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Current Opinion in Genetics & Development最新文献

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Insights and Interventions in Age-Associated Inflammation 年龄相关炎症的见解和干预措施。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-01-20 DOI: 10.1016/j.gde.2024.102306
Haoyan Huang , Jie Ren , Guang-Hui Liu
{"title":"Insights and Interventions in Age-Associated Inflammation","authors":"Haoyan Huang ,&nbsp;Jie Ren ,&nbsp;Guang-Hui Liu","doi":"10.1016/j.gde.2024.102306","DOIUrl":"10.1016/j.gde.2024.102306","url":null,"abstract":"<div><div>Aging is a systemic, complex, and heterogeneous process characterized by a progressive decline in physiological functions, rendering it a major risk factor for various chronic diseases. Chronic inflammation has emerged as both a hallmark and a driver in this complicated process. This persistent inflammatory state arises from a spectrum of stimuli, ranging from external pathogens to internal cellular remnants, to metabolic dysregulation, and to chronic stress. Here, we examine recent mechanistic advances into the driving forces behind age-related chronic inflammation, explore promising anti-inflammatory strategies to mitigate aging, and address current challenges, proposing future directions to propel this evolving field toward translational breakthrough.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102306"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015664","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
Beyond equilibrium: roles of RNAs in condensate control 超越平衡：rna在冷凝控制中的作用。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-01-14 DOI: 10.1016/j.gde.2024.102304
Fernando Muzzopappa, Fabian Erdel
{"title":"Beyond equilibrium: roles of RNAs in condensate control","authors":"Fernando Muzzopappa,&nbsp;Fabian Erdel","doi":"10.1016/j.gde.2024.102304","DOIUrl":"10.1016/j.gde.2024.102304","url":null,"abstract":"<div><div>Membraneless subcompartments organize various activities in the cell nucleus. Some of them are formed through phase separation that is driven by the polymeric and multivalent nature of biomolecules. Here, we discuss the role of RNAs in regulating nuclear subcompartments. On the one hand, chromatin-associated RNA molecules may act as binding platforms that recruit molecules to specific genomic loci. On the other hand, RNA molecules may act as multivalent scaffolds that stabilize biomolecular condensates. The active production and processing of RNAs inside of nuclear subcompartments drives them out of thermodynamic equilibrium and thereby modulates their properties. Accordingly, RNA content and transcriptional activity appear as key determinants of the biophysical and functional nature of nuclear substructures.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102304"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015661","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
Genome folding by cohesin 基因组内聚折叠。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-01-18 DOI: 10.1016/j.gde.2025.102310
Shutao Qi , Zhubing Shi , Hongtao Yu
{"title":"Genome folding by cohesin","authors":"Shutao Qi ,&nbsp;Zhubing Shi ,&nbsp;Hongtao Yu","doi":"10.1016/j.gde.2025.102310","DOIUrl":"10.1016/j.gde.2025.102310","url":null,"abstract":"<div><div>Chromosomes in eukaryotic cells undergo compaction at multiple levels and are folded into hierarchical structures to fit into the nucleus with limited dimensions. Three-dimensional genome organization needs to be coordinated with chromosome-templated processes, including DNA replication and gene transcription. As an ATPase molecular machine, the cohesin complex is a major driver of genome folding, which regulates transcription by modulating promoter–enhancer contacts. Here, we review our current understanding of genome folding by cohesin. We summarize the available evidence supporting a role of loop extrusion by cohesin in forming chromatin loops and topologically associating domains. We describe different conformations of cohesin and discuss the regulation of loop extrusion by cohesin-binding factors and loop-extrusion barriers. Finally, we propose a dimeric inchworm model for cohesin-mediated loop extrusion.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102310"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015663","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
Rewiring cancer: 3D genome determinants of cancer hallmarks 癌症重新布线：癌症特征的三维基因组决定因素。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-01-24 DOI: 10.1016/j.gde.2024.102307
Maria E Amodeo , Christine E Eyler , Sarah E Johnstone
