Wiley Interdisciplinary Reviews: RNA最新文献_第4页

Spatial analysis toolkits for RNA in situ sequencing. 用于 RNA 原位测序的空间分析工具包。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1842

Jiayu Chen, Rongqin Ke

{"title":"Spatial analysis toolkits for RNA in situ sequencing.","authors":"Jiayu Chen, Rongqin Ke","doi":"10.1002/wrna.1842","DOIUrl":"10.1002/wrna.1842","url":null,"abstract":"Spatial transcriptomics (ST) is featured by high-throughput gene expression profiling within their native cell and tissue context, offering a means to investigate gene regulatory networks in tissue microenvironment. In situ sequencing (ISS) is an imaging-based ST technology that simultaneously detects hundreds to thousands of genes at subcellular resolution. As a highly reproducible and robust technique, ISS has been widely adapted and undergone a series of technical iterations. As the interest in ISS-based spatial transcriptomic analysis grows, scalable and integrated data analysis workflows are needed to facilitate the applications of ISS in different research fields. This review presents the state-of-the-art bioinformatic toolkits for ISS data analysis, which covers the upstream and downstream analysis workflows, including image analysis, cell segmentation, clustering, functional enrichment, detection of spatially variable genes and cell clusters, spatial cell-cell interactions, and trajectory inference. To assist the community in choosing the right tools for their research, the application of each tool and its compatibility with ISS data are reviewed in detailed. Finally, future perspectives and challenges concerning how to integrate heterogeneous tools into a user-friendly analysis pipeline are discussed. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 2","pages":"e1842"},"PeriodicalIF":7.3,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854688","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: 0

Correction to "Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes". 更正 "Poly(A) tale：从 A 到 A；原核生物和真核生物中的 RNA 多腺苷酸化 "一文的更正。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1846

引用次数: 0

Emerging roles of RNA-binding proteins in fatty liver disease. RNA 结合蛋白在脂肪肝中的新作用。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1840

Oluwafolajimi Adesanya, Diptatanu Das, Auinash Kalsotra

{"title":"Emerging roles of RNA-binding proteins in fatty liver disease.","authors":"Oluwafolajimi Adesanya, Diptatanu Das, Auinash Kalsotra","doi":"10.1002/wrna.1840","DOIUrl":"10.1002/wrna.1840","url":null,"abstract":"A rampant and urgent global health issue of the 21st century is the emergence and progression of fatty liver disease (FLD), including alcoholic fatty liver disease and the more heterogenous metabolism-associated (or non-alcoholic) fatty liver disease (MAFLD/NAFLD) phenotypes. These conditions manifest as disease spectra, progressing from benign hepatic steatosis to symptomatic steatohepatitis, cirrhosis, and, ultimately, hepatocellular carcinoma. With numerous intricately regulated molecular pathways implicated in its pathophysiology, recent data have emphasized the critical roles of RNA-binding proteins (RBPs) in the onset and development of FLD. They regulate gene transcription and post-transcriptional processes, including pre-mRNA splicing, capping, and polyadenylation, as well as mature mRNA transport, stability, and translation. RBP dysfunction at every point along the mRNA life cycle has been associated with altered lipid metabolism and cellular stress response, resulting in hepatic inflammation and fibrosis. Here, we discuss the current understanding of the role of RBPs in the post-transcriptional processes associated with FLD and highlight the possible and emerging therapeutic strategies leveraging RBP function for FLD treatment. This article is categorized under: RNA in Disease and Development > RNA in Disease.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 2","pages":"e1840"},"PeriodicalIF":7.3,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11018357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140858114","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

RNA m6A modifications regulate crosstalk between tumor metabolism and immunity. RNA m6A修饰调节肿瘤代谢与免疫之间的相互关系。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-01-01 Epub Date: 2023-12-19 DOI: 10.1002/wrna.1829

Jinghua Gu, Huake Cao, Xiaoli Chen, Xu Dong Zhang, Rick F Thorne, Xiaoying Liu

{"title":"RNA m6A modifications regulate crosstalk between tumor metabolism and immunity.","authors":"Jinghua Gu, Huake Cao, Xiaoli Chen, Xu Dong Zhang, Rick F Thorne, Xiaoying Liu","doi":"10.1002/wrna.1829","DOIUrl":"10.1002/wrna.1829","url":null,"abstract":"In recent years, m6A modifications in RNA transcripts have arisen as a hot topic in cancer research. Indeed, a number of independent studies have elaborated that the m6A modification impacts the behavior of tumor cells and tumor-infiltrating immune cells, altering tumor cell metabolism along with the differentiation and functional activity of immune cells. This review elaborates on the links between RNA m6A modifications, tumor cell metabolism, and immune cell behavior, discussing this topic from the viewpoint of reciprocal regulation through \"RNA m6A-tumor cell metabolism-immune cell behavior\" and \"RNA m6A-immune cell behavior-tumor cell metabolism\" axes. In addition, we discuss the various factors affecting RNA m6A modifications in the tumor microenvironment, particularly the effects of hypoxia associated with cancer cell metabolism along with immune cell-secreted cytokines. Our analysis proposes the conclusion that RNA m6A modifications support widespread interactions between tumor metabolism and tumor immunity. With the current viewpoint that long-term cancer control must tackle cancer cell malignant behavior while strengthening anti-tumor immunity, the recognition of RNA m6A modifications as a key factor provides a new direction for the targeted therapy of tumors. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":" ","pages":"e1829"},"PeriodicalIF":7.3,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138804646","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: 0

