Virus-Mediated Targeted DNA Methylation Illuminates the Dynamics of Methylation in an Endogenous Plant Gene

Atsumi, Go; Matsuo, Kazuyuki; Fukuzawa, Noriho; Matsumura, Takeshi

doi:10.3390/ijms22084125

Cited by 3 publications

(3 citation statements)

References 45 publications

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“…Silencing constructs like RNA interference (RNAi) ( Přibylová et al., 2019 ; Zicola et al., 2019 ), artificial microRNAs (amiRNA), or virus-induced gene silencing (VIGS) ( Bond and Baulcombe, 2015 ; Atsumi et al., 2021 ) can weaken or temporary inactivate DNA methylation factors. Such mutants, developed for multiple crops, offer numerous advantages, including variable silencing strengths and simultaneous targeting of multiple homologs.…”

Section: Methodologies For Measuring Dna Methylationmentioning

confidence: 99%

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Agius

Kapazoglou²,

Avramidou³

et al. 2023

Front. Plant Sci.

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Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.

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Section: Methodologies For Measuring Dna Methylationmentioning

confidence: 99%

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Agius

Kapazoglou²,

Avramidou³

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…Many viruses dysregulate DNA replication and transcription and evade the cell‘s innate immune response. Viral infections use epigenetic pathways, more specifically CpG methylation that is responsible for enterocytosis and syncytium development [72–74] . Also, the biology of epigenetic mechanisms including histone acetylases, deacetylases, methylases, and DNA methylases must be further explored for the study and control of viral pathogenesis [75–78] .…”

Section: Treatment For Viral Infectionmentioning

confidence: 99%

“…Viral infections use epigenetic pathways, more specifically CpG methylation that is responsible for enterocytosis and syncytium development. [72][73][74] Also, the biology of epigenetic mechanisms including histone acetylases, deacetylases, meth-ylases, and DNA methylases must be further explored for the study and control of viral pathogenesis. [75][76][77][78] This area is to be more studied to develop pyrimidines and its mimics as epigenetic drugs for viral infections.…”

Section: Epigenetic Pathways As Target For Possible Viral Treatmentsmentioning

confidence: 99%

Synthesis and Antiviral Efficacy of Pyrimidine Analogs Targeting Viral Pathways

Basha¹,

Chandana²

2023

ChemistrySelect

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To date, viruses are known to cause chronic to acute pathogenesis. Nevertheless, antiviral drugs have been known for their medicinal applications for the last few decades to treat infections caused by these pathogens. Despite advancements in the field of vaccination and antiviral drugs, there is a need for a molecule that can eradicate or control viral infection without getting resistance from pathogens will be a real challenge. This review covers possible ways to treat viral infections with pyrimidine and its mimics compared to known antiviral drugs. A comprehensive study of the report accomplished synthetic routes of pyrimidine analogs and their target‐specific antiviral potential. The present review article covers literature from 2018 to 2022.

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In-Plant Persistence and Systemic Transport of Nicotiana benthamiana Retrozyme RNA

Lezzhov

Tolstyko

Atabekova

et al. 2022

IJMS

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Retrozymes are nonautonomous retrotransposons with hammerhead ribozymes in their long terminal repeats (LTRs). Retrozyme transcripts can be self-cleaved by the LTR ribozyme, circularized, and can undergo RNA-to-RNA replication. Here, we demonstrate that the Nicotiana benthamiana genome contains hundreds of retrozyme loci, of which nine represent full-length retrozymes. The LTR contains a promoter directing retrozyme transcription. Although retrozyme RNA is easily detected in plants, the LTR region is heavily methylated, pointing to its transcriptional silencing, which can be mediated by 24 nucleotide-long retrozyme-specific RNAs identified in N. benthamiana. A transcriptome analysis revealed that half of the retrozyme-specific RNAs in plant leaves have no exact matches to genomic retrozyme loci, containing up to 13% mismatches with the closest genomic sequences, and could arise as a result of many rounds of RNA-to-RNA replication leading to error accumulation. Using a cloned retrozyme copy, we show that retrozyme RNA is capable of replication and systemic transport in plants. The presented data suggest that retrozyme loci in the N. benthamiana genome are transcriptionally inactive, and that circular retrozyme RNA can persist in cells due to its RNA-to-RNA replication and be transported systemically, emphasizing functional and, possibly, evolutionary links of retrozymes to viroids—noncoding circular RNAs that infect plants.

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Virus-Mediated Targeted DNA Methylation Illuminates the Dynamics of Methylation in an Endogenous Plant Gene

Cited by 3 publications

References 45 publications

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Synthesis and Antiviral Efficacy of Pyrimidine Analogs Targeting Viral Pathways

In-Plant Persistence and Systemic Transport of Nicotiana benthamiana Retrozyme RNA

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