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Deciphering extrachromosomal circular DNA in Arabidopsis

Extrachromosomal circular DNA (eccDNA) is independent of the chromosome and exists in many eukaryotes. However, the nature and origin of eccDNA in plants remains unclear. In this study, we sequenced 12 samples from four tissues (leaf, flower, stem and root) with three biological replicates. In total...

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Autores principales: Wang, Keyi, Tian, Hui, Wang, Lequn, Wang, Lin, Tan, Yacong, Zhang, Ziting, Sun, Kai, Yin, Meng, Wei, Qinggong, Guo, Baohua, Han, Jinyu, Zhang, Peiru, Li, Han, Liu, Yulong, Zhao, Hongwei, Sun, Xiaoyong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899950/
https://www.ncbi.nlm.nih.gov/pubmed/33680359
http://dx.doi.org/10.1016/j.csbj.2021.01.043
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author Wang, Keyi
Tian, Hui
Wang, Lequn
Wang, Lin
Tan, Yacong
Zhang, Ziting
Sun, Kai
Yin, Meng
Wei, Qinggong
Guo, Baohua
Han, Jinyu
Zhang, Peiru
Li, Han
Liu, Yulong
Zhao, Hongwei
Sun, Xiaoyong
author_facet Wang, Keyi
Tian, Hui
Wang, Lequn
Wang, Lin
Tan, Yacong
Zhang, Ziting
Sun, Kai
Yin, Meng
Wei, Qinggong
Guo, Baohua
Han, Jinyu
Zhang, Peiru
Li, Han
Liu, Yulong
Zhao, Hongwei
Sun, Xiaoyong
author_sort Wang, Keyi
collection PubMed
description Extrachromosomal circular DNA (eccDNA) is independent of the chromosome and exists in many eukaryotes. However, the nature and origin of eccDNA in plants remains unclear. In this study, we sequenced 12 samples from four tissues (leaf, flower, stem and root) with three biological replicates. In total, we found 743 eccDNAs found in at least two samples. Most of eccDNA have inverted repeats ranging from 4 to 12 bp in the boundaries. Interestingly, eccDNA is not only related to transposon activity, but also hosts tRNA genes, suggesting that the eccDNAs may be associated with tRNA abundance which controls protein synthesis under conditions of stress. Our results provide an unprecedented view of eccDNA, which is still naïve in scope.
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spelling pubmed-78999502021-03-04 Deciphering extrachromosomal circular DNA in Arabidopsis Wang, Keyi Tian, Hui Wang, Lequn Wang, Lin Tan, Yacong Zhang, Ziting Sun, Kai Yin, Meng Wei, Qinggong Guo, Baohua Han, Jinyu Zhang, Peiru Li, Han Liu, Yulong Zhao, Hongwei Sun, Xiaoyong Comput Struct Biotechnol J Research Article Extrachromosomal circular DNA (eccDNA) is independent of the chromosome and exists in many eukaryotes. However, the nature and origin of eccDNA in plants remains unclear. In this study, we sequenced 12 samples from four tissues (leaf, flower, stem and root) with three biological replicates. In total, we found 743 eccDNAs found in at least two samples. Most of eccDNA have inverted repeats ranging from 4 to 12 bp in the boundaries. Interestingly, eccDNA is not only related to transposon activity, but also hosts tRNA genes, suggesting that the eccDNAs may be associated with tRNA abundance which controls protein synthesis under conditions of stress. Our results provide an unprecedented view of eccDNA, which is still naïve in scope. Research Network of Computational and Structural Biotechnology 2021-02-09 /pmc/articles/PMC7899950/ /pubmed/33680359 http://dx.doi.org/10.1016/j.csbj.2021.01.043 Text en © 2021 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Wang, Keyi
Tian, Hui
Wang, Lequn
Wang, Lin
Tan, Yacong
Zhang, Ziting
Sun, Kai
Yin, Meng
Wei, Qinggong
Guo, Baohua
Han, Jinyu
Zhang, Peiru
Li, Han
Liu, Yulong
Zhao, Hongwei
Sun, Xiaoyong
Deciphering extrachromosomal circular DNA in Arabidopsis
title Deciphering extrachromosomal circular DNA in Arabidopsis
title_full Deciphering extrachromosomal circular DNA in Arabidopsis
title_fullStr Deciphering extrachromosomal circular DNA in Arabidopsis
title_full_unstemmed Deciphering extrachromosomal circular DNA in Arabidopsis
title_short Deciphering extrachromosomal circular DNA in Arabidopsis
title_sort deciphering extrachromosomal circular dna in arabidopsis
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899950/
https://www.ncbi.nlm.nih.gov/pubmed/33680359
http://dx.doi.org/10.1016/j.csbj.2021.01.043
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