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Enhancer cooperativity in the folded genome 增强折叠基因组中的协同性
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2026-02-01 Epub Date: 2025-12-19 DOI: 10.1016/j.gde.2025.102416
Elias T Friman, Wendy A Bickmore
{"title":"Enhancer cooperativity in the folded genome","authors":"Elias T Friman,&nbsp;Wendy A Bickmore","doi":"10.1016/j.gde.2025.102416","DOIUrl":"10.1016/j.gde.2025.102416","url":null,"abstract":"<div><div>Transcriptional regulation involves the binding of thousands of transcription factors (TFs) to hundreds of thousands of enhancers and promoters. How do the collective activities of these proteins and cis-regulatory elements achieve precise and dynamic gene regulation? At an individual enhancer, TFs can interact to affect each other’s binding and the recruitment of different co-factors, resulting in cooperative outputs. More recently, new types of cooperative behaviour between enhancers have been discovered. In this review, we consider whether some of the same principles could contribute to both TF and enhancer cooperativity, focusing specifically on positive cooperativity (or synergy) and the role of 3D chromatin organisation.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"96 ","pages":"Article 102416"},"PeriodicalIF":3.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145792128","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
Block copolymer concepts of how transcription organizes the stem cell genome 嵌段共聚物概念的转录如何组织干细胞基因组
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2026-02-01 Epub Date: 2026-01-14 DOI: 10.1016/j.gde.2025.102428
Yuzhi Bao , Shaoqian Ma , Xiaohua Shen , Lennart Hilbert
{"title":"Block copolymer concepts of how transcription organizes the stem cell genome","authors":"Yuzhi Bao ,&nbsp;Shaoqian Ma ,&nbsp;Xiaohua Shen ,&nbsp;Lennart Hilbert","doi":"10.1016/j.gde.2025.102428","DOIUrl":"10.1016/j.gde.2025.102428","url":null,"abstract":"<div><div>Stem cells display a highly dispersed genome organization that supports flexible gene regulation. Here, we present block copolymer concepts to explore how transcriptional activity from specific genomic regions, or ‘blocks’, shapes and controls several features of this architecture. Nascent transcripts tethered to chromatin can disrupt compaction and promote the formation of a micro-dispersed state of euchromatin, explaining one typical feature of the stem cell genome. A second feature is long-lived transcriptional clusters, which form via condensation at super-enhancer blocks and mediate both long-range interactions and local transcription factor accumulation. Lastly, we conceptualize promoters and gene bodies as a two-block polymer, for which sequential switching on and off of the polymer blocks controls the association and subsequent release of developmental genes with the long-lived clusters. The presented block copolymer framework provides explanations as well as hypotheses of how transcription-associated processes contribute to distinct features of stem cell genome organization.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"96 ","pages":"Article 102428"},"PeriodicalIF":3.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145978554","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
Nonequilibrium polymer models for chromatin 染色质的非平衡聚合物模型
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2026-02-01 Epub Date: 2026-01-08 DOI: 10.1016/j.gde.2025.102426
Giada Forte , Chris A. Brackley , Nick Gilbert , Davide Marenduzzo
{"title":"Nonequilibrium polymer models for chromatin","authors":"Giada Forte ,&nbsp;Chris A. Brackley ,&nbsp;Nick Gilbert ,&nbsp;Davide Marenduzzo","doi":"10.1016/j.gde.2025.102426","DOIUrl":"10.1016/j.gde.2025.102426","url":null,"abstract":"<div><div>The cell nucleus is a dynamic environment where ATP-driven processes — like transcription, replication, and epigenetic modifications — continually drive the genome far from thermodynamic equilibrium. Recent interdisciplinary efforts combining cell biology and physics have introduced coarse-grained polymer models that reveal how these active processes shape chromosome organization in space and time. We review how these models have shed light on selected key features of nuclear function: the maintenance of epigenetic memory, the coupling between transcriptional activity and chromatin motion, and the emergence of replication factories. These approaches provide mechanistic insight and predictive power that are beyond experiments alone. We conclude by outlining future directions toward viewing the genome as an active polymer maintained far from equilibrium.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"96 ","pages":"Article 102426"},"PeriodicalIF":3.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145927355","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 advances in the neurogenomics of autism spectrum disorder 自闭症谱系障碍神经基因组学的最新进展
