Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation

Khan, Asif Ali; Yadav, Narendra Singh; Morgenstern, Yaakov; Zemach, Assaf; Grafi, Gideon

doi:10.1016/j.bbagrm.2016.07.012

Cited by 10 publications

(5 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The DNA methylation status in maize was affected in all APAP-contaminated variants. Compared with other studies, where increased levels of methylated DNA were observed in plants grown in polluted environments [74][75][76][77][78], this trend was confirmed. DNA hypermethylation directly lowers gene expression [25]; specifically, the downregulation of a considerable part of the genes is connected with hormone signaling pathways and the metabolism of oxidative stress regulation [79].…”

Section: Discussionsupporting

confidence: 59%

Effects of Acetaminophen Contamination on 5-Methylcytosine Content in Zea mays and Plant Physiological Parameters

et al. 2023

View full text Add to dashboard Cite

Zea mays L. plants were exposed to acetaminophen (APAP). Experiments were conducted in an experimental greenhouse with semi-controlled conditions. Experimental plants were grown in concentrations of APAP of 0, 200, 400, 600, 800, and 1000 mg L−1 for 14 days in an NFT hydroponic system. The impact of APAP contamination was observed on photosynthetic rate, water potential, proline content, and levels of 5-methylcytosine (5 mC%). The results showed that the selected parameters were influenced by different concentrations of APAP. High concentrations of APAP caused a decrease in transpiration rate, stomatal conductance, and water use efficiency. The water potential between the control and highest APAP concentration value increased by 388%. An upward trend of 5 mC% levels was observed, growing with APAP contamination. A 51% growth of 5 mC% was found between the control variant and the highest 1000 mg L−1 APAP contaminated variant. In most of the observed parameters, between 600 mg L−1 and 800 mg L−1 of APAP treatments, a turning point was shown with a noticeable increase in the stress in experimental plants according to the changes in the monitored parameters.

show abstract

Section: Discussionsupporting

confidence: 59%

Effects of Acetaminophen Contamination on 5-Methylcytosine Content in Zea mays and Plant Physiological Parameters

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Mutations in genes involved in DNA and histone methylation showed reductions in global cytosine methylation consequently resulting in more active chromatin [ 269 , 273 ]. DDM1 and RdDM pathways together with RdDM-independent pathways (such as CMT3-SUVH4/KYP) are accountable for methylation and silencing of nearly all transposable elements (TEs) and genome stability [ 273 , 274 , 275 ]. DNA demethylation is mediated via a subfamily of 5-methylcytosine glycosylases comprising REPRESSOR OF SILENCING 1 (ROS1), DEMETER (DME), DEMETER-LIKE2 (DML2), and DML3 [ 276 ].…”

Section: Plant Epigenetics and Epigenomics: Omics Studies (Methylome By Wgbs And Histone Modifications By Chip-seq)mentioning

confidence: 99%

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Gogolev

Ahmar

Akpınar³

et al. 2021

Plants

Self Cite

View full text Add to dashboard Cite

The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

show abstract

“…In an attempt to gain insight into the mechanism(s) by which transposable elements are activated in the course of protoplasting-induced cell dedifferentiation, we have shown previously that the class II, low-copy-number Tag1 transposable elements (TEs), which exist in Ler but not in Columbia (Col) ecotype is activated in dedifferentiating protoplasts and that CMT3 appears to be the major factor controlling their activity via inducing gene body CHG methylation [ 5 ]. Two copies of Tag1 elements are situated close to each other at the end of bottom arm of chromosome 1 (between At1g69650 and At1g69850 loci).…”

Section: Main Textmentioning

confidence: 99%

Arabidopsis mutants may represent recombinant introgression lines

2018

Self Cite

View full text Add to dashboard Cite

ObjectivesIt is a common practice in Arabidopsis to transfer a mutation generated in one genetic background to other genetic background via crossing. However, the drawback of this methodology is unavoidable presence of genomic fragments from the donor parent being often replacing desirable genomic fragments of the recurrent parent. Here, we highlighted problem of Arabidopsis mutants being recombinant introgression lines that can lead to unreliable and misinterpreted results.ResultsWe studied the regulation of low copy number transposable elements Tag1 and Evelknievel (EK), located at the end of the bottom arm of chromosome 1 and both are present in the Arabidopsis Landsberg erecta (Ler) but not in Columbia (Col) ecotype. Using various epigenetic mutants (cmt3, ddm1, kyp2, ago4, rdr2 hen1 etc.), we found that certain mutants in the Ler background are deficient of Tag1 or EK or both and represent recombinant introgression lines whereby chromosomal regions from Col have been recombined into the Ler genome. Our data support a recent proposal calling for formulating standards for authentication of plant lines that are used in plant research. Most important is to verify that a given trait or genomic locus under study is correctly identified, particularly when using mutants generated by crossing.Electronic supplementary materialThe online version of this article (10.1186/s13104-018-3326-5) contains supplementary material, which is available to authorized users.

show abstract

Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation

Cited by 10 publications

References 79 publications

Effects of Acetaminophen Contamination on 5-Methylcytosine Content in Zea mays and Plant Physiological Parameters

Effects of Acetaminophen Contamination on 5-Methylcytosine Content in Zea mays and Plant Physiological Parameters

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Arabidopsis mutants may represent recombinant introgression lines

Contact Info

Product

Resources

About