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Current Opinion in Genetics & Development最新文献

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Editorial overview: Drivers, droplets, and deeds of nuclear genome organization 编辑综述：核基因组组织的驱动力、液滴和契约。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-11-21 DOI: 10.1016/j.gde.2024.102281
Maya Capelson , Eda Yildirim
{"title":"Editorial overview: Drivers, droplets, and deeds of nuclear genome organization","authors":"Maya Capelson , Eda Yildirim","doi":"10.1016/j.gde.2024.102281","DOIUrl":"10.1016/j.gde.2024.102281","url":null,"abstract":"","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102281"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693795","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
Tile by tile: capturing the evolutionary mosaic of human conditions 一砖一瓦：捕捉人类环境的进化马赛克。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-12-19 DOI: 10.1016/j.gde.2024.102297
Nicolò Caporale , Oliviero Leonardi , Carlo Emanuele Villa , Alessandro Vitriolo , Cedric Boeckx , Giuseppe Testa
{"title":"Tile by tile: capturing the evolutionary mosaic of human conditions","authors":"Nicolò Caporale ,&nbsp;Oliviero Leonardi ,&nbsp;Carlo Emanuele Villa ,&nbsp;Alessandro Vitriolo ,&nbsp;Cedric Boeckx ,&nbsp;Giuseppe Testa","doi":"10.1016/j.gde.2024.102297","DOIUrl":"10.1016/j.gde.2024.102297","url":null,"abstract":"<div><div>The collection of <em>Homo sapiens</em> anatomical hallmarks hypothesized to support the ‘human condition’ did not appear at one specific time and place, but gradually, creating a reticulate evolutionary trajectory. The recent reconstruction of migration patterns and gene flows across different hominin species and populations draws a mosaic that we contend can be illuminated by genomic comparisons and specific experiments. Here, we first review key discoveries that could allow this experimental endeavor by describing recent advances in a variety of fields, stressing the importance of charting the current human neurodiversity as an interpretive substrate for evolutionary changes. Then, we identify key cellular and molecular observables. Finally, given the vast amount of possible variants, we focus the discussion on technologies that could allow their interrogation in a way that is compatible with the staggering amount of contemporary genomic and phenotypic characterization.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102297"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873355","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
Nuclear remodeling during cell fate transitions 细胞命运转变过程中的核重塑。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-12-03 DOI: 10.1016/j.gde.2024.102287
Xinyi Liu, Xiaoru Ling, Qi Tian, Zibin Huang, Junjun Ding
{"title":"Nuclear remodeling during cell fate transitions","authors":"Xinyi Liu,&nbsp;Xiaoru Ling,&nbsp;Qi Tian,&nbsp;Zibin Huang,&nbsp;Junjun Ding","doi":"10.1016/j.gde.2024.102287","DOIUrl":"10.1016/j.gde.2024.102287","url":null,"abstract":"<div><div>Totipotent stem cells, the earliest cells in embryonic development, can differentiate into complete embryos and extra-embryonic tissues, making them essential for understanding both development and regenerative medicine. This review examines recent advances in the dynamic remodeling of nuclear structures during the transition between totipotency and pluripotency, as well as other cell fate transition processes. Additionally, we highlight innovative experimental and computational methods that elucidate the relationship between nuclear architecture and cell fate decisions. By integrating these insights, we aim to enhance our understanding of how nuclear remodeling influences totipotency and other cell fate transitions, paving the way for future research in this critical field.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102287"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781759","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
Early central nervous system development and neuron regeneration 早期中枢神经系统发育和神经元再生。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-12-04 DOI: 10.1016/j.gde.2024.102286
Runhua Yang, Fen Ji, Jianwei Jiao