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2026-02-01 Epub Date: 2026-01-13 DOI: 10.1016/j.gde.2025.102431
Ashlesha Gogate , Maria H Chahrour
{"title":"Recent advances in the neurogenomics of autism spectrum disorder","authors":"Ashlesha Gogate ,&nbsp;Maria H Chahrour","doi":"10.1016/j.gde.2025.102431","DOIUrl":"10.1016/j.gde.2025.102431","url":null,"abstract":"<div><div>Neurogenomics has provided exceptional insights into the genetic architecture underlying autism spectrum disorder (ASD), which is increasingly understood as a collection of individually rare disorders. This review synthesizes current advancements in the field, examining how both rare and common genetic variants contribute to ASD etiology. To functionally interpret the convergence on biological pathways that has emerged despite this genetic heterogeneity, multiomic approaches have been applied to identify gene regulatory networks disrupted in ASD. High-throughput technologies, such as clustered regularly interspaced short palindromic repeats (CRISPR) editing and massively parallel reporter assays, have been employed in human induced pluripotent stem cells and organoids to bridge the gap between genetic association and biological function. Finally, machine learning methods play a pivotal role in integrating and leveraging these complex datasets to inform personalized interventions.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"96 ","pages":"Article 102431"},"PeriodicalIF":3.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145978552","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
Integrating machine learning and functional genomics to study cross-species gene regulatory evolution 结合机器学习和功能基因组学研究跨物种基因调控进化
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2026-02-01 Epub Date: 2025-12-19 DOI: 10.1016/j.gde.2025.102415
Erin N Gilbertson , Steven K Reilly
{"title":"Integrating machine learning and functional genomics to study cross-species gene regulatory evolution","authors":"Erin N Gilbertson ,&nbsp;Steven K Reilly","doi":"10.1016/j.gde.2025.102415","DOIUrl":"10.1016/j.gde.2025.102415","url":null,"abstract":"<div><div>Understanding the genetic basis of phenotypic differences across species has been a longstanding goal of evolutionary biology since Darwin. While a recent proliferation of mammalian genomes has provided an unprecedented inventory of sequence differences between species, the vast majority are in noncoding loci, where it remains challenging to link genetic changes to function. Cis-regulatory elements (CREs) control gene expression via combinatorial, redundant, and context-dependent interactions that are both evolutionarily amenable to change but render their gene regulatory logic difficult to decipher. Recent advances in comparative genomics, functional profiling across species, and high-throughput perturbation assays have begun to catalog cross-species differences in gene expression and CRE function. In parallel, machine learning approaches trained on these data are beginning to predict cis-regulatory activity differences from DNA sequences alone. Here, we highlight recent advances in both experimental and computational strategies to study gene regulatory evolution.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"96 ","pages":"Article 102415"},"PeriodicalIF":3.6,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145771942","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
Polygenic prediction of human complex traits using ancient DNA 利用古代DNA进行人类复杂性状的多基因预测
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-12-01 Epub Date: 2025-08-30 DOI: 10.1016/j.gde.2025.102396
Iain Mathieson
{"title":"Polygenic prediction of human complex traits using ancient DNA","authors":"Iain Mathieson","doi":"10.1016/j.gde.2025.102396","DOIUrl":"10.1016/j.gde.2025.102396","url":null,"abstract":"<div><div>Ancient DNA has revolutionized our understanding of human history and clarified many aspects of human evolution on a molecular level. In this article, I describe recent efforts to translate this into descriptions of phenotypic change over time and to predict phenotypes of ancient groups and individuals. I do not discuss the more challenging problem of distinguishing between adaptive and neutral evolution and instead focus entirely on whether phenotypes and their evolution can be accurately reconstructed. I begin by describing the conceptual and technical limitations of current approaches, and then discuss efforts to reconstruct various phenotypes and the extent to which they are reliable.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"95 ","pages":"Article 102396"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144916823","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
Human gut evolution: insights from stem cell models and single-cell genomics 人类肠道进化：来自干细胞模型和单细胞基因组学的见解。
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-12-01 Epub Date: 2025-09-24 DOI: 10.1016/j.gde.2025.102398
