Open Access
Plants, volume 12, issue 11, pages 2178
Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing
Publication type: Journal Article
Publication date: 2023-05-30
Plant Science
Ecology, Evolution, Behavior and Systematics
Ecology
Abstract
Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to stress are poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. Applying nanopore sequencing to the eccDNA molecules of epigenetically stressed Arabidopsis plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, whereas its combination with heat stress triggered the generation of full-length and various truncated eccDNAs of the ONSEN element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connections with various biological processes, such as eccDNA transcription and eccDNA-mediated TE silencing.
Citations by journals
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2
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Molecular Biology and Evolution
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Molecular Biology and Evolution
2 publications, 28.57%
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The Analyst
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The Analyst
1 publication, 14.29%
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International Journal of Molecular Sciences
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International Journal of Molecular Sciences
1 publication, 14.29%
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Briefings in Bioinformatics
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Briefings in Bioinformatics
1 publication, 14.29%
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BMC Genomics
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BMC Genomics
1 publication, 14.29%
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1
2
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Citations by publishers
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3
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Oxford University Press
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Oxford University Press
3 publications, 42.86%
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Royal Society of Chemistry (RSC)
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Royal Society of Chemistry (RSC)
1 publication, 14.29%
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
1 publication, 14.29%
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Springer Nature
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Springer Nature
1 publication, 14.29%
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3
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Merkulov P. et al. Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing // Plants. 2023. Vol. 12. No. 11. p. 2178.
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Merkulov P., Egorova E., Kirov I. Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing // Plants. 2023. Vol. 12. No. 11. p. 2178.
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TY - JOUR
DO - 10.3390/plants12112178
UR - https://doi.org/10.3390%2Fplants12112178
TI - Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing
T2 - Plants
AU - Merkulov, Pavel
AU - Egorova, Ekaterina
AU - Kirov, Ilya
PY - 2023
DA - 2023/05/30 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 2178
IS - 11
VL - 12
SN - 2223-7747
ER -
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@article{2023_Merkulov,
author = {Pavel Merkulov and Ekaterina Egorova and Ilya Kirov},
title = {Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing},
journal = {Plants},
year = {2023},
volume = {12},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {may},
url = {https://doi.org/10.3390%2Fplants12112178},
number = {11},
pages = {2178},
doi = {10.3390/plants12112178}
}
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Merkulov, Pavel, et al. “Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing.” Plants, vol. 12, no. 11, May. 2023, p. 2178. https://doi.org/10.3390%2Fplants12112178.
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