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Spatial metabolomics in tissue injury and regeneration 组织损伤和再生中的空间代谢组学
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-06-19 DOI: 10.1016/j.gde.2024.102223
Rosalie GJ Rietjens , Gangqi Wang , Bernard M van den Berg, Ton J Rabelink
{"title":"Spatial metabolomics in tissue injury and regeneration","authors":"Rosalie GJ Rietjens ,&nbsp;Gangqi Wang ,&nbsp;Bernard M van den Berg,&nbsp;Ton J Rabelink","doi":"10.1016/j.gde.2024.102223","DOIUrl":"https://doi.org/10.1016/j.gde.2024.102223","url":null,"abstract":"<div><p>Tissue homeostasis is intricately linked to cellular metabolism and metabolite exchange within the tissue microenvironment. The orchestration of adaptive cellular responses during injury and repair depends critically upon metabolic adaptation. This adaptation, in turn, shapes cell fate decisions required for the restoration of tissue homeostasis. Understanding the nuances of metabolic processes within the tissue context and comprehending the intricate communication between cells is therefore imperative for unraveling the complexity of tissue homeostasis and the processes of injury and repair. In this review, we focus on mass spectrometry imaging as an advanced platform with the potential to provide such comprehensive insights into the metabolic instruction governing tissue function. Recent advances in this technology allow to decipher the intricate metabolic networks that determine cellular behavior in the context of tissue resilience, injury, and repair. These insights not only advance our fundamental understanding of tissue biology but also hold implications for therapeutic interventions by targeting metabolic pathways critical for maintaining tissue homeostasis.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102223"},"PeriodicalIF":4.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000728/pdfft?md5=c94475248a825a6dadd8f9593cc3ab77&pid=1-s2.0-S0959437X24000728-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141429105","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
Recent insights into N6-methyladenosine during viral infection 病毒感染过程中 N6-甲基腺苷的最新研究成果
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-06-19 DOI: 10.1016/j.gde.2024.102213
Stacy M Horner , Jordan V Reaves
{"title":"Recent insights into N6-methyladenosine during viral infection","authors":"Stacy M Horner ,&nbsp;Jordan V Reaves","doi":"10.1016/j.gde.2024.102213","DOIUrl":"https://doi.org/10.1016/j.gde.2024.102213","url":null,"abstract":"<div><p>The RNA modification of N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) controls many aspects of RNA function that impact biological processes, including viral infection. In this review, we highlight recent work that shapes our current understanding of the diverse mechanisms by which m<sup>6</sup>A can regulate viral infection by acting on viral or cellular mRNA molecules. We focus on emerging concepts and understanding, including how viral infection alters the localization and function of m<sup>6</sup>A machinery proteins, how m<sup>6</sup>A regulates antiviral innate immunity, and the multiple roles of m<sup>6</sup>A in regulating specific viral infections. We also summarize the recent studies on m<sup>6</sup>A during SARS-CoV-2 infection, focusing on points of convergence and divergence. Ultimately, this review provides a snapshot of the latest research on m<sup>6</sup>A during viral infection.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102213"},"PeriodicalIF":4.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141429111","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
Interplay between N6-adenosine RNA methylation and mRNA splicing N6 腺苷 RNA 甲基化与 mRNA 剪接之间的相互作用
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-06-04 DOI: 10.1016/j.gde.2024.102211
Majid Mehravar, Justin J-L Wong
{"title":"Interplay between N6-adenosine RNA methylation and mRNA splicing","authors":"Majid Mehravar,&nbsp;Justin J-L Wong","doi":"10.1016/j.gde.2024.102211","DOIUrl":"https://doi.org/10.1016/j.gde.2024.102211","url":null,"abstract":"<div><p><em>N</em><sup><em>6</em></sup>-methyladenosine (m<sup>6</sup>A) is the most abundant modification to mRNAs. Loss-of-function studies of main m<sup>6</sup>A regulators have indicated the role of m<sup>6</sup>A in pre-mRNA splicing. Recent studies have reported the role of splicing in preventing m<sup>6</sup>A deposition. Understanding the interplay between m<sup>6</sup>A and mRNA splicing holds the potential to clarify the significance of these fundamental molecular mechanisms in cell development and function, thereby shedding light on their involvement in the pathogenesis of myriad diseases.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102211"},"PeriodicalIF":4.0,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000601/pdfft?md5=fd8e41b31a43b93bfe83fc06ed7cf249&pid=1-s2.0-S0959437X24000601-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141242471","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
Exploring pseudouridylation: dysregulation in disease and therapeutic potential 探索假苷酸化：疾病中的失调与治疗潜力
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-06-03 DOI: 10.1016/j.gde.2024.102210
Maria Guillen-Angel , Jean-Yves Roignant