{"title":"Rewiring cancer: 3D genome determinants of cancer hallmarks","authors":"Maria E Amodeo ,&nbsp;Christine E Eyler ,&nbsp;Sarah E Johnstone","doi":"10.1016/j.gde.2024.102307","DOIUrl":"10.1016/j.gde.2024.102307","url":null,"abstract":"<div><div>In modern cancer biology, Hanahan and Weinberg’s classic depiction of the Hallmarks of Cancer serves as a heuristic for understanding malignant phenotypes <span><span>[1]</span></span>. Genetic determinants of these phenotypes promote cancer induction and progression, and these mutations drive current approaches to understanding and treating cancer. Meanwhile, for over a century, pathologists have noted that profound alterations of nuclear structure accompany transformation, integrating these changes into diagnostic classifications (Figure 1). Nevertheless, the relationship of nuclear organization to malignant phenotypes has lagged. Recent advances yield profound insight into the 3D genome’s relationship with cancer phenotypes, suggesting that spatial genome organization influences many, if not all, of these malignant features. Here, we highlight recent discoveries elucidating connections between 3D genome organization and cancer phenotypes.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102307"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043279","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
Decoding N6-methyladenosine’s dynamic role in stem cell fate and early embryo development: insights into RNA–chromatin interactions 解码n6 -甲基腺苷在干细胞命运和早期胚胎发育中的动态作用：rna -染色质相互作用的见解
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-02-04 DOI: 10.1016/j.gde.2025.102311
Lei Yang , Mingli Ma , Yawei Gao , Jun Liu
{"title":"Decoding N6-methyladenosine’s dynamic role in stem cell fate and early embryo development: insights into RNA–chromatin interactions","authors":"Lei Yang ,&nbsp;Mingli Ma ,&nbsp;Yawei Gao ,&nbsp;Jun Liu","doi":"10.1016/j.gde.2025.102311","DOIUrl":"10.1016/j.gde.2025.102311","url":null,"abstract":"<div><div><em>N</em><sup>6</sup>-methyladenosine (m<sup>6</sup>A), a reversible and dynamic RNA modification, plays pivotal roles in regulating stem cell pluripotency and early embryogenesis. Disruptions in m<sup>6</sup>A homeostasis lead to profound developmental defects, impairing processes such as stem cell self-renewal, lineage specification, oocyte maturation, zygotic genome activation, and maternal RNA degradation after fertilization. Beyond its well-recognized roles in mRNA transport, stability, and translation, recent studies have highlighted m<sup>6</sup>A’s critical role in transcriptional regulation through intricate RNA–chromatin interactions, notably involving chromatin-associated regulatory RNAs (carRNAs) and retrotransposon RNAs. This review delves into the dynamic regulatory landscape of m<sup>6</sup>A, highlighting its critical interplay with chromatin modifications, and explores its broader implications in stem cell biology and early embryonic development.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102311"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143168794","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
Recipes and ingredients for deep learning models of 3D genome folding 3D基因组折叠的深度学习模型的配方和成分。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-01-24 DOI: 10.1016/j.gde.2024.102308
Paulina N Smaruj , Yao Xiao , Geoffrey Fudenberg
{"title":"Recipes and ingredients for deep learning models of 3D genome folding","authors":"Paulina N Smaruj ,&nbsp;Yao Xiao ,&nbsp;Geoffrey Fudenberg","doi":"10.1016/j.gde.2024.102308","DOIUrl":"10.1016/j.gde.2024.102308","url":null,"abstract":"<div><div>Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture, training, evaluation, and interpretation methods, highlighting the capabilities and limitations of different models. In each area, we highlight challenges, opportunities, and potential future directions for genome-folding models.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102308"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043275","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 connection between RNA splicing and intellectual disability 探索RNA剪接与智力缺陷之间的联系
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-02-08 DOI: 10.1016/j.gde.2025.102322
Anthony Caputo, Ashleigh E Schaffer
{"title":"Exploring the connection between RNA splicing and intellectual disability","authors":"Anthony Caputo,&nbsp;Ashleigh E Schaffer","doi":"10.1016/j.gde.2025.102322","DOIUrl":"10.1016/j.gde.2025.102322","url":null,"abstract":"<div><div>Intellectual disability (ID) is a broad diagnostic category that encompasses individuals with impaired cognitive ability. While these disorders have heterogeneous causes, recent developments in next-generation sequencing (NGS) are revealing the prevalence of genetic etiologies. In particular, germline mutations in genes that affect RNA splicing are increasingly common causes of ID disorders. Research to elucidate the functional relationship between splicing and neurodevelopment is critical since molecular therapeutics require a nuanced understanding of the pathological mechanism. In this review, we first summarize the trends that have led to the discovery of the RNA splicing–ID relationship, then discuss recent progress and future directions for research surrounding RNA splicing in neurodevelopment. Finally, we speak on how these results may serve as the foundation for burgeoning therapies.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102322"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143372310","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
