RNA silencing pathways in plant development and defense

Kryovrysanaki, Nikoleta; James, Anthony P.; Tselika, Martha; Bardani, Eirini; Kalantidis, Kriton

doi:10.1387/ijdb.210189kk

Cited by 12 publications

(20 citation statements)

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“…Plants have developed the function of using miRNA to regulate gene transcription in response to environmental factors and stress conditions such as temperature, light, water, and nutrient deficiency (Kryovrysanaki et al, 2022). Among the screened differentially expressed miRNAs in this study, miR398 played an important role in the regulatory network that responds to drought stress in C. oleifera.…”

Section: Mirna-mrna Network Under Drought Stress In Camellia Oleiferamentioning

confidence: 96%

Integration of mRNA and miRNA analysis reveals the differentially regulatory network in two different Camellia oleifera cultivars under drought stress

He¹,

Liu²,

Zhang³

et al. 2022

Front. Plant Sci.

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Camellia oleifera Abel. (C. oleifera) is an edible oil tree species that provide an important guarantee for targeted poverty alleviation strategy in China. Severe difficulties in irrigation leading to drought stress have become a major obstacle to the development of the C. oleifera planting industry. Breeding of drought-tolerant cultivars is the main idea for solving the problem of water shortage stress in C. oleifera cultivation. The photosynthetic physiology traits of C. oleifera cultivars ‘Xianglin No.1’ and ‘Hengdong No.2’ were affected by drought stress to different degrees, which demonstrated that the two cultivars suffered different degrees of damage. In the present study, we applied mRNA-seq and miRNA-seq to analyze the difference in molecular responses between drought stress and control, drought-tolerant and -sensitive cultivars, at mRNA and miRNA levels. The differentially expressed genes (DEGs) involved in photosynthesis-related, porphyrin, and chlorophyll metabolism, circadian rhythm system, and plant hormone signal transduction pathways were identified that might be candidates for drought stress tolerance genes. Subsequently, the miRNA-mRNA regulatory networks connected the differentially expressed miRNAs (DEMs) to their predicted target genes were established. miR398 and miR408-3p in C. oleifera showed that associated with the response to drought stress by negatively regulating genes encoding Downy Mildew Resistance 6 (DMR6) and Enhanced Disease Resistance 2 (EDR2), respectively, which might further improve drought tolerance via crosstalk between different stress-responsive pathways. The quantitation results of miRNA and mRNA were validated by quantitative real-time PCR (qRT-PCR). In summary, the integrated mRNA-seq and miRNA-seq analysis deepen our understanding of the regulatory network response to drought stress and variety-specific responses improving drought tolerance in C. oleifera.

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Section: Mirna-mrna Network Under Drought Stress In Camellia Oleiferamentioning

confidence: 96%

Integration of mRNA and miRNA analysis reveals the differentially regulatory network in two different Camellia oleifera cultivars under drought stress

He¹,

Liu²,

Zhang³

et al. 2022

Front. Plant Sci.

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“…DNA methylation is an epigenetic mechanism that regulates gene expression, imprinting and genome stability. In plants DNA methylation occurs at position 5 ( 5m C) of CG, CHG or CHH (H represents A, T or C) context (Erdmann and Picard, 2020;Gallego-Bartolome, 2020;Kryovrysanaki et al, 2022). CG is the predominant site for methylation, followed by CHG and CHH.…”

Section: Introductionmentioning

confidence: 99%

“…These siRNAs bind to non-coding RNAs (ncRNAs) produced by RNA POLYMERASE V (Pol V) by complementarity. Once the complex AGO4/6-siRNA-ncRNA-PolV is formed, the DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) catalyzes de novo DNA methylation (Zhang et al, 2018;Erdmann and Picard, 2020;Gallego-Bartolome, 2020;Kryovrysanaki et al, 2022). The second pathway is the non-canonical and is triggered by siRNAs produced by dsRNAs of different origins (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…Both biotic and abiotic stresses can interfere with DNA methylation mechanisms and mostly (but not only) influence gene expression (Wang et al, 2011;Wang et al, 2019;Erdmann and Picard, 2020;Liu and He, 2020;Kryovrysanaki et al, 2022;Lucibelli et al, 2022). Especially during infections, DNA methylation has been found to control replication and infectivity of various viruses.…”

Section: Introductionmentioning

confidence: 99%

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PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation

Tselika,

Belmezos,

Kallemi

et al. 2023

Front. Plant Sci.

