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Gao Z, Sun B, Fan Z, Su Y, Zheng C, Chen W, Yao Y, Ma C, Du Y. Vv-circSIZ1 mediated by pre-mRNA processing machinery contributes to salt tolerance. THE NEW PHYTOLOGIST 2023; 240:644-662. [PMID: 37530126 DOI: 10.1111/nph.19181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023]
Abstract
CircRNAs exist widely in plants, but the regulatory mechanisms for the biogenesis and function of plant circRNAs remain largely unknown. Using extensive mutagenesis of expression plasmids and genetic transformation methods, we analyzed the biogenesis and anti-salt functions of a new grape circRNA Vv-circSIZ1. We identified Vv-circSIZ1 that is mainly expressed in the cytoplasm of xylem. CircSIZ1 is species-specific, and genomic circSIZ1-forming region of seven tested species could be backspliced in Nicotiana benthamiana, but not in Arabidopsis. The retention length of Vv-circSIZ1 flanking introns was significantly positively correlated with its generation efficiency. The precise splicing of Vv-circSIZ1 does not depend on its mature exon sequence or internal intron sequences, but on the AG/GT splicing signal sites and branch site of the flanking introns. The spliceosome activity was inversely proportional to the expression level of Vv-circSIZ1. Furthermore, RNA-binding proteins can regulate the expression of Vv-circSIZ1. The overexpression of Vv-circSIZ1 improved salt tolerance of grape and N. benthamiana. Additionally, Vv-circSIZ1 could relieve the repressive effect of VvmiR3631 on its target VvVHAc1. Vv-circSIZ1 also promoted transcription of its parental gene. Overall, these results broaden our understanding of circRNAs in plants.
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Affiliation(s)
- Zhen Gao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Baozhen Sun
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zongbao Fan
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Yifan Su
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Weiping Chen
- Institute of Horticulture, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, 750002, China
| | - Yuxin Yao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuanpeng Du
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
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Yuan H, Liu F, Long J, Duan G, Yang H. A review on circular RNAs and bacterial infections. Int J Biol Macromol 2023:125391. [PMID: 37321437 DOI: 10.1016/j.ijbiomac.2023.125391] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
Bacterial infections and related diseases have been a major burden on social public health and economic stability around the world. However, the effective diagnostic methods and therapeutic approaches to treat bacterial infections are still limited. As a group of non-coding RNA, circular RNAs (circRNAs) that were expressed specifically in host cells and played a key regulatory role have the potential to be of diagnostic and therapeutic value. In this review, we systematically summarize the role of circRNAs in common bacterial infections and their potential roles as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Haitao Yuan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fang Liu
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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3
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Circular RNAs: Non-Canonical Observations on Non-Canonical RNAs. Cells 2023; 12:cells12020323. [PMID: 36672257 PMCID: PMC9856604 DOI: 10.3390/cells12020323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The existence of circular RNA (circRNA) research in mainstream science can be attributed to the contemporary synergism of big data and keen attention to detail by several research groups worldwide. Since the re-emergence of these non-canonical RNA transcripts, seminal advances have been made in understanding their biogenesis, interactome, and functions in diverse fields and a myriad of human diseases. However, most research outputs to date have focused on the ability of highly stable circRNAs to interact with, and impact signalling through, microRNAs. This is likely to be the result of seminal papers in the field ascribing a few remarkable circRNAs as "miRNA sponges". However, the stoichiometric ratio between the (often-lowly-expressed) circRNA and their (commonly-more-abundant) target is rarely in favour of a biologically relevant and functional consequence of these interactions. It is time for yet another revolution in circRNA research to uncover functions beyond their documented ability to bind miRNAs. This Special Issue aims to highlight non-canonical functions for this non-canonical family of RNA molecules.
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Liu R, Ma Y, Guo T, Li G. Identification, biogenesis, function, and mechanism of action of circular RNAs in plants. PLANT COMMUNICATIONS 2023; 4:100430. [PMID: 36081344 PMCID: PMC9860190 DOI: 10.1016/j.xplc.2022.100430] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded, closed RNA molecules with unique functions that are ubiquitously expressed in all eukaryotes. The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals. circRNAs mainly exert their biological functions by acting as microRNA sponges, forming R-loops, interacting with RNA-binding proteins, or being translated into polypeptides or proteins in human and animal cells. Genome-wide identification of circRNAs has been performed in multiple plant species, and the results suggest that circRNAs are abundant and ubiquitously expressed in plants. There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growth and development as well as in the responses to biotic and abiotic stress. However, compared with recent advances in human and animal systems, the roles of most circRNAs in plants are unclear at present. Here we review the identification, biogenesis, function, and mechanism of action of plant circRNAs, which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.
