Kovalchuk, Igor

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Browsing Kovalchuk, Igor by Subject "Arabidopsis thaliana"

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    Genomic and epigenomic changes in the progeny of cold-stressed Arabidopsis thaliana plants
    (MDPI, 2024) Rahman, Ashif; Yadav, Narendra Singh; Byeon, Boseon; Ilnytskyy, Yaroslav; Kovalchuk, Igor
    Plants are continuously exposed to various environmental stresses. Because they can not escape stress, they have to develop mechanisms of remembering stress exposures somatically and passing it to the progeny. We studied the Arabidopsis thaliana ecotype Columbia plants exposed to cold stress for 25 continuous generations. Our study revealed that multigenerational exposure to cold stress resulted in the changes in the genome and epigenome (DNA methylation) across generations. Main changes in the progeny were due to the high frequency of genetic mutations rather than epigenetic changes; the difference was primarily in single nucleotide substitutions and deletions. The progeny of cold-stressed plants exhibited the higher rate of missense non-synonymous mutations as compared to the progeny of control plants. At the same time, epigenetic changes were more common in the CHG (C = cytosine, H = cytosine, adenine or thymine, G = guanine) and CHH contexts and favored hypomethylation. There was an increase in the frequency of C to T (thymine) transitions at the CHH positions in the progeny of cold stressed plants; because this type of mutations is often due to the deamination of the methylated cytosines, it can be hypothesized that environment-induced changes in methylation contribute to mutagenesis and may be to microevolution processes and that RNA-dependent DNA methylation plays a crucial role. Our work supports the existence of heritable stress response in plants and demonstrates that genetic changes prevail.
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    Pattern recognition on read positioning in next generation sequencing
    (Public Library of Science, 2016) Byeon, Boseon; Kovalchuk, Igor
    The usefulness and the utility of the next generation sequencing (NGS) technology are based on the assumption that the DNA or cDNA cleavage required to generate short sequence reads is random. Several previous reports suggest the existence of sequencing bias of NGS reads. To address this question in greater detail, we analyze NGS data from four organisms with different GC content, Plasmodium falciparum (19.39%), Arabidopsis thaliana (36.03%), Homo sapiens (40.91%) and Streptomyces coelicolor (72.00%). Using machine learning techniques, we recognize the pattern that the NGS read start is positioned in the local region where the nucleotide distribution is dissimilar from the global nucleotide distribution. We also demonstrate that the mono-nucleotide distribution underestimates sequencing bias, and the recognized pattern is explained largely by the distribution of multinucleotides (di-, tri-, and tetra- nucleotides) rather than mono-nucleotides. This implies that the correction of sequencing bias needs to be performed on the basis of the multi-nucleotide distribution. Providing companion software to quantify the effect of the recognized pattern on read positioning, we exemplify that the bias correction based on the mono-nucleotide distribution may not be sufficient to clean sequencing bias.
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    The progeny of Arabidopsis thaliana plants exposed to salt exhibit changes in DNA methylation, histone modifications and gene expression
    (Public Library of Science, 2012) Bilichak, Andriy; Ilnytskyy, Yaroslav; Hollunder, Jens; Kovalchuk, Igor
    Plants are able to acclimate to new growth conditions on a relatively short time-scale. Recently, we showed that the progeny of plants exposed to various abiotic stresses exhibited changes in genome stability, methylation patterns and stress tolerance. Here, we performed a more detailed analysis of methylation patterns in the progeny of Arabidopsis thaliana (Arabidopsis) plants exposed to 25 and 75 mM sodium chloride. We found that the majority of gene promoters exhibiting changes in methylation were hypermethylated, and this group was overrepresented by regulators of the chromatin structure. The analysis of DNA methylation at gene bodies showed that hypermethylation in the progeny of stressed plants was primarily due to changes in the 59 and 39 ends as well as in exons rather than introns. All but one hypermethylated gene tested had lower gene expression. The analysis of histone modifications in the promoters and coding sequences showed that hypermethylation and lower gene expression correlated with the enrichment of H3K9me2 and depletion of H3K9ac histones. Thus, our work demonstrated a high degree of correlation between changes in DNA methylation, histone modifications and gene expression in the progeny of salt-stressed plants.
