Research Topic

Transitive and Systemic RNA Silencing in Plants

About this Research Topic

RNA silencing, including the action of micro RNAs (miRNAs), plays a major role in natural plant gene regulation and is associated with important biological processes such as plant reproduction, plant development, epigenetics, and stress responses. The sequence specificity of RNA silencing also spurred the development of its use in plant biotechnology. With the discovery of CRISPR/Cas technologies and their applicability to plant systems, research on biotechnological applications of RNA-mediated gene silencing in plants has receded into the background. However, the potential of RNA interference (RNAi) applications in plants are still far from being fully exploited. RNAi may serve to combat invading pests and pathogens and remains a useful tool to elucidate functions of plant genes. One of the advantages of RNAi over CRISPR/Cas9 is that silencing triggers (e.g. double-stranded RNA, dsRNA) can be exogenously applied to cover the entire plant, for example, to protect against fungi and insects. However, for virus defense and elucidation of gene functions, RNA silencing needs to be activated in the plant cell itself and should become systemic. Thus, transgene and virus-induced silencing technologies are frequently used. One other major advantage of RNAi is that unlike CRISPR, RNAi is dominant allowing gene suppression even in hemizygous states or in polyploid species with only one copy of a silencing trigger per multiple genomes.

To fully exploit RNAi technologies in plants, basic research is still needed to further understand the fundamental processes of RNAi and miRNA-mediated gene regulation pathways. For example, by using transgenic systems, the initiation of RNAi was demonstrated to efficiently trigger transitive and systemic silencing. Transitive silencing describes a process in which secondary (2°) small interfering RNAs (siRNAs) are produced. 2° siRNAs also map to regions up- and downstream of the sequence that was targeted by the primary RNAi trigger. Systemic silencing is suggested to be induced by a silencing signal that is produced in cells where silencing was initiated. By movement through the vascular system the signal re-initiates silencing in the distal parts of the plant. Since silencing is sequence-specific, it is assumed that the silencing signal consists of RNA but the nature of the mobile signal and its interactions are still unclear.

Although transitivity has been well documented to occur when transgenes were targeted, our understanding of the mechanistic details is still fragmentary. In general, 22-nt siRNAs or 22-nt miRNAs act much more readily as triggers of transitive silencing than 21-nt siRNA/miRNAs, but the molecular mechanisms underlying this phenomenon remain poorly understood. Systemic silencing and most probably also transitivity involve nuclear processes but how these nuclear steps feed into both pathways is still elusive. Transitive and systemic silencing both are dependent on the activity of RNA-directed RNA polymerase 6 (RDR6). RDR6 is assumed to transcribe aberrant RNA (abRNA) to produce dsRNA. AbRNA is suggested to consist of a “defective” mRNA that lacks a 5’ cap and/or a poly(A)-tail. However, it is not clear where abRNA derives from and where it acts, in the cytoplasm and/or the nucleus. In this context, it is remarkable that with a few exceptions, targeting endogenous genes is not associated with transitive and systemic silencing. One may speculate that endogenous gene expression is not or less associated with the accumulation of abRNA than transgene expression. In any case, the restrictiveness of endogenous silencing clearly limits applications that aim to combat viruses (RNAi-mediated immunization), to develop RNAi-based herbicides and to illuminate endogenous gene functions.

We welcome Original Research and Review articles dealing with detailed analysis of transitive and systemic RNA silencing in plants. Manuscripts should address, but not be restricted to, the following topics:
• How typical endogenous genes protect themselves against transitive and systemic silencing? Why some endogenous sequences are susceptible to transitive silencing and what do these sequences have in common?
• What is the nature of mobile silencing signals and which enzymes are involved in their production? How and where do mobile silencing signals re-initiate silencing?
• In which compartments of the cell are silencing-competent primary and 2° siRNAs generated? In this context, the analysis of the nature of abRNA and the significance of its localization (cytoplasm or nucleus) would be of specific interest.
• In which compartments of the cell do silencing components reside, and what would be the functional significance for this localization?
• Apart from their involvement in trans-acting siRNA generation, do miRNAs trigger transitivity of other endogenous transcripts (e.g. stress-responsive genes)?


