Epigenetic Modifications: An Unexplored Facet of Exogenous RNA Application in Plants

Dalakouras, Athanasios; Papadopoulou, Kalliope Κ.

doi:10.3390/plants9060673

Cited by 24 publications

(15 citation statements)

References 81 publications

(94 reference statements)

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“…In addition, it warrants more careful design and application of novel dsRNA sprays in plant protection ( 60 , 61 ) to avoid ‘off-target’ effects. Processing of exogenously applied antifungal or antiviral dsRNA in planta might result in sRNAs with partial complementarity to promoter sequences, which could induce heritable RdDM and consequently influence the expression of genes controlling agronomic traits ( 62 ).…”

Section: Discussionmentioning

confidence: 99%

Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs

Fei

Nyikó

Molnár

2021

Nucleic Acids Research

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Short non-coding RNA molecules (sRNAs) play a fundamental role in gene regulation and development in higher organisms. They act as molecular postcodes and guide AGO proteins to target nucleic acids. In plants, sRNA-targeted mRNAs are degraded, reducing gene expression. In contrast, sRNA-targeted DNA sequences undergo cytosine methylation referred to as RNA-directed DNA methylation (RdDM). Cytosine methylation can suppress transcription, thus sRNAs are potent regulators of gene expression. sRNA-mediated RdDM is involved in genome stability through transposon silencing, mobile signalling for epigenetic gene control and hybrid vigour. Since cytosine methylation can be passed on to subsequent generations, RdDM contributes to transgenerational inheritance of the epigenome. Using a novel approach, which can differentiate between primary (inducer) and secondary (amplified) sRNAs, we show that initiation of heritable RdDM does not require complete sequence complementarity between the sRNAs and their nuclear target sequences. sRNAs with up to four regularly interspaced mismatches are potent inducers of RdDM, however, the number and disruptive nature of nucleotide polymorphisms negatively correlate with their efficacy. Our findings contribute to understanding how sRNA can directly shape the epigenome and may be used in designing the next generation of RNA silencing constructs.

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Section: Discussionmentioning

confidence: 99%

Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs

Fei

Nyikó

Molnár

2021

Nucleic Acids Research

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“…In addition, SIGS has been shown to be more efficient under lab conditions compared to the HIGS strategy ( Koch et al, 2016 ). Nowadays, there is mounting evidence suggesting that topically-applied dsRNAs molecules are effective in silencing target genes aiming at plant resistance against a broad range of biotic factors ( Dubrovina and Kiselev, 2019 ; Dalakouras et al, 2020 ; Das and Sherif, 2020 ).…”

Section: An Overview Of Plant Breeding: From Ancient Times To Genetic...mentioning

confidence: 99%

CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture

Távora

Diniz

Rêgo-Machado

et al. 2022

Front. Bioeng. Biotechnol.

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Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated gene (Cas) system and RNA interference (RNAi)-based non-transgenic approaches are powerful technologies capable of revolutionizing plant research and breeding. In recent years, the use of these modern technologies has been explored in various sectors of agriculture, introducing or improving important agronomic traits in plant crops, such as increased yield, nutritional quality, abiotic- and, mostly, biotic-stress resistance. However, the limitations of each technique, public perception, and regulatory aspects are hindering its wide adoption for the development of new crop varieties or products. In an attempt to reverse these mishaps, scientists have been researching alternatives to increase the specificity, uptake, and stability of the CRISPR and RNAi system components in the target organism, as well as to reduce the chance of toxicity in nontarget organisms to minimize environmental risk, health problems, and regulatory issues. In this review, we discuss several aspects related to risk assessment, toxicity, and advances in the use of CRISPR/Cas and topical RNAi-based technologies in crop management and breeding. The present study also highlights the advantages and possible drawbacks of each technology, provides a brief overview of how to circumvent the off-target occurrence, the strategies to increase on-target specificity, the harm/benefits of association with nanotechnology, the public perception of the available techniques, worldwide regulatory frameworks regarding topical RNAi and CRISPR technologies, and, lastly, presents successful case studies of biotechnological solutions derived from both technologies, raising potential challenges to reach the market and being social and environmentally safe.

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“…Indeed, AGO4 is not required in IR-RdDM, at least not in Arabidopsis thaliana [ 41 ]. Collectively, these data suggest that RdDM is triggered not by siRNAs, but by long dsRNAs (>50 bp) [ 42 , 43 , 44 , 45 ]. According to our model, long dsRNAs appear to define the DNA region that will be methylated in a ruler-like fashion (Step 1, Figure 2 ).…”

Section: Rna-directed Dna Methylationmentioning

confidence: 99%

Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

Wassenegger

Dalakouras

2021

Cells

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Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.

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Epigenetic Modifications: An Unexplored Facet of Exogenous RNA Application in Plants

Cited by 24 publications

References 81 publications

Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs

Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs

CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture

Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

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