Wiley Interdisciplinary Reviews: RNA最新文献_第2页

Integrated Biochemical and Computational Methods for Deciphering RNA-Processing Codes. 破译 RNA 处理密码的生化和计算综合方法。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-11-01 DOI: 10.1002/wrna.1875

Chen Du, Weiliang Fan, Yu Zhou

{"title":"Integrated Biochemical and Computational Methods for Deciphering RNA-Processing Codes.","authors":"Chen Du, Weiliang Fan, Yu Zhou","doi":"10.1002/wrna.1875","DOIUrl":"https://doi.org/10.1002/wrna.1875","url":null,"abstract":"RNA processing involves steps such as capping, splicing, polyadenylation, modification, and nuclear export. These steps are essential for transforming genetic information in DNA into proteins and contribute to RNA diversity and complexity. Many biochemical methods have been developed to profile and quantify RNAs, as well as to identify the interactions between RNAs and RNA-binding proteins (RBPs), especially when coupled with high-throughput sequencing technologies. With the rapid accumulation of diverse data, it is crucial to develop computational methods to convert the big data into biological knowledge. In particular, machine learning and deep learning models are commonly utilized to learn the rules or codes governing the transformation from DNA sequences to intriguing RNAs based on manually designed or automatically extracted features. When precise enough, the RNA codes can be incredibly useful for predicting RNA products, decoding the molecular mechanisms, forecasting the impact of disease variants on RNA processing events, and identifying driver mutations. In this review, we systematically summarize the biochemical and computational methods for deciphering five important RNA codes related to alternative splicing, alternative polyadenylation, RNA localization, RNA modifications, and RBP binding. For each code, we review the main types of experimental methods used to generate training data, as well as the key features, strategic model structures, and advantages of representative tools. We also discuss the challenges encountered in developing predictive models using large language models and extensive domain knowledge. Additionally, we highlight useful resources and propose ways to improve computational tools for studying RNA codes.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 6","pages":"e1875"},"PeriodicalIF":6.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142629055","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

Three Stages of Nascent Protein Translocation Through the Ribosome Exit Tunnel. 新生蛋白质通过核糖体出口隧道转运的三个阶段

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-11-01 DOI: 10.1002/wrna.1873

Michal H Kolář, Hugo McGrath, Felipe C Nepomuceno, Michaela Černeková

{"title":"Three Stages of Nascent Protein Translocation Through the Ribosome Exit Tunnel.","authors":"Michal H Kolář, Hugo McGrath, Felipe C Nepomuceno, Michaela Černeková","doi":"10.1002/wrna.1873","DOIUrl":"https://doi.org/10.1002/wrna.1873","url":null,"abstract":"All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and recycling. In fact, peptide bonds are formed only during the elongation phase, which comprises periodic association of transfer RNAs and multiple auxiliary proteins with the ribosome and the addition of an amino acid to the nascent polypeptide one at a time. The protein spends a considerable amount of time attached to the ribosome. Here, we conceptually divide this portion of the protein lifetime into three stages. We define each stage on the basis of the position of the N-terminus of the nascent polypeptide within the ribosome exit tunnel and the context of the catalytic center. We argue that nascent polypeptides experience a variety of forces that determine how they translocate through the tunnel and interact with the tunnel walls. We review current knowledge about nascent polypeptide translocation and identify several white spots in our understanding of the birth of proteins.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 6","pages":"e1873"},"PeriodicalIF":6.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576877","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

Current Understandings and Open Hypotheses on Extracellular Circular RNAs. 关于细胞外环状 RNA 的现有认识和开放性假设。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-11-01 DOI: 10.1002/wrna.1872

Jasper Verwilt, Marieke Vromman

引用次数: 0

Decoding the role of RNA sequences and their interactions in influenza A virus infection and adaptation. 解码 RNA 序列及其相互作用在甲型流感病毒感染和适应中的作用。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-11-01 DOI: 10.1002/wrna.1871

