vector to infect them. The virus's own replication and systemic movement capabilities are utilized to express the target gene in the plant. Because this method utilizes the self-replicating ability of the virus to express the target gene, the use of vectors based on CMV or TMV, which have particularly high replication capabilities, can increase the amount of target gene expressed per plant cell.

[0024] Agroinfiltration is a method in which a culture solution of Agrobacterium transformed with a T-DNA vector containing a target gene is introduced into plant tissue by physical means (such as injection with a syringe or infiltration by vacuum) and the plant is infected, resulting in transient expression of the target gene in the plant. This method allows highly infectious Agrobacterium to be transferred and infected throughout the plant body by physical means (injection or infiltration), resulting in uniform expression of the target gene in all plant tissues. Agrobacterium is a general term for plant-pathogenic species of the genus Rhizobium, a gram-negative soil bacterium. An example of Agrobacterium is Agrobacterium tumefaciens, which is associated with crown gall disease. When using Agrobacterium-derived vectors to transiently express foreign genes in plants, the vector is usually introduced into plant tissues by physical methods (such as injection with a syringe or infiltration by reduced pressure) to infect the plant. Because Agrobacterium-derived vectors have strong infectivity due to the action of the T-DNA region, if they are transferred and infected throughout the plant body by physical methods (such as injection or infiltration), the foreign gene can be expressed uniformly and evenly throughout all plant tissues.

[0025] The magnICON® system involves introducing a TMV or PVX genome cDNA containing a gene of interest into a T-DNA vector, and then introducing a culture solution of Agrobacterium transformed with the resulting T-DNA vector into plant tissue by physical means (injection using a syringe or infiltration by reduced pressure) to infect the plant, thereby transiently expressing the gene of interest in the plant. Specifically, the vector is distributed throughout the plant body by physical means (injection or infiltration), thereby infecting the plant and expressing the gene of interest in all plant tissues. Furthermore, because the self-replicating ability of the virus (TMV or PVX) is utilized to express the gene of interest, the expression level of the gene of interest per plant cell can be increased. Thus, this method combines the advantages of the plant virus vector method and the agroinfiltration method described above. Furthermore, a nucleic acid molecule functionally combining a sequence corresponding to the RNA2 genome of Cucumber Mosaic Virus (CMV), in which part or all of the gene encoding the 2b protein has been replaced with a foreign gene, with an Agrobacterium T-DNA sequence can be introduced into a host plant that functionally expresses the CMV RNA1 and RNA3 genomes and protein 2b, and the plant can be cultivated to express the foreign gene. This allows the foreign gene to be transferred and expressed throughout the plant's cells, and the efficiency of foreign gene expression in each cell can be increased, achieving high expression throughout the plant (Patent Document 1). This method is comparable to the magnICON® system described above, which uses TMV or PVX, and allows for greater flexibility in the type of host plant and the size of the foreign gene that can be introduced.

[0026] The particle gun (particle bombardment) method is a technique for introducing target DNA into cells by ejecting metal particles, such as gold or tungsten, coated with DNA or vectors at high speed.

[0027] The vector used in the present invention for introducing the short dummy RNA is not particularly limited as long as it is capable of introducing the short dummy RNA into plant cells, but is typically a plant virus vector or a T-DNA vector, and is particularly preferably a plant virus vector. Plant virus vectors are not particularly limited as long as they can invade the nucleus of plant cells, and examples include vectors derived from various single-stranded RNA viruses such as tobacco mosaic virus (TMV), cucumber mosaic virus (CMV), potato virus X (PVX), and clover yellow vein virus (ClYVV); various single-stranded DNA viruses such as bean yellow dwarf virus (BeYDV), beet curly top virus (BCTV), cabbage leaf curl virus (CaLCuV), wheat dwarf virus (WDV), and tomato yellow leaf curl China virus (TYLCCNV); and double-stranded DNA viruses such as cauliflower mosaic virus (CaMV). Of these, vectors derived from the RNA virus cucumber mosaic virus (CMV) are particularly preferred, such as the CMV-A1 vector.