Fine-tuned programming of placenta trophoblast determines optimal maternal–fetal nutrient allocation 胎盘滋养细胞的精细编程决定了母胎营养的最佳分配。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-01-18 DOI: 10.1016/j.gde.2024.102305
Xin Yu , Qianqian Li , Xuan Shao , Amanda N Sferruzzi-Perri , Yan-Ling Wang
{"title":"Fine-tuned programming of placenta trophoblast determines optimal maternal–fetal nutrient allocation","authors":"Xin Yu ,&nbsp;Qianqian Li ,&nbsp;Xuan Shao ,&nbsp;Amanda N Sferruzzi-Perri ,&nbsp;Yan-Ling Wang","doi":"10.1016/j.gde.2024.102305","DOIUrl":"10.1016/j.gde.2024.102305","url":null,"abstract":"<div><div>Maternal health and fetal survival during pregnancy encapsulate a paradox of cooperation and competition. One particularly intriguing aspect of this paradox involves the optimal allocation of nutrients between the mother and fetus. Despite this, the precise mechanisms governing nutrient allocation remain elusive. This review aims to provide a summation of latest research that is improving our understanding of placental metabolism and nutrient allocation between the mother and the fetus. It highlights that in addition to transporter-mediated processes for glucose, fatty acid, and amino acid transport, the human placental trophoblast utilizes a unique macropinocytosis strategy to uptake large molecules from maternal circulation in conditions of nutrient stress. In addition, placental trophoblasts undergo intensive metabolic programming and post-translational modifications during the differentiation process, which regulate trophoblast cell fate, function, and pregnancy outcomes. A number of imprinted genes have been identified to play crucial roles in balancing allocation between the mother and the fetus, yet their role in trophoblast macropinocytosis and metabolic reprogramming requires study. Further work in this area of placental nutrient allocation is essential for identifying the pathogenesis of pregnancy disorders and developing novel therapeutic interventions.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102305"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015662","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
Principles of long-range gene regulation 远程基因调控原理
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-02-13 DOI: 10.1016/j.gde.2025.102323
Sanyami Zunjarrao, Maria Cristina Gambetta
{"title":"Principles of long-range gene regulation","authors":"Sanyami Zunjarrao,&nbsp;Maria Cristina Gambetta","doi":"10.1016/j.gde.2025.102323","DOIUrl":"10.1016/j.gde.2025.102323","url":null,"abstract":"<div><div>Transcription from gene promoters occurs in specific spatiotemporal patterns in multicellular organisms, controlled by genomic regulatory elements. The communication between a regulatory element and a promoter requires a certain degree of physical proximity between them; hence, most gene regulation occurs locally in the genome. However, recent discoveries have revealed long-range gene regulation strategies that enhance interactions between regulatory elements and promoters by overcoming the distances between them in the linear genome. These new findings challenge the traditional view of how gene expression patterns are controlled. This review examines long-range gene regulation strategies recently reported in Drosophila and mammals, offering insights into their mechanisms and evolution.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102323"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143396014","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
Genetic factors mediating long-range enhancer–promoter communication in mammalian development 哺乳动物发育过程中介导长程增强子-启动子通讯的遗传因素
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-11-22 DOI: 10.1016/j.gde.2024.102282
Grace Bower, Evgeny Z Kvon
{"title":"Genetic factors mediating long-range enhancer–promoter communication in mammalian development","authors":"Grace Bower,&nbsp;Evgeny Z Kvon","doi":"10.1016/j.gde.2024.102282","DOIUrl":"10.1016/j.gde.2024.102282","url":null,"abstract":"<div><div>Enhancers are remotely located noncoding DNA sequences that regulate gene expression in response to developmental, homeostatic, and environmental cues. Canonical short-range enhancers located &lt;50 kb from their cognate promoters function by binding transcription factors, coactivators, and chromatin modifiers. In this review, we discuss recent evidence that medium-range (50–400 kb) and long-range (&gt;400 kb) enhancers rely on additional mechanisms, including cohesin, CCCTC-binding factor, and high-affinity protein–protein interactions. These mechanisms are crucial for establishing the physical proximity and interaction between enhancers and their target promoters over extended genomic distances and ensuring robust gene activation during mammalian development. Future studies will be critical to unravel their prevalence and evolutionary significance across various genomic loci, cell types, and species.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102282"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696046","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
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