Wiley Interdisciplinary Reviews: RNA最新文献

The Functional Diversity of Chromatin-Associated RNA Binding Proteins in Transcriptional and Post-Transcriptional Regulation. 染色质相关RNA结合蛋白在转录和转录后调控中的功能多样性。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-05-01 DOI: 10.1002/wrna.70015

Min Zhou, Jun Yang, Chuan Huang

{"title":"The Functional Diversity of Chromatin-Associated RNA Binding Proteins in Transcriptional and Post-Transcriptional Regulation.","authors":"Min Zhou, Jun Yang, Chuan Huang","doi":"10.1002/wrna.70015","DOIUrl":"10.1002/wrna.70015","url":null,"abstract":"RNA-binding proteins (RBPs) are a diverse class of proteins that interact with their target RNA molecules to regulate gene expression at the transcriptional and post-transcriptional levels. RBPs contribute to almost all aspects of RNA processing with sequence-specific, structure-specific, and nonspecific binding modes. Advances in our understanding of the mechanisms of RBP-mediated regulatory networks consisting of DNAs, RNAs, and protein complexes and the association between these networks and human diseases have been made very recently. Here, we discuss the \"unconventional\" functions of RBPs in transcriptional regulation by focusing on the cutting-edge investigations of chromatin-associated RBPs (ChRBPs). We briefly introduce examples of how ChRBPs influence the genomic features and molecular structures at the level of transcription. In addition, we focus on the post-transcriptional functions of various RBPs that regulate the biogenesis, transportation, stability control, and translation ability of circular RNA molecules (circRNAs). Lastly, we raise several questions about the clinical significance and potential therapeutic utility of disease-relevant RBPs.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 3","pages":"e70015"},"PeriodicalIF":6.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128926","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

Post-Transcriptional Regulation of Gene Expression and the Intricate Life of Eukaryotic mRNAs. 基因表达的转录后调控和真核mrna的复杂生命。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70007

Carly L Lancaster, Kenneth H Moberg, Anita H Corbett

引用次数: 0

tRNA-Derived Fragments in Age-Related Diseases: A Systematic Review. 年龄相关疾病中的trna衍生片段：系统综述。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70013

Kamilla Bakowska-Zywicka, Alicja Rzepczak, Kinga Plawgo, Daria Sobanska, Agata Tyczewska

{"title":"tRNA-Derived Fragments in Age-Related Diseases: A Systematic Review.","authors":"Kamilla Bakowska-Zywicka, Alicja Rzepczak, Kinga Plawgo, Daria Sobanska, Agata Tyczewska","doi":"10.1002/wrna.70013","DOIUrl":"10.1002/wrna.70013","url":null,"abstract":"Aging is a progressive weakening of numerous functions of organisms resulting in diminished abilities to safeguard against environmental damage and augment physiological harmony. It is not a disease in itself; however, it is a main cause of debilitating and life-threatening chronic aging-related diseases (ARDs). tRNA-derived fragments (tDRs) are stable forms of tRNAs of 14-35 nt in length that function as regulatory small-RNA molecules. Here we aimed to perform a systematic review of original articles on the involvement of tDRs in the etiology of ARDs: their identification and characterization. The systematic review was conducted according to the Cochrane Handbook guidelines and the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) statement. Based on the eligibility criteria defined for the study, 21 original articles were included in this systematic review, covering 11 ARDs. The preferred research method used to study tDRs was high-throughput sequencing combined with RT-qPCR, and as a result, a number of tDRs were implicated in ARDs. Importantly, an in-depth analysis of the articles allowed us to identify several shortcomings: (i) the tDRs nomenclature varies between studies and articles, making it often difficult to precisely identify molecules differentiating in a given disease; (ii) the chosen tDRs have all been studied for a miRNA-like mechanism of action; however, tDRs also function in RNAi-independent ways, which need to be studied as well; (iii) to precisely identify tDRs, the sequencing techniques that overcome the issues of modifications harbored by tRNAs must be used.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 2","pages":"e70013"},"PeriodicalIF":6.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021530","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

Advances in Detection Methods for A-to-I RNA Editing. A-to-I RNA编辑检测方法研究进展

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70014

Yuxi Yang, Masayuki Sakurai

引用次数: 0

miR-135b: A Potential Biomarker for Pathological Diagnosis and Biological Therapy. miR-135b：病理诊断和生物治疗的潜在生物标志物

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70002

Dezhi Yan, Qingliu He, Chunjian Wang, Tian Li, Xueping Yi, Haisheng Yu, Wenfei Wu, Hanyun Yang, Wenzhao Wang, Liang Ma