[0028] The species of plants to which the present invention can be applied are not particularly limited, but typical examples include plants of the Poaceae, Fabaceae, Brassicaceae, Asteraceae, Solanaceae, Rosaceae, Cucurbitaceae, and Convolvulaceae families. Preferred plants include, for example, alfalfa, barley, kidney beans, canola, cowpeas, cotton, corn, clover, lotus, lentils, lupine, millet, oats, peas, peanuts, rice, rye, sweet clover, sunflower, sweet pea, soybean, sorghum, triticale, jicama, velvet bean, broad bean, wheat, wisteria, nut plants, Arabidopsis thaliana, bedweed, leek, snapdragon, honeywort, peanut, asparagus, scutellaria, oat, bamboo shoots, rapeseed, brome grass, bluebell, camellia, hemp, chili pepper, chickpea, chrysanthemum vulgare, chrysanthemum indicum, citrus, coffee tree, Job's tears, cucumber, Examples of suitable plants include pumpkin, larkspur, orchard grass, Datura stramonium, foxglove, dioscorea, oil palm, Zoysia japonica, fescue, strawberry, owl grass, soybean, sunflower, day lily, rubber tree, henbane, sweet potato, lettuce, lentil, lily, flax, ryegrass, lotus, tomato, marjoram, apple, mango, potato tree, alfalfa, African buttercup, tobacco, sainfoin, pelargonium, Japanese laurel, morning glory, Timothy grass, strawberry vine, cherry blossom, buttercup, radish, gooseberry, castor bean, brambleberry, sugarcane, salmenba, senecio, setaria, white mustard, eggplant, sorghum, lawn grass, cacao, sycamore, bellflower, and grapes.

[0029] Plant cells may be in any form, and may be unisolated cells present in a plant body, or cultured cells such as tissue cultures isolated from a plant body. In the case of cultured cells, they may be differentiated cells, dedifferentiated cells, or redifferentiated cells.

[0030] 3. Method for producing plants with desired traits By using the above-mentioned method for suppressing methylation of target DNA to suppress methylation of DNA involved in the expression of a desired trait in a plant, it is possible to produce a plant having the desired trait. Thus, in a second aspect of the present invention, there is provided a method for producing a plant having a desired trait, the method comprising using the above-mentioned method to suppress methylation of DNA involved in the expression of the desired trait in a plant.

[0031] [4. Method for producing plant-derived functional ingredients] Furthermore, by using the above-mentioned method for suppressing target DNA methylation, it is possible to easily and quickly produce a plant-derived functional component by suppressing methylation of DNA involved in the synthesis and accumulation of the plant-derived functional component. Therefore, in a third aspect of the present invention, there are provided a method for producing a plant-derived functional component, the method comprising: using the above-mentioned method to suppress methylation of DNA involved in the synthesis and accumulation of the plant-derived functional component, thereby accumulating the functional component in the plant cells, and then recovering the functional component from the plant cells; and an expression system for accumulating a plant-derived functional component, the expression system comprising: (A) a plant or plant cell that produces a scaffold RNA and an siRNA-AGO4 complex produced by transcription of DNA involved in the synthesis or accumulation of the plant-derived functional component in an RNA-directed DNA methylation system; and (B) a short dummy RNA containing a sequence complementary to the siRNA incorporated into the siRNA-AGO4 complex or a sequence complementary to at least a portion of the scaffold RNA.

