Wiley Interdisciplinary Reviews: RNA最新文献

Alternative Splicing and CaV-Associated Channelopathies. 选择性剪接和cav相关的通道病变。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-05-01 DOI: 10.1002/wrna.70016

Willy Munyao, Md Mostafizur Rahman, Samuel A Sabzanov, Elizabeth H Chu, Ruizhi Wang, Zhifei Wang, Yong Yu, Matteo Ruggiu

{"title":"Alternative Splicing and CaV-Associated Channelopathies.","authors":"Willy Munyao, Md Mostafizur Rahman, Samuel A Sabzanov, Elizabeth H Chu, Ruizhi Wang, Zhifei Wang, Yong Yu, Matteo Ruggiu","doi":"10.1002/wrna.70016","DOIUrl":"10.1002/wrna.70016","url":null,"abstract":"Voltage-gated calcium channels (VGCCs) are multi-subunit ion channel proteins that control and regulate a wide array of physiological processes. Their dysfunction has been implicated in several neurological, cardiac, psychiatric, endocrine, oncogenic, and muscular disorders. The diverse and specialized cellular functions involving VGCC-mediated calcium signaling stem from two primary mechanisms: differential and cell-specific expression of pore-forming (α1) and auxiliary subunit genes, and extensive alternative splicing of their pre-mRNA. All the 10 α1-encoding genes undergo alternative splicing to generate a wide array of cell-specific CaV variants with distinct biophysical, pharmacological, and protein-protein interaction properties. This proteomic diversity and the associated cell-specific expression signature of CaV splice variants are tightly regulated by trans-acting splicing factors-RNA-binding proteins that control the inclusion or skipping of alternatively spliced exons during post-transcriptional pre-mRNA processing. The discovery that several channelopathies are caused by aberrant splicing due to genetic mutations in either cis-acting binding elements on the pre-mRNA or in core splicing machinery components highlights the crucial role of alternative splicing in VGCC-related pathologies. These insights have opened new therapeutic avenues, as targeting the alternative splicing of disease-associated specific exons has recently emerged as a novel, promising treatment for neurodevelopmental disorders and channelopathies associated with splicing dysfunction.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 3","pages":"e70016"},"PeriodicalIF":6.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12149502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259041","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 Advances in Deep Learning Modeling of Polyadenylation Codes. 聚腺苷酸化代码的深度学习建模研究进展。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-05-01 DOI: 10.1002/wrna.70017

Emily Kunce Stroup, Tianjiao Sun, Qianru Li, John Carinato, Zhe Ji

{"title":"The Advances in Deep Learning Modeling of Polyadenylation Codes.","authors":"Emily Kunce Stroup, Tianjiao Sun, Qianru Li, John Carinato, Zhe Ji","doi":"10.1002/wrna.70017","DOIUrl":"10.1002/wrna.70017","url":null,"abstract":"3'-end cleavage and polyadenylation is an essential step of eukaryotic mRNA and lncRNA expression. The formation of a polyadenylation (polyA) site is determined by combinatory effects of multiple tandem motifs (~6 motifs in humans), each of which is bound by a protein subcomplex. However, motif occurrences and compositions are quite variable across individual polyA sites, leading to the technical challenge of quantifying polyadenylation activities and defining cleavage sites. Although conventional motif enrichment analyses and machine learning models identified contributing polyadenylation motifs, these cannot unbiasedly quantify motif crosstalk. Recently, several groups developed deep learning models to resolve sequence complexity, capture complex positional interactions among cis-regulatory motifs, examine polyA site formation, predict cleavage probability, and calculate site strength. These deep learning models have brought novel insights into polyadenylation biology, such as site configuration differences across species, cleavage heterogeneity, genomic parameters regulating site expression, and human genetic variants altering polyadenylation activities. In this review, we summarize the advances of deep learning models developed to address facets of polyadenylation regulation and discuss applications of the models.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 3","pages":"e70017"},"PeriodicalIF":6.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12138237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226884","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 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

The Role of 2'-O-Methylation in Epitranscriptomic Regulation: Gene Expression, Physiological Functions and Applications. 2'- o -甲基化在表转录组调控中的作用：基因表达、生理功能和应用。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2025-05-01 DOI: 10.1002/wrna.70018

Sayma Azeem, Imelda Margaretha Aritonang, Chi Peng, Yi-Shuian Huang

{"title":"The Role of 2'-O-Methylation in Epitranscriptomic Regulation: Gene Expression, Physiological Functions and Applications.","authors":"Sayma Azeem, Imelda Margaretha Aritonang, Chi Peng, Yi-Shuian Huang","doi":"10.1002/wrna.70018","DOIUrl":"10.1002/wrna.70018","url":null,"abstract":"Since the discovery of pseudouridine in the 1950s, the field of epitranscriptomics has expanded substantially, with over 330 RNA modifications now documented in the MODOMICS database. Among these, 2'-O-ribose methylation (2'-O-Me) is a prevalent modification characterized by the addition of a methyl group to the 2'-hydroxyl position of the ribose sugar, irrespective of the nucleotide bases. Initially detected in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA) in the 1970s, the methyltransferases responsible for 2'-O-Me were subsequently identified starting in the 1980s. Advancements in transcriptome-wide mapping techniques have since enabled precise identification of 2'-O-Me sites across various RNA species. Functional studies using knockdown or knockout models of specific 2'-O-Me methyltransferases have further elucidated their roles in different physiological processes. Notably, dysregulation of 2'-O-Me has been implicated in human diseases, including cancers and neurological disorders, underscoring its significance in controlling cellular homeostasis. This review covers the catalytic mechanisms and molecular functions of 2'-O-Me in different RNA species, discusses its physiological importance, and highlights the methods for transcriptome-wide mapping of this modification.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"16 3","pages":"e70018"},"PeriodicalIF":6.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310511","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