Wiley Interdisciplinary Reviews: RNA最新文献_第7页

RNA epigenetic modifications in ovarian cancer: The changes, chances, and challenges. 卵巢癌症的RNA表观遗传修饰：变化、机会和挑战。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-02-21 DOI: 10.1002/wrna.1784

Lele Ye, Xuyang Yao, Binbing Xu, Wenwen Chen, Han Lou, Xinya Tong, Su Fang, Ruanmin Zou, Yingying Hu, Zhibin Wang, Dan Xiang, Qiaoai Lin, Shiyu Feng, Xiangyang Xue, Gangqiang Guo

{"title":"RNA epigenetic modifications in ovarian cancer: The changes, chances, and challenges.","authors":"Lele Ye, Xuyang Yao, Binbing Xu, Wenwen Chen, Han Lou, Xinya Tong, Su Fang, Ruanmin Zou, Yingying Hu, Zhibin Wang, Dan Xiang, Qiaoai Lin, Shiyu Feng, Xiangyang Xue, Gangqiang Guo","doi":"10.1002/wrna.1784","DOIUrl":"10.1002/wrna.1784","url":null,"abstract":"Ovarian cancer (OC) is the most common female cancer worldwide. Patients with OC have high mortality because of its complex and poorly understood pathogenesis. RNA epigenetic modifications, such as m6 A, m1 A, and m5 C, are closely associated with the occurrence and development of OC. RNA modifications can affect the stability of mRNA transcripts, nuclear export of RNAs, translation efficiency, and decoding accuracy. However, there are few overviews that summarize the link between m6 A RNA modification and OC. Here, we discuss the molecular and cellular functions of different RNA modifications and how their regulation contributes to the pathogenesis of OC. By improving our understanding of the role of RNA modifications in the etiology of OC, we provide new perspectives for their use in OC diagnosis and treatment. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1784"},"PeriodicalIF":7.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10289907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Roles of non-coding RNAs in eye development and diseases. 非编码RNA在眼睛发育和疾病中的作用。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-02-27 DOI: 10.1002/wrna.1785

Xinrui Shi, Zhengbo Xue, Kaicheng Ye, Jian Yuan, Yan Zhang, Jia Qu, Jianzhong Su

{"title":"Roles of non-coding RNAs in eye development and diseases.","authors":"Xinrui Shi, Zhengbo Xue, Kaicheng Ye, Jian Yuan, Yan Zhang, Jia Qu, Jianzhong Su","doi":"10.1002/wrna.1785","DOIUrl":"10.1002/wrna.1785","url":null,"abstract":"The prevalence of ocular disorders is dramatically increasing worldwide, especially those that cause visual impairment and permanent loss of vision, including cataract, glaucoma, age-related macular degeneration, and diabetic retinopathy. Extensive evidence has shown that ncRNAs are key regulators in various biogenesis and biological functions, controlling gene expression related to histogenesis and cell differentiation in ocular tissues. Aberrant expression and function of ncRNA can lead to dysfunction of visual system and mediate progression of eye disorders. Here, we mainly offer an overview of the role of precise modulation of ncRNAs in eye development and function in patients with eye diseases. We also highlight the challenges and future perspectives in conducting ncRNA studies, focusing specifically on the role of ncRNAs that may hold expanded promise for their diagnostic and therapeutic applications in various eye diseases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1785"},"PeriodicalIF":7.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10226650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Physiological and engineered tRNA aminoacylation. 生理和工程tRNA氨基酰化。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-04-12 DOI: 10.1002/wrna.1789

Santiago Tijaro-Bulla, Samuel Protais Nyandwi, Haissi Cui

引用次数: 1

The DNA binding high mobility group box protein family functionally binds RNA. DNA结合的高迁移率基团盒蛋白家族在功能上结合RNA。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-01-16 DOI: 10.1002/wrna.1778

Desmond J Hamilton, Abigail E Hein, Deborah S Wuttke, Robert T Batey

{"title":"The DNA binding high mobility group box protein family functionally binds RNA.","authors":"Desmond J Hamilton, Abigail E Hein, Deborah S Wuttke, Robert T Batey","doi":"10.1002/wrna.1778","DOIUrl":"10.1002/wrna.1778","url":null,"abstract":"Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1778"},"PeriodicalIF":6.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10349909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10289412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Translation machinery captured in motion. 翻译机器在运动。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-05-03 DOI: 10.1002/wrna.1792