Satya P Sharma, Mamta Chawla-Sarkar, Rajat Sandhir, Dipanjan Dutta

{"title":"Decoding the role of RNA sequences and their interactions in influenza A virus infection and adaptation.","authors":"Satya P Sharma, Mamta Chawla-Sarkar, Rajat Sandhir, Dipanjan Dutta","doi":"10.1002/wrna.1871","DOIUrl":"https://doi.org/10.1002/wrna.1871","url":null,"abstract":"Influenza viruses (types A, B, C, and D) belong to the family orthomyxoviridae. Out of all the influenza types, influenza A virus (IAV) causes human pandemic outbreaks. Its pandemic potential is predominantly attributed to the genetic reassortment favored by a broad spectrum of host species that could lead to an antigenic shift along with a high rate of mutations in its genome, presenting a possibility of subtypes with heightened pathogenesis and virulence in humans (antigenic drift). In addition to antigenic shift and drift, there are several other inherent properties of its viral RNA species (vRNA, vmRNA, and cRNA) that significantly contribute to the success of specific stages of viral infection. In this review, we compile the key features of IAV RNA, such as sequence motifs and secondary structures, their functional significance in the infection cycle, and their overall impact on the virus's adaptive and evolutionary fitness. Because many of these motifs and folds are conserved, we also assess the existing antiviral approaches focused on targeting IAV RNA. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 6","pages":"e1871"},"PeriodicalIF":6.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583928","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 Definition of RNA Age Related to RNA Sequence Changes. 与RNA序列变化相关的RNA年龄的定义。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-11-01 DOI: 10.1002/wrna.1876

Zhongneng Xu, Shuichi Asakawa

{"title":"The Definition of RNA Age Related to RNA Sequence Changes.","authors":"Zhongneng Xu, Shuichi Asakawa","doi":"10.1002/wrna.1876","DOIUrl":"https://doi.org/10.1002/wrna.1876","url":null,"abstract":"Ribonucleic acid (RNA) undergoes dynamic changes in its structure and function under various intracellular and extracellular conditions over time. However, there is a lack of research on the concept of the RNA age to describe its diverse fates. This study proposes a definition of RNA age to address this issue. RNA age was defined as a sequence of numbers wherein the elements in the sequence were the nucleotide ages of the ribonucleotide residues in the RNA. Mean nucleotide age was used to represent RNA age. This definition describes the temporal properties of RNAs that have undergone diverse life histories and reflects the dynamic state of each ribonucleotide residue, which can be expressed mathematically. Notably, events (including base insertions, base deletions, and base substitutions) are likely to cause RNA to become younger or older when using mean nucleotide ages to represent the RNA age. Although information, including the presence of added markers in RNA, chemical modification structure of the RNA, and the excision of introns in the mRNA in cells, may provide a basis for identifying RNA age, little is known about determining the RNA age of extracellular RNA in the wild. Nonetheless, we believe that RNA age has an important relationship with the diverse biological properties of RNA under intracellular and extracellular conditions. Therefore, our proposed definition of RNA age offers new perspectives for studying dynamic changes in RNA function, RNA aging, ancient RNA, environmental RNA, and the ages of other biomolecules.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 6","pages":"e1876"},"PeriodicalIF":6.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142772813","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 landscape of lncRNAs in cell granules: Insights into their significance in cancer. 细胞颗粒中的 lncRNAs 景观：洞察它们在癌症中的意义

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-09-01 DOI: 10.1002/wrna.1870

Carolina Mathias, Ana Carolina Rodrigues, Suelen Cristina Soares Baal, Alexandre Luiz Korte de Azevedo, Vanessa Nascimento Kozak, Leticia Ferreira Alves, Jaqueline Carvalho de Oliveira, Sonia Guil, Daniela Fiori Gradia