{"title":"miR-135b: A Potential Biomarker for Pathological Diagnosis and Biological Therapy.","authors":"Dezhi Yan, Qingliu He, Chunjian Wang, Tian Li, Xueping Yi, Haisheng Yu, Wenfei Wu, Hanyun Yang, Wenzhao Wang, Liang Ma","doi":"10.1002/wrna.70002","DOIUrl":"10.1002/wrna.70002","url":null,"abstract":"MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs found in eukaryotes with post-transcriptional regulatory functions. A variety of miRNAs is differentially expressed in cancer tissues and thus can be used as biomarkers. microRNA-135b-5p (miR-135b) has been shown to be involved in the pathological processes of a variety of neoplastic and non-neoplastic diseases. Under different conditions, miR-135b has different tumor suppressive and carcinogenic effects. miR-135b regulates the development of cancer, including metabolism, proliferation, apoptosis, invasion, fibrosis, angiogenesis, immunomodulation, and drug resistance. miR-135b can be used as a new biomarker for tumor diagnosis and prognosis, which has the potential for clinical guidance. This article reviews the relevant research on miR-135B in the field of tumors, including the biogenesis background of miR-135b, the expression of miR-135b in tumors, and the related targets and signaling pathways of miR-135b mediating tumor progression in order to sort out and explore the clinical transformation value of miR-135b.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 2","pages":"e70002"},"PeriodicalIF":6.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143543773","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

The Role of Non-Coding RNA in Systemic Sclerosis: From Mechanism to Translation. 非编码RNA在系统性硬化症中的作用：从机制到翻译。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70003

Ruixuan Zhu, Zixin Pi, Yaqian Shi, Yangfan Xiao, Rong Xiao

引用次数: 0

Understanding GEMIN5 Interactions: From Structural and Functional Insights to Selective Translation. 理解GEMIN5相互作用：从结构和功能的见解到选择性翻译。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70008

Encarnacion Martinez-Salas, Salvador Abellan, Rosario Francisco-Velilla

{"title":"Understanding GEMIN5 Interactions: From Structural and Functional Insights to Selective Translation.","authors":"Encarnacion Martinez-Salas, Salvador Abellan, Rosario Francisco-Velilla","doi":"10.1002/wrna.70008","DOIUrl":"10.1002/wrna.70008","url":null,"abstract":"GEMIN5 is a predominantly cytoplasmic protein, initially identified as a member of the survival of motor neurons (SMN) complex. In addition, this abundant protein modulates diverse aspects of RNA-dependent processes, executing its functions through the formation of multi-component complexes. The modular organization of structural domains present in GEMIN5 enables this protein to perform various functions through its interaction with distinct partners. The protein is responsible for the recognition of small nuclear (sn)RNAs through its N-terminal region, and therefore for snRNP assembly. Beyond its role in spliceosome assembly, GEMIN5 regulates translation through the interaction with either RNAs or proteins. In the central region, a robust dimerization domain acts as a hub for protein-protein interaction, while a non-canonical RNA-binding site is located towards the C-terminus. Interestingly, GEMIN5 regulates the partitioning of mRNAs into polysomes, likely due to its RNA-binding capacity and its ability to bind native ribosomes. Understanding the functional and structural organization of the protein has brought an increasing interest in the last years with important implications in human disease. Patients carrying GEMIN5 biallelic variants suffer from neurodevelopmental delay, hypotonia, and cerebellar ataxia. This review discusses recent relevant works aimed at understanding the molecular mechanisms of GEMIN5 activity in gene expression, and also the challenges to discover new functions.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 2","pages":"e70008"},"PeriodicalIF":6.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11965781/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143773637","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

PiRNAs, PiRNA-Like, and PIWI Proteins in Somatic Cells: From Genetic Regulation to Disease Mechanisms. 体细胞中的pirna、pirna样蛋白和PIWI蛋白：从遗传调控到疾病机制。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70012

Jakub Dudzik, Paulina Czechowicz, Anna Więch-Walów, Jakub Sławski, James F Collawn, Rafal Bartoszewski

{"title":"PiRNAs, PiRNA-Like, and PIWI Proteins in Somatic Cells: From Genetic Regulation to Disease Mechanisms.","authors":"Jakub Dudzik, Paulina Czechowicz, Anna Więch-Walów, Jakub Sławski, James F Collawn, Rafal Bartoszewski","doi":"10.1002/wrna.70012","DOIUrl":"10.1002/wrna.70012","url":null,"abstract":"PIWI-interacting RNAs (piRNAs) are small non-coding RNA molecules that were originally described as responsible for binding to PIWI proteins to silence transposons in the germline genome. Here we discuss their controversial influence in regulating gene expression in human somatic cells. Although their functions in human somatic cells remain controversial, current research has focused on their potential contribution to human diseases including cancers and cardiovascular diseases (CVDs). These small RNA molecules directly interact with PIWI proteins to form piRNA-induced silencing complexes (piRISC). These complexes regulate not only long non-coding RNAs (lncRNAs) but also mRNAs in their 3' untranslated region. The controversy in human somatic cells occurs because not all of the reports demonstrate a direct interaction between the small non-coding RNAs and the PIWI proteins and also whether these established complexes have silencing activities. Therefore, their importance in human physiology and pathology continues to remain controversial. Here we discuss the challenges and limitations that need to be addressed in order to establish and harness the potential of these ncRNAs in potential clinical applications. In this review, we distinguish those examples that have been shown to function as silencing complexes (piRNAs) from those that appear to be silencing complexes based only on their ability to bind to PIWI proteins (piRNA-like) in human somatic cells.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 2","pages":"e70012"},"PeriodicalIF":6.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143987507","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