Hassan Zafar, Ahmed H Hassan, Gabriel Demo

引用次数: 0

Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function. 肌苷三磷酸焦磷酸酶：细胞核苷酸库的守护者和RNA功能的潜在介质。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-04-24 DOI: 10.1002/wrna.1790

Jacob H Schroader, Mark T Handley, Kaalak Reddy

{"title":"Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function.","authors":"Jacob H Schroader, Mark T Handley, Kaalak Reddy","doi":"10.1002/wrna.1790","DOIUrl":"10.1002/wrna.1790","url":null,"abstract":"Inosine triphosphate pyrophosphatase (ITPase), encoded by the ITPA gene in humans, is an important enzyme that preserves the integrity of cellular nucleotide pools by hydrolyzing the noncanonical purine nucleotides (deoxy)inosine and (deoxy)xanthosine triphosphate into monophosphates and pyrophosphate. Variants in the ITPA gene can cause partial or complete ITPase deficiency. Partial ITPase deficiency is benign but clinically relevant as it is linked to altered drug responses. Complete ITPase deficiency causes a severe multisystem disorder characterized by seizures and encephalopathy that is frequently associated with fatal infantile dilated cardiomyopathy. In the absence of ITPase activity, its substrate noncanonical nucleotides have the potential to accumulate and become aberrantly incorporated into DNA and RNA. Hence, the pathophysiology of ITPase deficiency could arise from metabolic imbalance, altered DNA or RNA regulation, or from a combination of these factors. Here, we review the known functions of ITPase and highlight recent work aimed at determining the molecular basis for ITPA-associated pathogenesis which provides evidence for RNA dysfunction. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1790"},"PeriodicalIF":7.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10235876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution. 利用功能性无细胞提取物以单分子分辨率剖析核糖核蛋白复合物生物学。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-04-12 DOI: 10.1002/wrna.1787

Elizabeth Duran, Andreas Schmidt, Robb Welty, Ameya P Jalihal, Sethuramasundaram Pitchiaya, Nils G Walter

{"title":"Utilizing functional cell-free extracts to dissect ribonucleoprotein complex biology at single-molecule resolution.","authors":"Elizabeth Duran, Andreas Schmidt, Robb Welty, Ameya P Jalihal, Sethuramasundaram Pitchiaya, Nils G Walter","doi":"10.1002/wrna.1787","DOIUrl":"10.1002/wrna.1787","url":null,"abstract":"Cellular machineries that drive and regulate gene expression often rely on the coordinated assembly and interaction of a multitude of proteins and RNA together called ribonucleoprotein complexes (RNPs). As such, it is challenging to fully reconstitute these cellular machines recombinantly and gain mechanistic understanding of how they operate and are regulated within the complex environment that is the cell. One strategy for overcoming this challenge is to perform single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts. This strategy enables elucidation of the interaction and kinetic behavior of specific fluorescently labeled biomolecules within RNPs under conditions that approximate native cellular environments. In this review, we describe single molecule fluorescence microcopy approaches that dissect RNP-driven processes within cellular extracts, highlighting general strategies used in these methods. We further survey biological advances in the areas of pre-mRNA splicing and transcription regulation that have been facilitated through this approach. Finally, we conclude with a summary of practical considerations for the implementation of the featured approaches to facilitate their broader future implementation in dissecting the mechanisms of RNP-driven cellular processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1787"},"PeriodicalIF":6.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10524090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10237746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer. Pol III转录组：癌症的基本特征、复发模式和新出现的作用。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-02-08 DOI: 10.1002/wrna.1782