Keywords: RNA silencing, Transitive and systemic silencing, Mobile silencing sequences, Localization


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

RNA silencing, including the action of micro RNAs (miRNAs), plays a major role in natural plant gene regulation and is associated with important biological processes such as plant reproduction, plant development, epigenetics, and stress responses. The sequence specificity of RNA silencing also spurred the development of its use in plant biotechnology. With the discovery of CRISPR/Cas technologies and their applicability to plant systems, research on biotechnological applications of RNA-mediated gene silencing in plants has receded into the background. However, the potential of RNA interference (RNAi) applications in plants are still far from being fully exploited. RNAi may serve to combat invading pests and pathogens and remains a useful tool to elucidate functions of plant genes. One of the advantages of RNAi over CRISPR/Cas9 is that silencing triggers (e.g. double-stranded RNA, dsRNA) can be exogenously applied to cover the entire plant, for example, to protect against fungi and insects. However, for virus defense and elucidation of gene functions, RNA silencing needs to be activated in the plant cell itself and should become systemic. Thus, transgene and virus-induced silencing technologies are frequently used. One other major advantage of RNAi is that unlike CRISPR, RNAi is dominant allowing gene suppression even in hemizygous states or in polyploid species with only one copy of a silencing trigger per multiple genomes.

To fully exploit RNAi technologies in plants, basic research is still needed to further understand the fundamental processes of RNAi and miRNA-mediated gene regulation pathways. For example, by using transgenic systems, the initiation of RNAi was demonstrated to efficiently trigger transitive and systemic silencing. Transitive silencing describes a process in which secondary (2°) small interfering RNAs (siRNAs) are produced. 2° siRNAs also map to regions up- and downstream of the sequence that was targeted by the primary RNAi trigger. Systemic silencing is suggested to be induced by a silencing signal that is produced in cells where silencing was initiated. By movement through the vascular system the signal re-initiates silencing in the distal parts of the plant. Since silencing is sequence-specific, it is assumed that the silencing signal consists of RNA but the nature of the mobile signal and its interactions are still unclear.

Although transitivity has been well documented to occur when transgenes were targeted, our understanding of the mechanistic details is still fragmentary. In general, 22-nt siRNAs or 22-nt miRNAs act much more readily as triggers of transitive silencing than 21-nt siRNA/miRNAs, but the molecular mechanisms underlying this phenomenon remain poorly understood. Systemic silencing and most probably also transitivity involve nuclear processes but how these nuclear steps feed into both pathways is still elusive. Transitive and systemic silencing both are dependent on the activity of RNA-directed RNA polymerase 6 (RDR6). RDR6 is assumed to transcribe aberrant RNA (abRNA) to produce dsRNA. AbRNA is suggested to consist of a “defective” mRNA that lacks a 5’ cap and/or a poly(A)-tail. However, it is not clear where abRNA derives from and where it acts, in the cytoplasm and/or the nucleus. In this context, it is remarkable that with a few exceptions, targeting endogenous genes is not associated with transitive and systemic silencing. One may speculate that endogenous gene expression is not or less associated with the accumulation of abRNA than transgene expression. In any case, the restrictiveness of endogenous silencing clearly limits applications that aim to combat viruses (RNAi-mediated immunization), to develop RNAi-based herbicides and to illuminate endogenous gene functions.

We welcome Original Research and Review articles dealing with detailed analysis of transitive and systemic RNA silencing in plants. Manuscripts should address, but not be restricted to, the following topics:
• How typical endogenous genes protect themselves against transitive and systemic silencing? Why some endogenous sequences are susceptible to transitive silencing and what do these sequences have in common?
• What is the nature of mobile silencing signals and which enzymes are involved in their production? How and where do mobile silencing signals re-initiate silencing?
• In which compartments of the cell are silencing-competent primary and 2° siRNAs generated? In this context, the analysis of the nature of abRNA and the significance of its localization (cytoplasm or nucleus) would be of specific interest.
• In which compartments of the cell do silencing components reside, and what would be the functional significance for this localization?
• Apart from their involvement in trans-acting siRNA generation, do miRNAs trigger transitivity of other endogenous transcripts (e.g. stress-responsive genes)?


Keywords: RNA silencing, Transitive and systemic silencing, Mobile silencing sequences, Localization


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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30 June 2020 Manuscript

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Manuscripts can be submitted to this Research Topic via the following journals:

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Submission Deadlines

30 June 2020 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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