[0032] The present invention will be described in more detail below with reference to examples. However, the present invention is not limited to the following examples and can be practiced with appropriate modifications. [Example]

[0033] [Experiment 1] Creation of short dummy RNA constructs The sequences (underlined) on the 35S promoter (SEQ ID NO: 1) that synthesize siRNAs homologous to the short dummy RNA constructs are shown in Figure 4. To clone the siRNA-expressing SD-51 (5'-TAAGGGAGGACGCACAATCCCCCTAT-3'; SEQ ID NO: 2) homologous to this sequence for use in a DNA methylation model based on the capture of siRNA-AGO4 complexes (Figure 2) and / or a DNA methylation model based on the blocking of scaffold RNA-AGO4 binding by short dummy RNAs (Figure 3), we synthesized oligonucleotides 35S(-)-sdRNA-(-51)-5St (5'-CGAGGCCTTAAGGGATGACGCACAATCCCACTA-3'; SEQ ID NO: 3) and 35S(-)-sdRNA-(-51)-3Ml (5'-CGCACGCGTATAGTGGGATTGTGCGTCATCCCTTA-3'; SEQ ID NO: 4) with StuI and MluI restriction sites at the 5' end, respectively, and converted them into double-stranded DNA by PCR. This was inserted into the cloning site (StuI and MluI restriction sites) of an infectious cDNA clone plasmid of a CMV-A1 vector in a standard manner.

[0034] [Experiment 2] Inoculation of short dummy RNA constructs (1) Short dummy RNA (SD-51) inoculation In this experiment, the benthamiana 208RED line, which we developed, was used as a material. The development and characteristics of 208RED are as follows. First, the benthamiana 16c line (see Non-Patent Document 4), which emits GFP fluorescence due to an introduced GFP gene, was infected with a CMV-A1 vector (see Non-Patent Document 5) incorporating a sequence homologous to the 35S promoter linked to the GFP gene. Infection with this CMV-A1 vector induced cytosine methylation via the RdDM pathway within the 35S promoter sequence, resulting in the induction of transcriptional gene silencing (TGS) in the GFP gene and the loss of GFP fluorescence. Individuals that maintained TGS of the GFP gene were selected in each generation from the self-pollinated progeny of this infected individual, and the line that stably maintained TGS in the third self-pollinated generation (S3) was used in this experiment as the 208RED line. When 208RED, in which GFP fluorescence had disappeared, were inoculated with a CMV-A1 vector containing a short dummy RNA (SD-51) construct (CMV-A1-SD-51), GFP fluorescence was restored in approximately 30% of the inoculated individuals (Figure 5). On the other hand, in 208RED that had not been inoculated with CMV-A1-SD-51, fluorescence did not return in any of the individuals tested (Figure 5). These results suggest that in individuals in which fluorescence was restored by infection with CMV-A1-SD-51, the TGS of the GFP gene was released by the short dummy RNA (SD-51).

[0035] (2) Progeny inoculated with short dummy RNA (SD-51) Seeds were collected from 208RED individuals (16c type) whose fluorescence was restored to the same level as that of 16c (the original GFP-expressing Benthamiana plant) by infection with CMV-A1-SD-51, and the next generation (S1) and the next generation (S2) were grown. GFP fluorescence was observed in each generation. In both generations, GFP fluorescence restoration was observed in the stem and gradually spread throughout the plant (Figure 6). The GFP fluorescence phenotype was classified into five groups: RED (no fluorescence), stem, petiole, and leaf, and 16c type (which showed GFP fluorescence at a level equivalent to that of 16c) (Figure 7). In the S1 and S2 individuals in which GFP fluorescence was restored, GFP fluorescence gradually returned with growth, and in S2, approximately 40% of the individuals showed GFP fluorescence at a level equivalent to that of 16c (Table 1).

