Wiley Interdisciplinary Reviews: RNA最新文献_第3页

Origin of functional de novo genes in humans from "hopeful monsters". 人类功能性新基因源自 "希望的怪物"。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1845

Xiaoge Liu, Chunfu Xiao, Xinwei Xu, Jie Zhang, Fan Mo, Jia-Yu Chen, Nicholas Delihas, Li Zhang, Ni A An, Chuan-Yun Li

{"title":"Origin of functional de novo genes in humans from \"hopeful monsters\".","authors":"Xiaoge Liu, Chunfu Xiao, Xinwei Xu, Jie Zhang, Fan Mo, Jia-Yu Chen, Nicholas Delihas, Li Zhang, Ni A An, Chuan-Yun Li","doi":"10.1002/wrna.1845","DOIUrl":"10.1002/wrna.1845","url":null,"abstract":"For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a \"motherless\" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely \"motherless\" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or \"hopeful monsters,\" for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":null,"pages":null},"PeriodicalIF":7.3,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140858115","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

RNA base editors: The emerging approach of RNA therapeutics. RNA 碱基编辑器：新出现的 RNA 治疗方法。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1844

Jinghui Song, Nan Luo, Liting Dong, Jinying Peng, Chengqi Yi

引用次数: 0

RNA-binding proteins in pain. 疼痛中的 RNA 结合蛋白

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1843

Patrick R Smith, Zachary T Campbell

引用次数: 0

To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes. 启动还是不启动？对 eIF2A、eIF2D 和 MCT-1-DENR 将启动子 tRNA 运送到核糖体的关键评估。

IF 6.4 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1833

Daisy J Grove, Paul J Russell, Michael G Kearse

{"title":"To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes.","authors":"Daisy J Grove, Paul J Russell, Michael G Kearse","doi":"10.1002/wrna.1833","DOIUrl":"10.1002/wrna.1833","url":null,"abstract":"Selection of the correct start codon is critical for high-fidelity protein synthesis. In eukaryotes, this is typically governed by a multitude of initiation factors (eIFs), including eIF2·GTP that directly delivers the initiator tRNA (Met-tRNAi Met ) to the P site of the ribosome. However, numerous reports, some dating back to the early 1970s, have described other initiation factors having high affinity for the initiator tRNA and the ability of delivering it to the ribosome, which has provided a foundation for further work demonstrating non-canonical initiation mechanisms using alternative initiation factors. Here we provide a critical analysis of current understanding of eIF2A, eIF2D, and the MCT-1·DENR dimer, the evidence surrounding their ability to initiate translation, their implications in human disease, and lay out important key questions for the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Mechanisms Translation > Regulation.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11260288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140022765","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

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

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1837

Ahmadreza Mofayezi, Mahdieh Jadaliha, Fatemeh-Zahra Zangeneh, Vahid Khoddami

{"title":"Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes.","authors":"Ahmadreza Mofayezi, Mahdieh Jadaliha, Fatemeh-Zahra Zangeneh, Vahid Khoddami","doi":"10.1002/wrna.1837","DOIUrl":"10.1002/wrna.1837","url":null,"abstract":"Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":null,"pages":null},"PeriodicalIF":7.3,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140132710","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

Multiple structural flavors of RNase P in precursor tRNA processing. RNase P 在前体 tRNA 处理过程中的多种结构。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1835

Sagar Sridhara

{"title":"Multiple structural flavors of RNase P in precursor tRNA processing.","authors":"Sagar Sridhara","doi":"10.1002/wrna.1835","DOIUrl":"10.1002/wrna.1835","url":null,"abstract":"The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":null,"pages":null},"PeriodicalIF":7.3,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140120813","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

Navigating the landscapes of spatial transcriptomics: How computational methods guide the way. 空间转录组学的导航：计算方法如何指引方向。

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1839

Runze Li, Xu Chen, Xuerui Yang

{"title":"Navigating the landscapes of spatial transcriptomics: How computational methods guide the way.","authors":"Runze Li, Xu Chen, Xuerui Yang","doi":"10.1002/wrna.1839","DOIUrl":"10.1002/wrna.1839","url":null,"abstract":"Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single-cell, multi-cellular, or sub-cellular resolution, while retaining the information of geometric localizations of cells in complex tissues. The coupling of cell spatial information and its molecular characteristics generates a novel multi-modal high-throughput data source, which poses new challenges for the development of analytical methods for data-mining. Spatial transcriptomic data are often highly complex, noisy, and biased, presenting a series of difficulties, many unresolved, for data analysis and generation of biological insights. In addition, to keep pace with the ever-evolving spatial transcriptomic experimental technologies, the existing analytical theories and tools need to be updated and reformed accordingly. In this review, we provide an overview and discussion of the current computational approaches for mining of spatial transcriptomics data. Future directions and perspectives of methodology design are proposed to stimulate further discussions and advances in new analytical models and algorithms. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Computational Analyses of RNA RNA Export and Localization > RNA Localization.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":null,"pages":null},"PeriodicalIF":7.3,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140289106","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

Small-RNA-guided histone modifications and somatic genome elimination in ciliates. 小核糖核酸引导的组蛋白修饰与纤毛虫体细胞基因组的消除

IF 7.3 2区生物学

Wiley Interdisciplinary Reviews: RNA Pub Date : 2024-03-01 DOI: 10.1002/wrna.1848

Thomas Balan, Leticia Koch Lerner, Daniel Holoch, Sandra Duharcourt

{"title":"Small-RNA-guided histone modifications and somatic genome elimination in ciliates.","authors":"Thomas Balan, Leticia Koch Lerner, Daniel Holoch, Sandra Duharcourt","doi":"10.1002/wrna.1848","DOIUrl":"10.1002/wrna.1848","url":null,"abstract":"Transposable elements and other repeats are repressed by small-RNA-guided histone modifications in fungi, plants and animals. The specificity of silencing is achieved through base-pairing of small RNAs corresponding to the these genomic loci to nascent noncoding RNAs, which allows the recruitment of histone methyltransferases that methylate histone H3 on lysine 9. Self-reinforcing feedback loops enhance small RNA production and ensure robust and heritable repression. In the unicellular ciliate Paramecium tetraurelia, small-RNA-guided histone modifications lead to the elimination of transposable elements and their remnants, a definitive form of repression. In this organism, germline and somatic functions are separated within two types of nuclei with different genomes. At each sexual cycle, development of the somatic genome is accompanied by the reproducible removal of approximately a third of the germline genome. Instead of recruiting a H3K9 methyltransferase, small RNAs corresponding to eliminated sequences tether Polycomb Repressive Complex 2, which in ciliates has the unique property of catalyzing both lysine 9 and lysine 27 trimethylation of histone H3. These histone modifications that are crucial for the elimination of transposable elements are thought to guide the endonuclease complex, which triggers double-strand breaks at these specific genomic loci. The comparison between ciliates and other eukaryotes underscores the importance of investigating small-RNAs-directed chromatin silencing in a diverse range of organisms. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action.","PeriodicalId":23886,"journal":{"name":"Wiley Interdisciplinary Reviews: RNA","volume":null,"pages":null},"PeriodicalIF":7.3,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854687","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

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":null,"pages":null},"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