Genome-wide Repression of Extrachromosomal Circular DNA in Plants: A Review

Umar Azam *

Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad, Pakistan.

Ali Haider

Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad, Pakistan.

Bismillah Fiaz

Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad, Pakistan.

Sadaf Batool

Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad, Pakistan.

Ayesha Ashraf

Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad, Pakistan.

Maham Ashraf

Department of Microbiology, Faculty of Veterinary Sciences, University of Agriculture Faisalabad, Faisalabad, Punjab, Pakistan.

Abdul Rehman Shah

Department of Seed Science and Technology, Faculty of Agriculture, University of Agriculture Faisalabad, Faisalabad, Pakistan.

Kiran Shahzadi

Department of Botany, Faculty of Basic Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan.

Amina Zia

Department of Microbiology, Faculty of Veterinary Sciences, University of Agriculture Faisalabad, Faisalabad, Punjab, Pakistan.

Ibtisham Elahi

Department of Microbiology, Faculty of Veterinary Sciences, University of Agriculture Faisalabad, Faisalabad, Punjab, Pakistan.

*Author to whom correspondence should be addressed.


Abstract

Many years ago, scientists keenly absorbed and paid attention to the Cytoplasmic genes and nucleus Chromosomes. In this era, Scientists also focused on the nucleus chromosomes since 1965. There are a lot of things that are fortunately or unfortunately neglected by the scientific community one is eccDNA. Mostly in the eukaryotic cell exons and eccDNA is a not-rare process. When the sequencing techniques have come into view this is highly appreciated that this eccDNA is due to the repeats again and again in genomic sequence, new and fresh studies and scientists admit that this eccDNA is due to the different regions of the genome taking part to the eccDNA pool. This eccDNA may be extra but plays a role as a DNA in the cell. Sometimes this is very dangerous for the wheat and in some conditions, it is very may be helpful and show their gene expression in the different plants to control their mechanisms such as stress and adaptation, this may also show the phenotypic effect as well as genotypic effect. In this review, we discuss different approaches and technologies that facilitate eccDNA identification and early discoveries in the eccDNA in wheat.

Keywords: DNA, EccDNA, genome, centromere, plants genomics


How to Cite

Azam , U., Haider , A., Fiaz , B., Batool , S., Ashraf , A., Ashraf , M., Rehman Shah , A., Shahzadi , K., Zia , A., & Elahi , I. (2024). Genome-wide Repression of Extrachromosomal Circular DNA in Plants: A Review. Asian Journal of Biotechnology and Genetic Engineering, 7(1), 85–95. Retrieved from https://journalajbge.com/index.php/AJBGE/article/view/127

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References

Li R, Wang Y, Li J, Zhou X. Extrachromosomal circular DNA (ECCDNA): An emerging star in cancer. Biomarker Research. 2022a;10(1):53. Available:https://doi.org/10.1186/s40364-022-00399-9

Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants—Science Direct. (n.d.); 2023. Available:https://www.sciencedirect.com/science/article/pii/S1369526622000929

Kinoshita Y, Ohnishi N, Yamada Y, Kunisada T, Yamagishi H. Extrachromosomal circular DNA from the nuclear fraction of higher plants. Plant and Cell Physiology. 1985;26(7):1401–1409.

Liao Z, Jiang W, Ye L, Li T, Yu X, Liu L. Classification of extrachromosomal circular DNA with a focus on the role of extrachromosomal DNA (ECDNA) in tumor heterogeneity and progression. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer. 2020;1874(1):188392.

Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JS. Chromothripsis drives the evolution of gene amplification in cancer. Nature. 2021;591(7848):137–141.

Dillon LW, Kumar P, Shibata Y, Wang YH, Willcox S, Griffith JD, Pommier Y, Takeda S, Dutta A. Production of extrachromosomal micro DNAs is linked to mismatch repair pathways and transcriptional activity. Cell Reports. 2015;11(11):1749–1759.

Verhaak RG, Bafna V, Mischel PS. Extrachromosomal oncogene amplification in tumor pathogenesis and evolution. Nature Reviews Cancer. 2019;19(5):283–288.