[0036] [Table 1] (3) DNA methylation rate in the 35S promoter in the current and next generations after short dummy RNA (SD-51) inoculation DNA was extracted from leaves of 208RED plants and the current and subsequent generations of 208RED plants inoculated with CMV-A1-SD-51 using the Illustra DNA Extraction Kit Nucleon Phytopure (GE Healthcare). The extracted DNA was then subjected to bisulfite treatment using the EZ DNA Methylation-Lightning Kit (Zymo Research) to convert unmethylated cytosines to uracils. The 35S promoter region was amplified from the bisulfite-treated DNA using TaKaRa EpiTaq HS for bisulfite-treated DNA (TaKaRa). The PCR primers for detecting the plus strand were 35S-346F-bisuT (5'-ATTGAGAYTTTTYAAYAAAGGGTA-3'; SEQ ID NO: 5) and 35S+1A-bisuA (5'-CTCTCCAAATGAAATGAACTTC-3'; SEQ ID NO: 6). The primers used for PCR to detect the minus strand were 35S(-)-5-BS (5'-TTATATAGAGGAAGGGTYTTGYGAAG-3': SEQ ID NO: 7) and 35S(-)-3-BS (5'-CAATTRARACTTTTCAACAAAR-3': SEQ ID NO: 8). The resulting PCR product was ligated into pTAC1 vector using the Dyna Express TA PCR Cloning Kit (BioDynamics Laboratory). This was transformed into E. coli JM109 Competent Cells (TaKaRa), and the plasmid was extracted after growth. The extracted plasmid was sequenced according to standard methods. Based on the sequencing results, the methylation frequencies of cytosine in the 35S promoter region were compared for CG, CHG (H = A / C / T), and CHH sites. Cytosine demethylation was confirmed at all sites in the SD-51-inoculated plants (Table 2).

[0037] [Table 2]

Claims

1. 1. A method for suppressing target DNA methylation in a plant cell, comprising: The method includes a step of inhibiting binding of a scaffold RNA produced by transcription of the target DNA to an siRNA-AG04 complex in an RNA-directed DNA methylation mechanism; wherein the step of inhibiting the binding of the scaffold RNA to the siRNA-AG04 complex is achieved by introducing a short dummy RNA into the plant cell; the short dummy RNA comprises either i) a sequence complementary to the siRNA incorporated into the siRNA-AG04 complex and capturing the siRNA-AG04 complex, or ii) a sequence complementary to at least a portion of the scaffold RNA and blocking the binding of the scaffold RNA to the siRNA-AG04 complex through binding to the scaffold RNA (excluding sequences that eliminate the scaffold RNA), the length of the short dummy RNA is 20 bp to 50 bp, and The method, wherein the target DNA is a promoter that controls a gene that expresses a desired trait in a plant cell.

2. The method according to claim 1, wherein the gene that expresses the desired trait is a gene that encodes the amino acid sequence of an enzyme that controls the synthesis or accumulation of a plant-derived functional component.

3. 3. The method according to claim 1, wherein the short dummy RNA is introduced into plant cells by a plant virus vector method, agroinfiltration method, or particle gun method.

4. The method according to any one of claims 1 to 3, wherein the plant cells are non-isolated cells of a plant body.

5. The method according to any one of claims 1 to 3, wherein the plant cells are cultured cells.

6. A method for producing a plant having a desired trait, the method comprising suppressing methylation of DNA involved in expression of the desired trait in a plant using the method according to any one of claims 1 to 5.

7. A method for producing a plant-derived functional ingredient, the method comprising: using the method according to any one of claims 1 to 5 to suppress methylation of DNA involved in the synthesis or accumulation of the plant-derived functional ingredient, thereby accumulating the functional ingredient in the plant cells; and recovering the functional ingredient from the plant cells.

8. An expression system for accumulating a plant-derived functional component, the expression system comprising: (A) a plant body or plant cell that produces a scaffold RNA and an siRNA-AG04 complex produced by transcription of a promoter that controls a gene involved in the synthesis or accumulation of the plant-derived functional component in an RNA-directed DNA methylation mechanism; and (B) i) a sequence complementary to the siRNA incorporated into the siRNA-AG04 complex, and a sequence that captures the siRNA-AG04 complex; or ii) a sequence complementary to at least a portion of the scaffold RNA, and a sequence that blocks the binding of the scaffold RNA to the siRNA-AG04 complex through binding to the scaffold RNA (excluding those that erase the scaffold RNA), wherein the length of the short dummy RNA is 20 bp to 50 bp; and An expression system in which the short dummy RNA inhibits the binding of the scaffold RNA to the siRNA-AG04 complex, thereby suppressing methylation of the promoter, thereby causing the functional component to accumulate in the plant body or plant cells.

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