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Viroids are small circular RNAs infecting a wide range of plants. They do not code for any protein or peptide and therefore rely on their structure for their biological cycle. Observed phenotypes of viroid infected plants are thought to occur through changes at the transcriptional/translational level of the host. A mechanism involved in such changes is RNA-directed DNA methylation (RdDM). Till today, there are contradictory works about viroids interference of RdDM. In this study, we investigated the epigenetic effect of viroid infection in Nicotiana benthamiana plants. Using potato spindle tuber viroid (PSTVd) as the triggering pathogen and via bioinformatic analyses, we identified endogenous gene promoters and transposable elements targeted by 24 nt host siRNAs that differentially accumulated in PSTVd-infected and healthy plants. The methylation status of these targets was evaluated following digestion with methylation-sensitive restriction enzymes coupled with PCR amplification, and bisulfite sequencing. In addition, we used Methylation Sensitive Amplification Polymorphism (MSAP) followed by sequencing (MSAP-seq) to study genomic DNA methylation of 5-methylcytosine (5mC) in CG sites upon viroid infection. In this study we identified a limited number of target loci differentially methylated upon PSTVd infection. These results enhance our understanding of the epigenetic host changes as a result of pospiviroid infection.

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“…PTGS involves sequence-specific degradation of target RNAs triggered by complementary 21-22-nt siRNAs, which are produced in Arabidopsis by DICER-LIKE4 (DCL4) and DCL2, respectively. TGS is associated with DNA methylation of promoter segments guided by DCL3dependent 24-nt siRNAs in a process referred to as RNA-directed DNA methylation (RdDM) (Uslu and Wassenegger, 2020;El-Sappah et al, 2021;Kryovrysanaki et al, 2022) In Arabidopsis, factors required for PTGS and TGS, such as DCL enzymes and ARGONAUTE (AGO) silencing effector proteins, have been detected in CBs by immunofluorescence microscopy (Li et al, 2006;Pontes and Pikaard, 2008;Pontes et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

AGFPsplicing reporter in acoilinmutant background reveals links between alternative splicing, siRNAs and coilin function inArabidopsis thaliana

Kanno

Chiou

et al. 2022

Preprint

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Coilin is a scaffold protein essential for the structure of Cajal bodies, which are nucleolar-associated, nonmembranous organelles that coordinate the assembly of nuclear ribonucleoproteins including spliceosomal snRNPs. To learn more about coilin functions and pathways in plants, we conducted a genetic suppressor screen using a coilin mutant in Arabidopsis thaliana and performed an immunoprecipitation-mass spectrometry analysis on coilin protein. The coi1 mutations modify alternative splicing of a GFP reporter gene, resulting in a hyper-GFP phenotype in young coi1 seedlings relative to the intermediate wild-type level. As shown here, this hyper-GFP phenotype is extinguished in older coi1 seedlings by posttranscriptional gene silencing triggered by siRNAs derived from aberrant splice variants of GFP pre-mRNA. In the coi1 suppressor screen, we identified suppressor mutations in WRAP53, a putative coilin-interacting protein; SMU2, a predicted splicing factor; and ZC3HC1, an incompletely characterized zinc finger protein. These suppressor mutations return the hyper-GFP fluorescence of young coi1 seedlings to the intermediate wild-type level. Additionally, zc3hc1 coi1 mutants display more extensive GFP silencing and elevated levels of GFP siRNAs, suggesting the involvement of wild-type ZC3HC1 in siRNA biogenesis or stability. The immunoprecipitation-mass spectrometry analysis reinforced the roles of coilin in pre-mRNA splicing, nucleolar chromatin structure, and rRNA processing. The participation of coilin in these processes, at least some of which incorporate small RNAs, supports the hypothesis that coilin acts as a chaperone for small noncoding RNAs. Our study demonstrates the usefulness of the GFP splicing reporter for investigating alternative splicing, ribosome biogenesis, and siRNA-mediated silencing in the context of coilin function.

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RNA silencing pathways in plant development and defense

Cited by 12 publications

References 0 publications

Integration of mRNA and miRNA analysis reveals the differentially regulatory network in two different Camellia oleifera cultivars under drought stress

Integration of mRNA and miRNA analysis reveals the differentially regulatory network in two different Camellia oleifera cultivars under drought stress

PSTVd infection in Nicotiana benthamiana plants has a minor yet detectable effect on CG methylation

AGFPsplicing reporter in acoilinmutant background reveals links between alternative splicing, siRNAs and coilin function inArabidopsis thaliana

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