Ter-Avanesyan M, Derkatch I, Baskakov I, Kushnirov V. [No title found]. Genome Biology. 2005;6(13):366. Available:https://doi.org/10.1186/gb-2005-6-13-366

Møller HD, Parsons L, Jørgensen TS, Botstei D, Regenberg B. Extrachromosomal circular DNA is common in yeast. Proceedings of the National Academy of Sciences. 2015;112(24):E3114–E3122.

Sinclair DA, Guarente L. Extrachromosomal rDNA circles—A cause of aging in yeast. Cell. 1997;91(7):1033–1042.

Fpls-13-1080993.pdf. (n.d.).

Mansisidor A, Molinar T, Srivastava P, Dartis DD, Delgado AP, Blitzblau HG, Klein H, Hochwagen A.. Genomic copy-number loss is rescued by the self-limiting production of DNA circles. Molecular Cell. 2018;72(3):583–593.

Koo DH, Molin WT, Saski CA, Jiang J, Putta K, Jugulam M, Friebe B, Gill BS. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proceedings of the National Academy of Sciences. 2018;115(13):3332–3337. Available:https://doi.org/10.1073/pnas.1719354115

Yang L, Jia R, Ge T, Ge S, Zhuang A, Chai P, Fan X. Extrachromosomal circular DNA: Biogenesis, structure, functions and diseases. Signal Transduction and Targeted Therapy. 2022;7(1). Article 1. Available:https://doi.org/10.1038/s41392-022-01176-8

Wang M, Chen X, Yu F, Ding H, Zhang Y, Wang K. Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer. International Journal of Biological Sciences. 2021a;17(4):1010–1025.

Available:https://doi.org/10.7150/ijbs.54614

Arrey G, Keating ST, Regenberg B. A unifying model for extrachromosomal circular DNA load in eukaryotic cells. Seminars in Cell and Developmental Biology. 2022;128:40–50.

Available:https://doi.org/10.1016/j.semcdb.2022.03.002

Zhao Y, Yu L, Zhang S, Su X, Zhou X. Extrachromosomal circular DNA: Current status and prospects. ELIFE. 2022a;11:e81412. Available:https://doi.org/10.7554/eLife.81412

Cao X, Wang S, Ge L, Zhang W, Huang J, Sun W. Extrachromosomal circular DNA: Category, biogenesis, recognition, and functions. Frontiers in Veterinary Science. 2021a;8:693641.

Peng H, Mirouze M, Bucher E. Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants. Current Opinion in Plant Biology. 2022a;69:102263. Available:https://doi.org/10.1016/j.pbi.2022.102263

Peng H, Mirouze M, Bucher E. Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants. Current Opinion in Plant Biology. 2022b;69:102263.

Khan SU, Khan MU. Extra chromosomal circular DNA: Recent advances in research. Journal of Biomedical Research and Environmental Sciences. 2022a;3(4):445–452.

Available:https://doi.org/10.37871/jbres1463

Fromm M, Walbot V. Transient Expression of DNA in Plant Cells. In Hohn T, Schell J. (Eds.), Plant DNA Infectious Agents. Springer Vienna. 1987;303–310. Available:https://doi.org/10.1007/978-3-7091-6977-3_13

Li R, Wang Y, Li J, Zhou X. Extrachromosomal circular DNA (ECCDNA): An emerging star in cancer. Biomarker Research. 2022b;10(1):53. Available:https://doi.org/10.1186/s40364-022-00399-9

Zuo S, Yi Y, Wang C, Li X, Zhou M, Peng Q, Zhou J, Yang Y, He Q. Extrachromosomal Circular DNA (ECCDNA): From Chaos to Function. Frontiers in Cell and Developmental Biology. 2022a;9:792555.

Available:https://doi.org/10.3389/fcell.2021.792555

Cao X, Wang S, Ge L, Zhang W, Huang J, Sun W. Extrachromosomal circular DNA: Category, biogenesis, recognition, and functions. Frontiers in Veterinary Science. 2021b;8:693641. Available:https://doi.org/10.3389/fvets.2021.693641

Zhao Y, Yu L, Zhang S, Su X, Zhou X. Extrachromosomal circular DNA: Current status and prospects. ELIFE. 2022b;11:e81412. Available:https://doi.org/10.7554/eLife.81412

Khan SU, Khan MU. Extra chromosomal circular DNA: Recent advances in research. Journal of Biomedical Research and Environmental Sciences. 2022b;3(4):445–452. Available:https://doi.org/10.37871/jbres1463