{"title":"The landscape of lncRNAs in cell granules: Insights into their significance in cancer.","authors":"Carolina Mathias, Ana Carolina Rodrigues, Suelen Cristina Soares Baal, Alexandre Luiz Korte de Azevedo, Vanessa Nascimento Kozak, Leticia Ferreira Alves, Jaqueline Carvalho de Oliveira, Sonia Guil, Daniela Fiori Gradia","doi":"10.1002/wrna.1870","DOIUrl":"https://doi.org/10.1002/wrna.1870","url":null,"abstract":"Cellular compartmentalization, achieved through membrane-based compartments, is a fundamental aspect of cell biology that contributes to the evolutionary success of cells. While organelles have traditionally been the focus of research, membrane-less organelles (MLOs) are emerging as critical players, exhibiting distinct morphological features and unique molecular compositions. Recent research highlights the pivotal role of long noncoding RNAs (lncRNAs) in MLOs and their involvement in various cellular processes across different organisms. In the context of cancer, dysregulation of MLO formation, influenced by altered lncRNA expression, impacts chromatin organization, oncogenic transcription, signaling pathways, and telomere lengthening. This review synthesizes the current understanding of lncRNA composition within MLOs, delineating their functions and exploring how their dysregulation contributes to human cancers. Environmental challenges in tumorigenesis, such as nutrient deprivation and hypoxia, induce stress granules, promoting cancer cell survival and progression. Advancements in biochemical techniques, particularly single RNA imaging methods, offer valuable tools for studying RNA functions within live cells. However, detecting low-abundance lncRNAs remains challenging due to their limited expression levels. The correlation between lncRNA expression and pathological conditions, particularly cancer, should be explored, emphasizing the importance of single-cell studies for precise biomarker identification and the development of personalized therapeutic strategies. This article is categorized under: RNA Export and Localization > RNA Localization RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 5","pages":"e1870"},"PeriodicalIF":6.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142296748","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

Orchestrated centers for the production of proteins or "translation factories". 精心策划的蛋白质生产中心或 "翻译工厂"。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-07-01 DOI: 10.1002/wrna.1867

Robert A Crawford, Matthew Eastham, Martin R Pool, Mark P Ashe

引用次数: 0

Pericentromeric satellite RNAs as flexible protein partners in the regulation of nuclear structure. 核周边卫星 RNA 是调节核结构的灵活蛋白质伙伴。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-07-01 DOI: 10.1002/wrna.1868

Mariana Lopes, Sandra Louzada, Margarida Gama-Carvalho, Raquel Chaves

{"title":"Pericentromeric satellite RNAs as flexible protein partners in the regulation of nuclear structure.","authors":"Mariana Lopes, Sandra Louzada, Margarida Gama-Carvalho, Raquel Chaves","doi":"10.1002/wrna.1868","DOIUrl":"https://doi.org/10.1002/wrna.1868","url":null,"abstract":"Pericentromeric heterochromatin is mainly composed of satellite DNA sequences. Although being historically associated with transcriptional repression, some pericentromeric satellite DNA sequences are transcribed. The transcription events of pericentromeric satellite sequences occur in highly flexible biological contexts. Hence, the apparent randomness of pericentromeric satellite transcription incites the discussion about the attribution of biological functions. However, pericentromeric satellite RNAs have clear roles in the organization of nuclear structure. Silencing pericentromeric heterochromatin depends on pericentromeric satellite RNAs, that, in a feedback mechanism, contribute to the repression of pericentromeric heterochromatin. Moreover, pericentromeric satellite RNAs can also act as scaffolding molecules in condensate subnuclear structures (e.g., nuclear stress bodies). Since the formation/dissociation of nuclear condensates provides cell adaptability, pericentromeric satellite RNAs can be an epigenetic platform for regulating (sub)nuclear structure. We review current knowledge about pericentromeric satellite RNAs that, irrespective of the meaning of biological function, should be functionally addressed in regular and disease settings. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA in Disease and Development > RNA in Disease.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 4","pages":"e1868"},"PeriodicalIF":6.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555613","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

