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
CircRNAs,widely found throughout the human bodies,play a crucial role in regulating various biological processes and are closely linked to complex human diseases.Investigating potential associations between circRNAs a...CircRNAs,widely found throughout the human bodies,play a crucial role in regulating various biological processes and are closely linked to complex human diseases.Investigating potential associations between circRNAs and diseases can enhance our understanding of diseases and provide new strategies and tools for early diagnosis,treatment,and disease prevention.However,existing models have limitations in accurately capturing similarities,handling the sparse and noise attributes of association networks,and fully leveraging bioinformatical aspects from multiple viewpoints.To address these issues,this study introduces a new non-negative matrix factorization-based framework called NMFMSN.First,we incorporate circRNA sequence data and disease semantic information to compute circRNA and disease similarity,respectively.Given the sparse known associations between circRNAs and diseases,we reconstruct the network to complete more associations by imputing missing links based on neighboring circRNA and disease interactions.Finally,we integrate these two similarity networks into a non-negative matrix factorization framework to identify potential circRNA-disease associations.Upon conducting 5-fold cross-validation and leave-one-out cross-validation,the AUC values for NMFMSN reach 0.9712 and 0.9768,respectively,outperforming the currently most advanced models.Case studies on lung cancer and hepatocellular carcinoma show that NMFMSN is a good way to predict new associations between circRNAs and diseases.展开更多
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the Gansu Province Industrial Support Plan(No.2023CYZC-25)Natural Science Foundation of Gansu Province(No.23JRRA770)the National Natural Science Foundation of China(No.62162040)。
文摘CircRNAs,widely found throughout the human bodies,play a crucial role in regulating various biological processes and are closely linked to complex human diseases.Investigating potential associations between circRNAs and diseases can enhance our understanding of diseases and provide new strategies and tools for early diagnosis,treatment,and disease prevention.However,existing models have limitations in accurately capturing similarities,handling the sparse and noise attributes of association networks,and fully leveraging bioinformatical aspects from multiple viewpoints.To address these issues,this study introduces a new non-negative matrix factorization-based framework called NMFMSN.First,we incorporate circRNA sequence data and disease semantic information to compute circRNA and disease similarity,respectively.Given the sparse known associations between circRNAs and diseases,we reconstruct the network to complete more associations by imputing missing links based on neighboring circRNA and disease interactions.Finally,we integrate these two similarity networks into a non-negative matrix factorization framework to identify potential circRNA-disease associations.Upon conducting 5-fold cross-validation and leave-one-out cross-validation,the AUC values for NMFMSN reach 0.9712 and 0.9768,respectively,outperforming the currently most advanced models.Case studies on lung cancer and hepatocellular carcinoma show that NMFMSN is a good way to predict new associations between circRNAs and diseases.