Peng H, Mirouze M, Bucher E. Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants. Current Opinion in Plant Biology. 2022c;69:102263. Available:https://doi.org/10.1016/j.pbi.2022.102263

Wang M, Chen X, Yu F, Ding H, Zhang Y, Wang K. Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer. International Journal of Biological Sciences. 2021b;17(4):1010–1025. Available:https://doi.org/10.7150/ijbs.54614

Pereira L, Dunning LT. Extrachromosomal circular DNA as a vehicle for gene transfer in plants. Plant Physiology. 2023;193(1).Article 1. Available:https://doi.org/10.1093/plphys/kiad380

Extrachromosomal circular DNA. In Wikipedia; 2023b. Available:https://en.wikipedia.org/w/index.php?title=Extrachromosomal_circular_DNA&oldid=1170218116

Dong Y, He Q, Chen X, Yang F, He L, Zheng Y. Extrachromosomal DNA (ECDNA) in cancer: Mechanisms, functions, and clinical implications. Frontiers in Oncology. 2023;13. Available:https://doi.org/10.3389/fonc.2023.1194405

Extrachromosomal circular DNA. In Wikipedia; 2023c. Available:https://en.wikipedia.org/w/index.php?title=Extrachromosomal_circular_DNA&oldid=1170218116

Zuo S, Yi Y, Wang C, Li X, Zhou M, Peng Q, Zhou J, Yang Y, He Q. Extrachromosomal Circular DNA (ECCDNA): From Chaos to Function. Frontiers in Cell and Developmental Biology. 2022b;9. Available:https://www.frontiersin.org/articles/10.3389/fcell.2021.792555

Paulsen T, Kumar P, Koseoglu MM, Dutta A. Discoveries of extrachromosomal circles of DNA in normal and tumor cells. Trends in Genetics : TIG. 2018;34(4):270–278. Available:https://doi.org/10.1016/j.tig.2017.12.010

Li R, Wang Y, Li J, Zhou X. Extrachromosomal circular DNA (ECCDNA): An emerging star in cancer. Biomarker Research. 2022c;10(1).Article 1. Available:https://doi.org/10.1186/s40364-022-00399-9

Raffeiner M, Zhu S, González-Fuente M, Üstün S. The interplay between autophagy and proteasome during protein turnover. Trends in Plant Science. 2023;28(6):698–714. Available:https://doi.org/10.1016/j.tplants.2023.01.013

Liu WJ, Ye L, Huang WF, Guo LJ, Xu ZG, Wu HL, Yang C, Liu HF. P62 links the autophagy pathway and the ubiquitin-proteasome system upon ubiquitinated protein degradation. Cellular and Molecular Biology Letters. 2016;21(1):29. Available:https://doi.org/10.1186/s11658-016-0031-z

10.4: The Structure and Function of Cellular Genomes. Biology LibreTexts; 2016. Available:https://bio.libretexts.org/ Bookshelves/Microbiology/Microbiology_(OpenStax)/10%3A_Biochemistry_of_ the_Genome/10.04%3A_The_ Structure_and_Function_of_Cellular_Genomes

81412. pdf. (n.d.); 2023. Available:https://elifesciences.org/articles/81412.pdf

Extrachromosomal circular DNA. In Wikipedia; 2023a. Available:https://en.wikipedia.org/w/index.php?title=Extrachromosomal_circular_DNA&oldid=1170218116

Extrachromosomal circular DNA: biogenesis, structure, functions, and diseases. Signal Transduction and Targeted Therapy. (n.d.); 2023. Available:https://www.nature.com/articles/s41392-022-01176-8

Kiad380.pdf. (n.d.).

Nucleases | Exonucleases and Endonucleases—YouTube. (n.d.); 2023

Available:https://www.youtube.com/watch?v=kLpNHnRt_64&t=12

Nucleases in higher plants and their possible involvement in DNA degradation during leaf senescence. Journal of Experimental Botany. Oxford Academic. (n.d.); 2023. Available:https://academic.oup.com/jxb/article/65/14/3835/2877468

S13059-017-1265-4.pdf. (n.d.).

The Plant Journal—2022—Kwolek.pdf. (n.d.).