Sihang Zhou, Kevin Van Bortle

{"title":"The Pol III transcriptome: Basic features, recurrent patterns, and emerging roles in cancer.","authors":"Sihang Zhou, Kevin Van Bortle","doi":"10.1002/wrna.1782","DOIUrl":"10.1002/wrna.1782","url":null,"abstract":"The RNA polymerase III (Pol III) transcriptome is universally comprised of short, highly structured noncoding RNA (ncRNA). Through RNA-protein interactions, the Pol III transcriptome actuates functional activities ranging from nuclear gene regulation (7SK), splicing (U6, U6atac), and RNA maturation and stability (RMRP, RPPH1, Y RNA), to cytoplasmic protein targeting (7SL) and translation (tRNA, 5S rRNA). In higher eukaryotes, the Pol III transcriptome has expanded to include additional, recently evolved ncRNA species that effectively broaden the footprint of Pol III transcription to additional cellular activities. Newly evolved ncRNAs function as riboregulators of autophagy (vault), immune signaling cascades (nc886), and translation (Alu, BC200, snaR). Notably, upregulation of Pol III transcription is frequently observed in cancer, and multiple ncRNA species are linked to both cancer progression and poor survival outcomes among cancer patients. In this review, we outline the basic features and functions of the Pol III transcriptome, and the evidence for dysregulation and dysfunction for each ncRNA in cancer. When taken together, recurrent patterns emerge, ranging from shared functional motifs that include molecular scaffolding and protein sequestration, overlapping protein interactions, and immunostimulatory activities, to the biogenesis of analogous small RNA fragments and noncanonical miRNAs, augmenting the function of the Pol III transcriptome and further broadening its role in cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Processing of Small RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1782"},"PeriodicalIF":6.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10289430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Web tools support predicting protein-nucleic acid complexes stability with affinity changes. 网络工具支持预测蛋白质-核酸复合物的亲和力变化稳定性。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-01-24 DOI: 10.1002/wrna.1781

Xiao Zhang, Long-Can Mei, Yang-Yang Gao, Ge-Fei Hao, Bao-An Song

{"title":"Web tools support predicting protein-nucleic acid complexes stability with affinity changes.","authors":"Xiao Zhang, Long-Can Mei, Yang-Yang Gao, Ge-Fei Hao, Bao-An Song","doi":"10.1002/wrna.1781","DOIUrl":"10.1002/wrna.1781","url":null,"abstract":"Numerous biological processes, such as transcription, replication, and translation, rely on protein-nucleic acid interactions (PNIs). Demonstrating the binding stability of protein-nucleic acid complexes is vital to deciphering the code for PNIs. Numerous web-based tools have been developed to attach importance to protein-nucleic acid stability, facilitating the prediction of PNIs characteristics rapidly. However, the data and tools are dispersed and lack comprehensive integration to understand the stability of PNIs better. In this review, we first summarize existing databases for evaluating the stability of protein-nucleic acid binding. Then, we compare and evaluate the pros and cons of web tools for forecasting the interaction energies of protein-nucleic acid complexes. Finally, we discuss the application of combining models and capabilities of PNIs. We may hope these web-based tools will facilitate the discovery of recognition mechanisms for protein-nucleic acid binding stability. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1781"},"PeriodicalIF":7.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10289425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Functional and regulatory impact of chimeric RNAs in human normal and cancer cells. 嵌合RNA在人类正常细胞和癌症细胞中的功能和调节影响。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-09-01 Epub Date: 2023-01-12 DOI: 10.1002/wrna.1777

Sumit Mukherjee, Sunanda Biswas Mukherjee, Milana Frenkel-Morgenstern

{"title":"Functional and regulatory impact of chimeric RNAs in human normal and cancer cells.","authors":"Sumit Mukherjee, Sunanda Biswas Mukherjee, Milana Frenkel-Morgenstern","doi":"10.1002/wrna.1777","DOIUrl":"10.1002/wrna.1777","url":null,"abstract":"Fusions of two genes can lead to the generation of chimeric RNAs, which may have a distinct functional role from their original molecules. Chimeric RNAs could encode novel functional proteins or serve as novel long noncoding RNAs (lncRNAs). The appearance of chimeric RNAs in a cell could help to generate new functionality and phenotypic diversity that might facilitate this cell to survive against new environmental stress. Several recent studies have demonstrated the functional roles of various chimeric RNAs in cancer progression and are considered as biomarkers for cancer diagnosis and sometimes even drug targets. Further, the growing evidence demonstrated the potential functional association of chimeric RNAs with cancer heterogeneity and drug resistance cancer evolution. Recent studies highlighted that chimeric RNAs also have functional potentiality in normal physiological processes. Several functionally potential chimeric RNAs were discovered in human cancer and normal cells in the last two decades. This could indicate that chimeric RNAs are the hidden layer of the human transcriptome that should be explored from the functional insights to better understand the functional evolution of the genome and disease development that could facilitate clinical practice improvements. This review summarizes the current knowledge of chimeric RNAs and highlights their functional, regulatory, and evolutionary impact on different cancers and normal physiological processes. Further, we will discuss the potential functional roles of a recently discovered novel class of chimeric RNAs named sense-antisense/cross-strand chimeric RNAs generated by the fusion of the bi-directional transcripts of the same gene. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"14 5","pages":"e1777"},"PeriodicalIF":7.3,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10235305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2