{"title":"Exploring pseudouridylation: dysregulation in disease and therapeutic potential","authors":"Maria Guillen-Angel ,&nbsp;Jean-Yves Roignant","doi":"10.1016/j.gde.2024.102210","DOIUrl":"https://doi.org/10.1016/j.gde.2024.102210","url":null,"abstract":"<div><p>Pseudouridine (Ψ), the most abundant RNA modification, plays a role in pre-mRNA splicing, RNA stability, protein translation efficiency, and cellular responses to environmental stress. Dysregulation of pseudouridylation is linked to human diseases. This review explores recent insights into the role of RNA pseudouridylation alterations in human disorders and the therapeutic potential of Ψ. We discuss the impact of the reduction of Ψ levels in ribosomal, messenger, and transfer RNA in RNA processing, protein translation, and consequently its role in neurodevelopmental diseases and cancer. Furthermore, we review the success of N1-methyl-Ψ messenger RNA vaccines against COVID-19 and the development of RNA-guided pseudouridylation enzymes for treating genetic diseases caused by premature stop codons.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102210"},"PeriodicalIF":4.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000595/pdfft?md5=fcabdf580120488af4c595d5ccc4e7c3&pid=1-s2.0-S0959437X24000595-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141242470","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
Exploring the role of ribosomal RNA modifications in cancer. 探索核糖体 RNA 修饰在癌症中的作用。
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-06-01 Epub Date: 2024-05-17 DOI: 10.1016/j.gde.2024.102204
Judith López, Sandra Blanco
{"title":"Exploring the role of ribosomal RNA modifications in cancer.","authors":"Judith López, Sandra Blanco","doi":"10.1016/j.gde.2024.102204","DOIUrl":"10.1016/j.gde.2024.102204","url":null,"abstract":"<p><p>Recent advances have highlighted the significant roles of post-transcriptional modifications in rRNA in various cancers. Evidence suggests that dysregulation of rRNA modifications acts as a common denominator in cancer development, with alterations in these modifications conferring competitive advantages to cancer cells. Specifically, rRNA modifications modulate protein synthesis and favor the specialized translation of oncogenic programs, thereby contributing to the formation of a protumorigenic proteome in cancer cells. These findings reveal a novel regulatory layer mediated by changes in the deposition of rRNA chemical modifications. Moreover, inhibition of these modifications in vitro and in preclinical studies demonstrates potential therapeutic applications. The recurrence of altered rRNA modification patterns across different types of cancer underscores their importance in cancer progression, proposing them as potential biomarkers and novel therapeutic targets. This review will highlight the latest insights into how post-transcriptional rRNA modifications contribute to cancer progression and summarize the main developments and ongoing challenges in this research area.</p>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"86 ","pages":"102204"},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140960858","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
Clinical Perspectives in Epitranscriptomics 表观转录组学的临床视角
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-06-01 DOI: 10.1016/j.gde.2024.102209
Eloy Santos-Pujol , Carlos Quero-Dotor , Manel Esteller
{"title":"Clinical Perspectives in Epitranscriptomics","authors":"Eloy Santos-Pujol ,&nbsp;Carlos Quero-Dotor ,&nbsp;Manel Esteller","doi":"10.1016/j.gde.2024.102209","DOIUrl":"10.1016/j.gde.2024.102209","url":null,"abstract":"<div><p>Epitranscriptomics, the study of reversible and dynamic chemical marks on the RNA, is rapidly emerging as a pivotal field in post-transcriptional gene expression regulation. Increasing knowledge about epitranscriptomic landscapes implicated in disease pathogenesis proves an invaluable opportunity for the identification of epitranscriptomic biomarkers and the development of new potential therapeutic drugs. Hence, recent advances in the characterization of these marks and associated enzymes in both health and disease blaze a trail toward the use of epitranscriptomics approaches for clinical applications. Here, we review the latest studies to provide a wide and comprehensive perspective of clinical epitranscriptomics and emphasize its transformative potential in shaping future health care paradigms.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102209"},"PeriodicalIF":4.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0959437X24000583/pdfft?md5=83ac12829bb0fe78db8f5cc5f476c05c&pid=1-s2.0-S0959437X24000583-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141200959","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
Quantitative mapping of the mammalian epitranscriptome 哺乳动物表转录组的定量绘图。
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-05-31 DOI: 10.1016/j.gde.2024.102212
Bo He , Yuting Chen , Chengqi Yi
{"title":"Quantitative mapping of the mammalian epitranscriptome","authors":"Bo He ,&nbsp;Yuting Chen ,&nbsp;Chengqi Yi","doi":"10.1016/j.gde.2024.102212","DOIUrl":"10.1016/j.gde.2024.102212","url":null,"abstract":"<div><p>The epitranscriptome encompasses a diverse array of dynamic and reversible RNA modifications, affecting both coding and noncoding RNAs. Over 170 types of RNA chemical modifications have been identified, underscoring the need for innovative detection methods to deepen our understanding of RNA modification roles and mechanisms. In particular, the base resolution and quantitative information on RNA modifications are critical for understanding the regulation and functions of RNA modifications. Based on detection throughput and principles, existing quantitative RNA modification detection methods can be categorized into two groups, including next-generation sequencing and nanopore direct RNA sequencing. In this review, we focus on methodologies for elucidating the base resolution and stoichiometric information of RNA modifications. In addition, we further discuss the challenges and the potential prospects of the quantitative RNA modification detection methods.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102212"},"PeriodicalIF":4.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141187118","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