Synthetic antibodies for accelerated RNA crystallography. 用于加速 RNA 晶体学的合成抗体。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-07-01 DOI: 10.1002/wrna.1869

Saurja DasGupta

{"title":"Synthetic antibodies for accelerated RNA crystallography.","authors":"Saurja DasGupta","doi":"10.1002/wrna.1869","DOIUrl":"https://doi.org/10.1002/wrna.1869","url":null,"abstract":"RNA structure is crucial to a wide range of cellular processes. The intimate relationship between macromolecular structure and function necessitates the determination of high-resolution structures of functional RNA molecules. X-ray crystallography is the predominant technique used for macromolecular structure determination; however, solving RNA structures has been more challenging than their protein counterparts, as reflected in their poor representation in the Protein Data Bank (<1%). Antibody-assisted RNA crystallography is a relatively new technique that promises to accelerate RNA structure determination by employing synthetic antibodies (Fabs) as crystallization chaperones that are specifically raised against target RNAs. Antibody chaperones facilitate the formation of ordered crystal lattices by minimizing RNA flexibility and replacing unfavorable RNA-RNA contacts with contacts between chaperone molecules. Atomic coordinates of these antibody fragments can also be used as search models to obtain phase information during structure determination. Antibody-assisted RNA crystallography has enabled the structure determination of 15 unique RNA targets, including 11 in the last 6 years. In this review, I cover the historical development of antibody fragments as crystallization chaperones and their application to diverse RNA targets. I discuss how the first structures of antibody-RNA complexes informed the design of second-generation antibodies and led to the development of portable crystallization modules that have greatly reduced the uncertainties associated with RNA crystallography. Finally, I outline unexplored avenues that can increase the impact of this technology in structural biology research and discuss potential applications of antibodies as affinity reagents for interrogating RNA biology outside of their use in crystallography. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 4","pages":"e1869"},"PeriodicalIF":6.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074091","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

Novel insights on the positive correlation between sense and antisense pairs on gene expression. 有义和反义配对基因表达正相关的新见解。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-07-01 DOI: 10.1002/wrna.1864

Subhadeep Das, Maria Paula Zea Rojas, Elizabeth J Tran

{"title":"Novel insights on the positive correlation between sense and antisense pairs on gene expression.","authors":"Subhadeep Das, Maria Paula Zea Rojas, Elizabeth J Tran","doi":"10.1002/wrna.1864","DOIUrl":"10.1002/wrna.1864","url":null,"abstract":"A considerable proportion of the eukaryotic genome undergoes transcription, leading to the generation of noncoding RNA molecules that lack protein-coding information and are not subjected to translation. These noncoding RNAs (ncRNAs) are well recognized to have essential roles in several biological processes. Long noncoding RNAs (lncRNAs) represent the most extensive category of ncRNAs found in the human genome. Much research has focused on investigating the roles of cis-acting lncRNAs in the regulation of specific target gene expression. In the majority of instances, the regulation of sense gene expression by its corresponding antisense pair occurs in a negative (discordant) manner, resulting in the suppression of the target genes. The notion that a negative correlation exists between sense and antisense pairings is, however, not universally valid. In fact, several recent studies have reported a positive relationship between corresponding cis antisense pairs within plants, budding yeast, and mammalian cancer cells. The positive (concordant) correlation between anti-sense and sense transcripts leads to an increase in the level of the sense transcript within the same genomic loci. In addition, mechanisms such as altering chromatin structure, the formation of R loops, and the recruitment of transcription factors can either enhance transcription or stabilize sense transcripts through their antisense pairs. The primary objective of this work is to provide a comprehensive understanding of both aspects of antisense regulation, specifically focusing on the positive correlation between sense and antisense transcripts in the context of eukaryotic gene expression, including its implications towards cancer progression. This article is categorized under: RNA Processing > 3' End Processing Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":"15 4","pages":"e1864"},"PeriodicalIF":6.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11626863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861106","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