Recent insights into the world of dual-function bacterial sRNAs. 对双功能细菌srna世界的最新见解。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-12-01 DOI: 10.1002/wrna.1824

Sebastian Benjamin Schnoor, Peter Neubauer, Matthias Gimpel

引用次数: 0

Fates and functions of RNA-binding proteins under stress. 应激条件下rna结合蛋白的命运和功能。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-11-28 DOI: 10.1002/wrna.1825

Binita Goswami, Sharanya Nag, Partho Sarothi Ray

{"title":"Fates and functions of RNA-binding proteins under stress.","authors":"Binita Goswami, Sharanya Nag, Partho Sarothi Ray","doi":"10.1002/wrna.1825","DOIUrl":"10.1002/wrna.1825","url":null,"abstract":"Exposure to stress activates a well-orchestrated set of changes in gene expression programs that allow the cell to cope with and adapt to the stress, or undergo programmed cell death. RNA-protein interactions, mediating all aspects of post-transcriptional regulation of gene expression, play crucial roles in cellular stress responses. RNA-binding proteins (RBPs), which interact with sequence/structural elements in RNAs to control the steps of RNA metabolism, have therefore emerged as central regulators of post-transcriptional responses to stress. Following exposure to a variety of stresses, the dynamic alterations in the RNA-protein interactome enable cells to respond to intracellular or extracellular perturbations by causing changes in mRNA splicing, polyadenylation, stability, translation, and localization. As RBPs play a central role in determining the cellular proteome both qualitatively and quantitatively, it has become increasingly evident that their abundance, availability, and functions are also highly regulated in response to stress. Exposure to stress initiates a series of signaling cascades that converge on post-translational modifications (PTMs) of RBPs, resulting in changes in their subcellular localization, association with stress granules, extracellular export, proteasomal degradation, and RNA-binding activities. These alterations in the fate and function of RBPs directly impact their post-transcriptional regulatory roles in cells under stress. Adopting the ubiquitous RBP HuR as a prototype, three scenarios illustrating the changes in nuclear-cytoplasmic localization, RNA-binding activity, export and degradation of HuR in response to inflammation, genotoxic stress, and heat shock depict the complex and interlinked regulatory mechanisms that control the fate and functions of RBPs under stress. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":" ","pages":"e1825"},"PeriodicalIF":7.3,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138446417","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: 0

Roles of the CCR4-Not complex in translation and dynamics of co-translation events. ccr4 -不复杂在翻译中的作用及共译事件的动态。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-11-27 DOI: 10.1002/wrna.1827

Martine A Collart, Léna Audebert, Martin Bushell

引用次数: 0

Long noncoding RNAs and their complex role in shaping and regulating arachidonic acid metabolism: Learning to love the (not-really) junk. 长链非编码rna及其在形成和调节花生四烯酸代谢中的复杂作用:学会热爱(并非真正的)垃圾。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-11-23 DOI: 10.1002/wrna.1828