Two Birds With One Stone: RNA Virus Strategies to Manipulate G3BP1 and Other Stress Granule Components. 一石二鸟：RNA病毒策略操纵G3BP1和其他压力颗粒成分。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70005

Moh Egy Rahman Firdaus, Eliana Dukhno, Rupali Kapoor, Piotr Gerlach

{"title":"Two Birds With One Stone: RNA Virus Strategies to Manipulate G3BP1 and Other Stress Granule Components.","authors":"Moh Egy Rahman Firdaus, Eliana Dukhno, Rupali Kapoor, Piotr Gerlach","doi":"10.1002/wrna.70005","DOIUrl":"10.1002/wrna.70005","url":null,"abstract":"Stress granules (SGs) are membrane-less organelles forming in the cytoplasm in response to various types of stress, including viral infection. SGs and SG-associated proteins can play either a proviral role, by facilitating viral replication, or an antiviral role, by limiting the translation capacity, sequestering viral RNA, or contributing to the innate immune response of the cell. Consequently, viruses frequently target stress granules while counteracting cellular translation shut-off and the antiviral response. One strategy is to sequester SG components, not only to impair their assembly but also to repurpose and incorporate them into viral replication sites. G3BP1 is a key SG protein, driving its nucleation through protein-protein and protein-RNA interactions. Many cellular proteins, including other SG components, interact with G3BP1 via their ΦxFG motifs. Notably, SARS-CoV N proteins and alphaviral nsP3 proteins contain similar motifs, allowing them to compete for G3BP1. Several SG proteins have been shown to interact with the flaviviral capsid protein, which is primarily responsible for anchoring the viral genome inside the virion. There are also numerous examples of structured elements within coronaviral and flaviviral RNAs recruiting or sponging SG proteins. Despite these insights, the structural and biochemical details of SG-virus interactions remain largely unexplored and are known only for a handful of cases. Exploring their molecular relevance for infection and discovering new examples of direct SG-virus contacts is highly important, as advances in this area will open new possibilities for the design of targeted therapies and potentially broad-spectrum antivirals.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 2","pages":"e70005"},"PeriodicalIF":6.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143765260","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

Metabolism Meets Translation: Dietary and Metabolic Influences on tRNA Modifications and Codon Biased Translation. 代谢与翻译：饮食和代谢对tRNA修饰和密码子偏向翻译的影响。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-03-01 DOI: 10.1002/wrna.70011

Sherif Rashad, Aseel Marahleh

{"title":"Metabolism Meets Translation: Dietary and Metabolic Influences on tRNA Modifications and Codon Biased Translation.","authors":"Sherif Rashad, Aseel Marahleh","doi":"10.1002/wrna.70011","DOIUrl":"10.1002/wrna.70011","url":null,"abstract":"Transfer RNA (tRNA) is not merely a passive carrier of amino acids, but an active regulator of mRNA translation controlling codon bias and optimality. The synthesis of various tRNA modifications is regulated by many \"writer\" enzymes, which utilize substrates from metabolic pathways or dietary sources. Metabolic and bioenergetic pathways, such as one-carbon (1C) metabolism and the tricarboxylic acid (TCA) cycle produce essential substrates for tRNA modifications synthesis, such as S-Adenosyl methionine (SAM), sulfur species, and α-ketoglutarate (α-KG). The activity of these metabolic pathways can directly impact codon decoding and translation via regulating tRNA modifications levels. In this review, we discuss the complex interactions between diet, metabolism, tRNA modifications, and mRNA translation. We discuss how nutrient availability, bioenergetics, and intermediates of metabolic pathways, modulate the tRNA modification landscape to fine-tune protein synthesis. Moreover, we highlight how dysregulation of these metabolic-tRNA interactions contributes to disease pathogenesis, including cancer, metabolic disorders, and neurodegenerative diseases. We also discuss the new emerging field of GlycoRNA biology drawing parallels from glycobiology and metabolic diseases to guide future directions in this area. Throughout our discussion, we highlight the links between specific modifications, their metabolic/dietary precursors, and various diseases, emphasizing the importance of a metabolism-centric tRNA view in understanding many pathologies. Future research should focus on uncovering the interplay between metabolism and tRNA in specific cellular and disease contexts. Addressing these gaps will guide new research into novel disease interventions.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 2","pages":"e70011"},"PeriodicalIF":6.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677347","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