Rubén López-Sandoval , Stefano Secchia , Joep Beumer , Jarrett Gray Camp
{"title":"Human gut evolution: insights from stem cell models and single-cell genomics","authors":"Rubén López-Sandoval ,&nbsp;Stefano Secchia ,&nbsp;Joep Beumer ,&nbsp;Jarrett Gray Camp","doi":"10.1016/j.gde.2025.102398","DOIUrl":"10.1016/j.gde.2025.102398","url":null,"abstract":"<div><div>The gastrointestinal (GI) tract evolved in response to dietary changes and pathogen exposures that varied throughout history. As a major interface between the host and environment, the GI epithelia have evolved specialized barrier and immune functions while optimizing nutrient processing and absorption. Recent technological breakthroughs in modeling human biology <em>in vitro</em> and comparative single-cell genomics are providing novel insights into the genetic, cellular, and ontogenic basis of human evolution. In this review, we provide a broad overview of human-specific gut changes and how GI organoids and single-cell technologies can offer a mechanistic understanding of the specific features of human GI tract physiology.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"95 ","pages":"Article 102398"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151709","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
Evolutionary genetics meets ecological immunology: insights into the evolution of immune systems 进化遗传学满足生态免疫学：洞察免疫系统的进化。
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-12-01 Epub Date: 2025-10-29 DOI: 10.1016/j.gde.2025.102411
Alexander E Downie , Jenny Tung
{"title":"Evolutionary genetics meets ecological immunology: insights into the evolution of immune systems","authors":"Alexander E Downie ,&nbsp;Jenny Tung","doi":"10.1016/j.gde.2025.102411","DOIUrl":"10.1016/j.gde.2025.102411","url":null,"abstract":"<div><div>Immune genes show remarkably consistent evidence of selection, modification, and diversification across the tree of life. Parasites are a key force in this process, but many questions remain about the genetic and phenotypic targets of parasite-mediated selection and how these connect to each other. Ecological immunology — the study of immune variation in natural settings — can complement genetic inference by providing an organismal perspective on immune evolution, including how immune adaptation may be explained or constrained by host life history and ecological context. In this review, we outline key questions in immune evolution where ecological immunology offers insights for evolutionary geneticists, and we explore the value of evolutionary genetic approaches for testing fundamental assumptions in ecological immunology.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"95 ","pages":"Article 102411"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145410717","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
Editorial overview: Molecular and genetic basis of disease (2025): post-transcriptional regulation of neurodevelopment and associated disorders 编辑概述：疾病的分子和遗传基础（2025）：神经发育和相关疾病的转录后调控
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-12-01 Epub Date: 2025-10-31 DOI: 10.1016/j.gde.2025.102409
Naiara Akizu , Jozef Gecz
{"title":"Editorial overview: Molecular and genetic basis of disease (2025): post-transcriptional regulation of neurodevelopment and associated disorders","authors":"Naiara Akizu ,&nbsp;Jozef Gecz","doi":"10.1016/j.gde.2025.102409","DOIUrl":"10.1016/j.gde.2025.102409","url":null,"abstract":"","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"95 ","pages":"Article 102409"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416827","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
Behavioral evolution by diverging cell type composition 分化细胞类型组成的行为进化
IF 3.6 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-12-01 Epub Date: 2025-09-03 DOI: 10.1016/j.gde.2025.102397
Andres Bendesky
{"title":"Behavioral evolution by diverging cell type composition","authors":"Andres Bendesky","doi":"10.1016/j.gde.2025.102397","DOIUrl":"10.1016/j.gde.2025.102397","url":null,"abstract":"<div><div>Recent advances in single-cell genomics are propelling a flurry of discoveries about the cellular composition of the brain and other organs across species. These discoveries, coupled with experimental manipulations, have begun to reveal how variation between species in the proportion of cell types, including the outright disappearance of some cell types and the emergence of new ones, contributes to the evolution of behavior. This review highlights these emerging findings in the context of more traditional approaches to study the evolution of behavior and discusses important outstanding questions in this field.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"95 ","pages":"Article 102397"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144932407","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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