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    A systemic increase in the recombination frequency upon local infection of Arabidopsis thaliana plants with oilseed rape mosaic virus depends on plant age, the initial inoculum concentration and the time for virus replication
    (Frontiers Media, 2013) Yao, Youli; Kathiria, Palak; Kovalchuk, Igor
    In the past, we showed that loca linfection of tobacco leaves with either tobacco mosaic virus or oilseed rape mosaic virus (ORMV) resulted in a systemic increase in the homologous recombination frequency (HRF). Later on, we showed that a similar phenomenon occurs in Arabidopsis thaliana plant sinfected with ORMV. Here, we tested whether the time of removing the infected leaves as well as viral titer have any effect on the degree of changes in HRF in systemic tissues. An increase in HRF in systemic non-infected tissues was more pronounced when the infected leaves were detached from the infected plants at 60–96 h post-infection, rather than at earlier time. Next, we found that exposure to higher concentrations of inoculum was much more efficient in triggering an increase in HRF than exposure to lower concentrations. Finally, we showed that older plants exhibited a higher increase in HRF than younger plants. We found that an increase in genome instability in systemic tissues of locally infected plants depends on plant age, the concentration of initial in oculums and the time of viral replication.
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    Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of dicer-like proteins
    (Public Library of Science, 2010) Boyko, Alexander; Blevins, Todd; Yao, Youli; Golubov, Andrey; Bilichak, Andriy; Ilnytskyy, Yaroslav; Hollunder, Jens; Meins, Frederick; Kovalchuk, Igor
    Epigenetic states and certain environmental responses in mammals and seed plants can persist in the next sexual generation. These transgenerational effects have potential adaptative significance as well as medical and agronomic ramifications. Recent evidence suggests that some abiotic and biotic stress responses of plants are transgenerational. For example, viral infection of tobacco plants and exposure of Arabidopsis thaliana plants to UVC and flagellin can induce transgenerational increases in homologous recombination frequency (HRF). Here we show that exposure of Arabidopsis plants to stresses, including salt, UVC, cold, heat and flood, resulted in a higher HRF, increased global genome methylation, and higher tolerance to stress in the untreated progeny. This transgenerational effect did not, however, persist in successive generations. Treatment of the progeny of stressed plants with 5-azacytidine was shown to decrease global genomic methylation and enhance stress tolerance. Dicer-like (DCL) 2 and DCL3 encode Dicer activities important for small RNAdependent gene silencing. Stress-induced HRF and DNA methylation were impaired in dcl2 and dcl3 deficiency mutants, while in dcl2 mutants, only stress-induced stress tolerance was impaired. Our results are consistent with the hypothesis that stress-induced transgenerational responses in Arabidopsis depend on altered DNA methylation and smRNA silencing pathways.
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    Transgenerational adaptation to heavy metal salts in Arabidopsis
    (Frontiers Media, 2011) Rahavi, Mohammad Reza; Migicovsky, Zoë; Titov, Viktor; Kovalchuk, Igor
    Exposure to abiotic and biotic stress results in changes in plant physiology and triggers genomic instability. Recent reports suggest that the progeny of stressed plants also exhibit changes in genome stability, stress tolerance, and methylation. Here we analyzed whether exposure to Ni2+, Cd2+, and Cu2+ salts leads to transgenerational changes in homologous recombination frequency and stress tolerance. We found that the immediate progeny of stressed plants exhibited an increased rate of recombination. However, when the progeny of stressed plants was propagated without stress, recombination reverted to normal levels. Exposure of plants to heavy metals for five consecutive generations (S1–S5) resulted in recombination frequency being maintained at a high level. Skipping stress following two to three generations of propagation with 50mM Ni2+ or Cd2+ did not decrease the recombination frequency, suggesting plant acclimation to upregulated recombination. Analysis of the progeny of plants exposed to Cu2+ and Ni2+ indicated higher stress tolerance to the heavy metal parental plants were exposed to. Tolerance was higher in plants propagated with stress for three to five generations, which resulted in longer roots than plants propagated on heavy metals for only one to two generations.Tolerancewas also more prominent upon exposure to a higher concentration of salts.The progeny of stressed plants were also more tolerant to NaCl and methyl methane sulfonate.
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    Transgenic plants as sensors of environmental pollution genotoxicity
    (M D P I A G, 2008) Kovalchuk, Igor; Kovalchuk, Olga
    Rapid technological development is inevitably associated with many environmental problems which primarily include pollution of soil, water and air. In many cases, the presence of contamination is difficult to assess. It is even more difficult to evaluate its potential danger to the environment and humans. Despite the existence of several whole organism-based and cell-based models of sensing pollution and evaluation of toxicity and mutagenicity, there is no ideal system that allows one to make a quick and cheap assessment. In this respect, transgenic organisms that can be intentionally altered to be more sensitive to particular pollutants are especially promising. Transgenic plants represent an ideal system, since they can be grown at the site of pollution or potentially dangerous sites. Plants are ethically more acceptable and esthetically more appealing than animals as sensors of environmental pollution. In this review, we will discuss various transgenic plant-based models that have been successfully used for biomonitoring genotoxic pollutants. We will also discuss the benefits and potential drawbacks of these systems and describe some novel ideas for the future generation of efficient transgenic phytosensors.