NAT10 and cytidine acetylation in mRNA: intersecting paths in development and disease NAT10 和 mRNA 中的胞苷乙酰化：发育和疾病的交叉路径。
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-05-30 DOI: 10.1016/j.gde.2024.102207
Cyrinne Achour, Shalini Oberdoerffer
{"title":"NAT10 and cytidine acetylation in mRNA: intersecting paths in development and disease","authors":"Cyrinne Achour,&nbsp;Shalini Oberdoerffer","doi":"10.1016/j.gde.2024.102207","DOIUrl":"10.1016/j.gde.2024.102207","url":null,"abstract":"<div><p>N4-acetylcytidine (ac4C) is an RNA modification that is catalyzed by the enzyme NAT10. Constitutively found in tRNA and rRNA, ac4C displays a dynamic presence in mRNA that is shaped by developmental and induced shifts in NAT10 levels. However, deciphering ac4C functions in mRNA has been hampered by its context-dependent influences in translation and the complexity of isolating effects on specific mRNAs from other NAT10 activities. Recent advances have begun to overcome these obstacles by leveraging natural variations in mRNA acetylation in cancer, developmental transitions, and immune responses. Here, we synthesize the current literature with a focus on nuances that may fuel the perception of cellular discrepancies toward the development of a cohesive model of ac4C function in mRNA.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102207"},"PeriodicalIF":4.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141184951","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
Chromatin insulator mechanisms ensure accurate gene expression by controlling overall 3D genome organization 染色质绝缘体机制通过控制三维基因组的整体组织，确保基因的准确表达。
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-05-28 DOI: 10.1016/j.gde.2024.102208
Mallika Bhattacharya , Savanna F Lyda , Elissa P Lei
{"title":"Chromatin insulator mechanisms ensure accurate gene expression by controlling overall 3D genome organization","authors":"Mallika Bhattacharya ,&nbsp;Savanna F Lyda ,&nbsp;Elissa P Lei","doi":"10.1016/j.gde.2024.102208","DOIUrl":"10.1016/j.gde.2024.102208","url":null,"abstract":"<div><p>Chromatin insulators are DNA–protein complexes that promote specificity of enhancer–promoter interactions and maintain distinct transcriptional states through control of 3D genome organization. In this review, we highlight recent work visualizing how mammalian CCCTC-binding factor acts as a boundary to dynamic DNA loop extrusion mediated by cohesin. We also discuss new studies in both mammals and <em>Drosophila</em> that elucidate biological redundancy of chromatin insulator function and interplay with transcription with respect to topologically associating domain formation. Finally, we present novel concepts in spatiotemporal regulation of chromatin insulator function during differentiation and development and possible consequences of disrupted insulator activity on cellular proliferation.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"87 ","pages":"Article 102208"},"PeriodicalIF":4.0,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141176814","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
Dysregulation of transcriptional condensates in human disease: mechanisms, biological functions, and open questions 人类疾病中转录凝聚物的失调：机制、生物功能和未决问题
IF 4 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-05-23 DOI: 10.1016/j.gde.2024.102203
Kaeli M Mathias , Yiman Liu , Liling Wan
{"title":"Dysregulation of transcriptional condensates in human disease: mechanisms, biological functions, and open questions","authors":"Kaeli M Mathias ,&nbsp;Yiman Liu ,&nbsp;Liling Wan","doi":"10.1016/j.gde.2024.102203","DOIUrl":"https://doi.org/10.1016/j.gde.2024.102203","url":null,"abstract":"<div><p>Precise gene expression, crucial for normal development and health, depends on the co-ordinated assembly and function of various factors within the crowded nucleus. Recent evidence suggests that this process is in part regulated by mesoscale compartmentalization and concentration of transcriptional components within condensates, offering a new perspective on gene regulation. Dysregulation of transcriptional condensates is increasingly associated with diseases, indicating a potential role in pathogenesis. In this mini-review, we provide a concise overview of the current understanding of the formation and function of transcriptional condensates, with a specific focus on recent advances in their dysregulation and implications in diseases, notably cancer. We also address limitations in the field and highlight open questions for future research.</p></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"86 ","pages":"Article 102203"},"PeriodicalIF":4.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141089998","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
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