Samuel Z Desind, Samira K Bell, Zachary M Davidson, Carol S Lutz

{"title":"Long noncoding RNAs and their complex role in shaping and regulating arachidonic acid metabolism: Learning to love the (not-really) junk.","authors":"Samuel Z Desind, Samira K Bell, Zachary M Davidson, Carol S Lutz","doi":"10.1002/wrna.1828","DOIUrl":"https://doi.org/10.1002/wrna.1828","url":null,"abstract":"Long noncoding RNAs (lncRNAs) have emerged as critical regulators in numerous biological processes. The arachidonic acid (AA) metabolic pathway is a fundamental biochemical pathway responsible for the enzymatic conversion of AA, a 20-carbon omega-six polyunsaturated fatty acid, into a variety of potent lipid signaling molecules known as eicosanoids. Eicosanoids are produced through the cyclooxygenase and lipoxygenase arms of the AA pathway and have diverse biological roles in both healthy and disease states, including cancer and inflammatory diseases. Cyclooxygenase 2 (COX-2), the inducible, rate-limiting enzyme of the cyclooxygenase arm, produces two main forms of eicosanoids: prostaglandins and thromboxanes. AA metabolized through the lipoxygenase arm by the action of 5-lipoxygenase (ALOX5) produces eicosanoids known as leukotrienes. COX-2 and ALOX5 gene expression are regulated through many different lncRNAs and microRNA (miRNA)-mediated mechanisms. As previously reviewed, noncoding RNAs affect transcription, splicing, alternative polyadenylation, messenger RNA stability, translation, and miRNA regulation of COX-2 and ALOX5 (Lutz and Cornett, 2013, Wiley Interdisciplinary Reviews. RNA, 4(5), 593-605). This current review discusses the intricate roles of lncRNAs, including MALAT1, NEAT1, HOTAIR, PACER, and others, in modulating the AA pathway. In this review update, we will delve into advancements in our understanding of AA gene expression regulation. We will explore the mechanisms of lncRNAs and their associated miRNAs and proteins known to regulate key components of the AA signaling pathway. We will also discuss the therapeutic potential of targeting lncRNA-mediated regulation, with a focus on modulating COX-2 and ALOX5 activity and downstream eicosanoid production for applications in inflammatory and oncological conditions. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":" ","pages":"e1828"},"PeriodicalIF":7.3,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138296152","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: 0

p53 and RNA viruses: The tug of war. p53和RNA病毒:拉锯战。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-11-20 DOI: 10.1002/wrna.1826

Apala Pal, Sachin Kumar Tripathi, Priya Rani, Meghana Rastogi, Saumitra Das

{"title":"p53 and RNA viruses: The tug of war.","authors":"Apala Pal, Sachin Kumar Tripathi, Priya Rani, Meghana Rastogi, Saumitra Das","doi":"10.1002/wrna.1826","DOIUrl":"https://doi.org/10.1002/wrna.1826","url":null,"abstract":"Host factors play essential roles in viral infection, and their interactions with viral proteins are necessary for establishing effective pathogenesis. p53 is a host factor that maintains genomic integrity by controlling cell-cycle progression and cell survival. It is a well-known tumor suppressor protein that gets activated by various stress signals, thereby regulating cellular pathways. The cellular outcomes from different stresses are tightly related to p53 dynamics, including its alterations at gene, mRNA, or protein levels. p53 also contributes to immune responses leading to the abolition of viral pathogens. In turn, the viruses have evolved strategies to subvert p53-mediated host responses to improve their life cycle and pathogenesis. Some viruses attenuate wild-type p53 (WT-p53) function for successful pathogenesis, including degradation and sequestration of p53. In contrast, some others exploit the WT-p53 function through regulation at the transcriptional/translational level to spread infection. One area in which the importance of such host factors is increasingly emerging is the positive-strand RNA viruses that cause fatal viral infections. In this review, we provide insight into all the possible mechanisms of p53 modulation exploited by the positive-strand RNA viruses to establish infection. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Regulation RNA in Disease and Development > RNA in Disease.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":" ","pages":"e1826"},"PeriodicalIF":7.3,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138177434","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: 0

Exploring the interplay between PARP1 and circRNA biogenesis and function. 探索PARP1与circRNA生物发生和功能之间的相互作用。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2023-11-13 DOI: 10.1002/wrna.1823

Hejer Dhahri, Yvonne N Fondufe-Mittendorf

{"title":"Exploring the interplay between PARP1 and circRNA biogenesis and function.","authors":"Hejer Dhahri, Yvonne N Fondufe-Mittendorf","doi":"10.1002/wrna.1823","DOIUrl":"10.1002/wrna.1823","url":null,"abstract":"PARP1 (poly-ADP-ribose polymerase 1) is a multidomain protein with a flexible and self-folding structure that allows it to interact with a wide range of biomolecules, including nucleic acids and target proteins. PARP1 interacts with its target molecules either covalently via PARylation or non-covalently through its PAR moieties induced by auto-PARylation. These diverse interactions allow PARP1 to participate in complex regulatory circuits and cellular functions. Although the most studied PARP1-mediated functions are associated with DNA repair and cellular stress response, subsequent discoveries have revealed additional biological functions. Based on these findings, PARP1 is now recognized as a major modulator of gene expression. Several discoveries show that this multifunctional protein has been intimately connected to several steps of mRNA biogenesis, from transcription initiation to mRNA splicing, polyadenylation, export, and translation of mRNA to proteins. Nevertheless, our understanding of PARP1's involvement in the biogenesis of both coding and noncoding RNA, notably circular RNA (circRNA), remains restricted. In this review, we outline the possible roles of PARP1 in circRNA biogenesis. A full examination of the regulatory roles of PARP1 in nuclear processes with an emphasis on circRNA may reveal new avenues to control dysregulation implicated in the pathogenesis of several diseases such as neurodegenerative disorders and cancers. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Processing > Splicing Regulation/Alternative Splicing.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":" ","pages":"e1823"},"PeriodicalIF":7.3,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11089078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92156780","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