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Current Opinion in Genetics & Development最新文献

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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 : 2025-01-24 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":"2025-01-24","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
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 : 2025-01-24 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":"2025-01-24","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
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 : 2025-01-20 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":"2025-01-20","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
Recent insights into the in vitro culture systems for mammalian embryos 哺乳动物胚胎体外培养系统的最新进展。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-01-18 DOI: 10.1016/j.gde.2025.102309
Zhiyuan Guo , Wentao Zhao , Hongmei Wang , Jinglei Zhai
{"title":"Recent insights into the in vitro culture systems for mammalian embryos","authors":"Zhiyuan Guo ,&nbsp;Wentao Zhao ,&nbsp;Hongmei Wang ,&nbsp;Jinglei Zhai","doi":"10.1016/j.gde.2025.102309","DOIUrl":"10.1016/j.gde.2025.102309","url":null,"abstract":"<div><div>Mammalian early embryonic development is the cornerstone for a healthy life. Any aberrations during early embryonic development may lead to adverse pregnancy outcomes. Therefore, the comprehensive study of embryonic developmental events is essential for understanding biological and pathological pregnancy. However, due to mammalian embryo development taking place in the uterus, it is hard to directly observe the developing embryos that are undergoing dramatic and complex morphologies, proliferation, and differentiation. The <em>in vitro</em> culture (IVC) of mammalian embryos is a pivotal model for studying developmental events. Recent advancements in establishing long-term culture systems for early mammalian embryos have allowed researchers to culture human embryos up to the embryonic day (E) 14 ethical limitations and extend mouse and macaque embryos to early organogenesis. Here, we review the development of IVC systems for mammalian embryos, emphasize the important improvements in culture elements, and offer our perspectives on potential future optimizations of IVC systems.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102309"},"PeriodicalIF":3.7,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015665","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
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 : 2025-01-18 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":"2025-01-18","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
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 : 2025-01-18 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":"2025-01-18","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
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 : 2025-01-14 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":"2025-01-14","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
Editorial overview: Regaining architecture and cell cross-talk upon regeneration 编辑综述：再生时恢复结构和细胞交叉对话。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-12-28 DOI: 10.1016/j.gde.2024.102302
Anne Grapin-Botton, Jonathan Y-H Loh
{"title":"Editorial overview: Regaining architecture and cell cross-talk upon regeneration","authors":"Anne Grapin-Botton,&nbsp;Jonathan Y-H Loh","doi":"10.1016/j.gde.2024.102302","DOIUrl":"10.1016/j.gde.2024.102302","url":null,"abstract":"","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102302"},"PeriodicalIF":3.7,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903906","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
Inferring human phenotypes using ancient DNA: from molecules to populations 利用古代DNA推断人类表型：从分子到种群
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-29 DOI: 10.1016/j.gde.2024.102283
Manuel Ferrando-Bernal , Colin M Brand , John A Capra
{"title":"Inferring human phenotypes using ancient DNA: from molecules to populations","authors":"Manuel Ferrando-Bernal ,&nbsp;Colin M Brand ,&nbsp;John A Capra","doi":"10.1016/j.gde.2024.102283","DOIUrl":"10.1016/j.gde.2024.102283","url":null,"abstract":"<div><div>The increasing availability of ancient DNA (aDNA) from human groups across space and time has yielded deep insights into the movements of our species. However, given the challenges of mapping from genotype to phenotype, aDNA has revealed less about the phenotypes of ancient individuals. In this review, we highlight recent advances in inferring ancient phenotypes — from the molecular to population scale — with a focus on applications enabled by new machine learning approaches. The genetic architecture of complex traits across human groups suggests that the prediction of individual-level complex traits, like behavior or disease risk, is often challenging across the relevant evolutionary distances. Thus, we propose an approach that integrates predictions of molecular phenotypes, whose mechanisms are more conserved, with nongenetic data.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102283"},"PeriodicalIF":3.7,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142747917","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
In vitro dynamics of DNA loop extrusion by structural maintenance of chromosomes complexes 染色体复合物结构维持 DNA 环挤压的体外动态变化
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2024-11-26 DOI: 10.1016/j.gde.2024.102284
Marius Rutkauskas, Eugene Kim
{"title":"In vitro dynamics of DNA loop extrusion by structural maintenance of chromosomes complexes","authors":"Marius Rutkauskas,&nbsp;Eugene Kim","doi":"10.1016/j.gde.2024.102284","DOIUrl":"10.1016/j.gde.2024.102284","url":null,"abstract":"<div><div>Genomic DNA inside the cell’s nucleus is highly organized and tightly controlled by the structural maintenance of chromosomes (SMC) protein complexes. These complexes fold genomes by creating and processively enlarging loops, a process called loop extrusion. After more than a decade of accumulating indirect evidence, recent <em>in vitro</em> single-molecule studies confirmed loop extrusion as an evolutionarily conserved function among eukaryotic and prokaryotic SMCs. These studies further provided important insights into mechanisms and regulations of these universal molecular machines, which will be discussed in this minireview.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102284"},"PeriodicalIF":3.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142699491","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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