Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),w...Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),which has attracted much attention from the plant circRNA community.Here,we report an updated PlantcircBase(v.7.0),which contains 171,118 circRNAs from 21 plant species.Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing(RNAseq)datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study.A plant multiple conservation score(PMCS),based on the conservation of both sequence and expression profiles,was calculated for each circRNA to quantify and compare the conservation of all circRNAs.A new parameter,plant circRNA confidence level(PCCL),is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA.All this information and other details of circRNAs can be browsed,searched,and downloaded from PlantcircBase 7.0,which also provides online bioinformatics tools for visualization and sequence alignment.PlantcircBase 7.0 is publicly and freely accessible at http://ibi.zju.edu.cn/plantcircbase/.展开更多
Circular RNAs(circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, bind...Circular RNAs(circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding mi RNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and,particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue-or developmentspecific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circ RNA studies.展开更多
CircularRNAs(circRNAs)are a class of single-stranded,closedRNAmolecules with unique functions that are ubiquitously expressed in all eukaryotes.The biogenesis of circRNAs is regulated by specific cis-acting elements a...CircularRNAs(circRNAs)are a class of single-stranded,closedRNAmolecules 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 performedin 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 growthanddevelopment as well as inthe responses to bioticandabiotic 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.展开更多
基金supported by the National Natural Science Foundation of China(32101729,31871589,and 91740108)the National Postdoctoral Program for Innovative Talents(BX20200301).
文摘Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),which has attracted much attention from the plant circRNA community.Here,we report an updated PlantcircBase(v.7.0),which contains 171,118 circRNAs from 21 plant species.Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing(RNAseq)datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study.A plant multiple conservation score(PMCS),based on the conservation of both sequence and expression profiles,was calculated for each circRNA to quantify and compare the conservation of all circRNAs.A new parameter,plant circRNA confidence level(PCCL),is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA.All this information and other details of circRNAs can be browsed,searched,and downloaded from PlantcircBase 7.0,which also provides online bioinformatics tools for visualization and sequence alignment.PlantcircBase 7.0 is publicly and freely accessible at http://ibi.zju.edu.cn/plantcircbase/.
基金supported by grants of Key project of intergovernmental International Science and Technology Innovation Cooperation, MOST of China (2022YFE0100500)the National Key Laboratory of Crop Genetic Improvement Self-research Program (ZW18B0102)。
文摘Circular RNAs(circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding mi RNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and,particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue-or developmentspecific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circ RNA studies.
基金funded by the National Science Foundation of China(31770333 and 31370329)the Program for New Century Excellent Talents in University(NCET-12–0896)+1 种基金the Fundamental Research Funds for the Central Universities(GK202103067 and GK202202006)the Natural Science Foundation of Shaanxi Province,China(2022JQ-218).
文摘CircularRNAs(circRNAs)are a class of single-stranded,closedRNAmolecules 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 performedin 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 growthanddevelopment as well as inthe responses to bioticandabiotic 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.