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Affiliation(s)
- Ruiqi Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Yu Ma
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.
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Zhang X, Liang Z, Wang C, Shen Z, Sun S, Gong C, Hu X. Viral Circular RNAs and Their Possible Roles in Virus-Host Interaction. Front Immunol 2022; 13:939768. [PMID: 35784275 PMCID: PMC9247149 DOI: 10.3389/fimmu.2022.939768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/26/2022] [Indexed: 11/24/2022] Open
Abstract
Circular RNAs (circRNAs) as novel regulatory molecules have been recognized in diverse species, including viruses. The virus-derived circRNAs play various roles in the host biological process and the life cycle of the viruses. This review summarized the circRNAs from the DNA and RNA viruses and discussed the biogenesis of viral and host circRNAs, the potential roles of viral circRNAs, and their future perspective. This review will elaborate on new insights gained on viruses encoded circRNAs during virus infection.
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Affiliation(s)
- Xing Zhang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Zi Liang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Chonglong Wang
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Zeen Shen
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Sufei Sun
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
| | - Chengliang Gong
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
- *Correspondence: Xiaolong Hu, ; Chengliang Gong,
| | - Xiaolong Hu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, China
- Institute of Agricultural Biotechnology and Ecological Research, Soochow University, Suzhou, China
- *Correspondence: Xiaolong Hu, ; Chengliang Gong,
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Nowis K, Jackowiak P, Figlerowicz M, Philips A. At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format. Database (Oxford) 2021; 2021:6425494. [PMID: 34788390 PMCID: PMC8594480 DOI: 10.1093/database/baab074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022]
Abstract
Circular RNAs (circRNAs) are a large class of noncoding RNAs with functions that, in most
cases, remain unknown. Recent genome-wide analysis of circRNAs using RNA-Seq has revealed
that circRNAs are abundant and some of them conserved in plants. Furthermore, it has been
shown that the expression of circRNAs in plants is regulated in a tissue-specific manner.
Arabidopsis thaliana circular RNA database is a new resource designed
to integrate and standardize the data available for circRNAs in a model plant A.
thaliana, which is currently the best-characterized plant in terms of circRNAs.
The resource integrates all applicable publicly available RNA-seq datasets. These datasets
were subjected to extensive reanalysis and curation, yielding results in a unified format.
Moreover, all data were normalized according to our optimized approach developed for
circRNA identification in plants. As a result, the database accommodates circRNAs
identified across organs and seedlings of wild-type A. thaliana and its
single-gene knockout mutants for genes related to splicing. The database provides free
access to unified data and search functionalities, thus enabling comparative analyses of
A. thaliana circRNAs between organs, variants and studies for the first
time. Database URLhttps://plantcircrna.ibch.poznan.pl/
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Affiliation(s)
- Katarzyna Nowis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
| | - Anna Philips
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego str. 12/14, Poznan 61-704, Poland
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NGS Methodologies and Computational Algorithms for the Prediction and Analysis of Plant Circular RNAs. Methods Mol Biol 2021; 2362:119-145. [PMID: 34195961 DOI: 10.1007/978-1-0716-1645-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded RNAs derived from exonic, intronic, and intergenic regions from precursor messenger RNAs (pre-mRNA), where a noncanonical back-splicing event occurs, in which the 5' and 3' ends are attached by covalent bond. CircRNAs participate in the regulation of gene expression at the transcriptional and posttranscriptional level primarily as miRNA and RNA-binding protein (RBP) sponges, but also involved in the regulation of alternative RNA splicing and transcription. CircRNAs are widespread and abundant in plants where they have been involved in stress responses and development. Through the analysis of all publications in this field in the last five years, we can summarize that the identification of these molecules is carried out through next generation sequencing studies, where samples have been previously treated to eliminate DNA, rRNA, and linear RNAs as a means to enrich circRNAs. Once libraries are prepared, they are sequenced and subsequently studied from a bioinformatics point of view. Among the different tools for identifying circRNAs, we can highlight CIRI as the most used (in 60% of the published studies), as well as CIRCExplorer (20%) and find_circ (20%). Although it is recommended to use more than one program in combination, and preferably developed specifically to treat with plant samples, this is not always the case. It should also be noted that after identifying these circular RNAs, most of the authors validate their findings in the laboratory in order to obtain bona fide results.
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