{"title":"Early central nervous system development and neuron regeneration","authors":"Runhua Yang,&nbsp;Fen Ji,&nbsp;Jianwei Jiao","doi":"10.1016/j.gde.2024.102286","DOIUrl":"10.1016/j.gde.2024.102286","url":null,"abstract":"<div><div>The nervous system is the most complex system in the human body, and the normal development of the central nervous system (CNS) is essential for maintaining the healthy life activities of the individual. CNS development requires the orchestration of multiple internal or external or direct or indirect factors to regulate neural stem cell fate specification. Here, we provide a broad overview of the regulatory system of nerve cell fate decisions and discuss the latest technological approaches to achieve neural regeneration. Understanding the CNS development and regeneration mechanisms has shifted the paradigm from traditional experiments to high-throughput sequencing.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102286"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142786668","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
Archaic hominin admixture and its consequences for modern humans 古人类混居及其对现代人类的影响。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-11-21 DOI: 10.1016/j.gde.2024.102280
Debashree Tagore, Joshua M Akey
{"title":"Archaic hominin admixture and its consequences for modern humans","authors":"Debashree Tagore,&nbsp;Joshua M Akey","doi":"10.1016/j.gde.2024.102280","DOIUrl":"10.1016/j.gde.2024.102280","url":null,"abstract":"<div><div>As anatomically modern humans dispersed out of Africa, they encountered and mated with now extinct hominins, including Neanderthals and Denisovans. It is now well established that all non-African individuals derive approximately 2% of their genome from Neanderthal ancestors and individuals of Melanesian and Australian aboriginal ancestry inherited an additional 2%–5% of their genomes from Denisovan ancestors. Attention has started to shift from documenting amounts of archaic admixture and identifying introgressed segments to understanding their molecular, phenotypic, and evolutionary consequences and refining models of human history. Here, we review recent insights into admixture between modern and archaic humans, emphasizing methodological innovations and the functional and phenotypic effects Neanderthal and Denisovan sequences have in contemporary individuals.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102280"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693792","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 : 2025-02-01 Epub 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":"2025-02-01","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
Exploring the interplay between enhancer–promoter interactions and transcription 探索增强子-启动子相互作用与转录之间的相互作用。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2025-01-14 DOI: 10.1016/j.gde.2024.102303
Ryan H Kittle , Michal Levo
{"title":"Exploring the interplay between enhancer–promoter interactions and transcription","authors":"Ryan H Kittle ,&nbsp;Michal Levo","doi":"10.1016/j.gde.2024.102303","DOIUrl":"10.1016/j.gde.2024.102303","url":null,"abstract":"<div><div>Enhancers in metazoan genomes are known to activate their target genes across both short and long genomic distances. Recent advances in chromosome conformation capture assays and single-cell imaging have shed light on the underlying chromatin contacts and dynamics. Yet the relationship between 3D physical enhancer–promoter (E-P) interactions and transcriptional activation remains unresolved. In this brief review, we discuss recent studies exploring this relationship across scales: from developmental stages to the minutes surrounding transcriptional activation and from the tissue level to single-allele subcellular dynamics. We discuss how seemingly contradictory observations might be reconciled and contribute to a refined causal relationship between E-P interactions and transcription, with mutual influences.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102303"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985474","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
Interphase chromatin biophysics and mechanics: new perspectives and open questions 间期染色质生物物理学和力学：新观点和开放问题。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-12-25 DOI: 10.1016/j.gde.2024.102296
Antoine Coulon
{"title":"Interphase chromatin biophysics and mechanics: new perspectives and open questions","authors":"Antoine Coulon","doi":"10.1016/j.gde.2024.102296","DOIUrl":"10.1016/j.gde.2024.102296","url":null,"abstract":"<div><div>The physical organization and properties of chromatin within the interphase nucleus are intimately linked to a wide range of functional DNA-based processes. In this context, interphase chromatin mechanics — that is, how chromatin, physically, responds to forces — is gaining increasing attention. Recent methodological advances for probing the force–response of chromatin <em>in cellulo</em> open new avenues for research, as well as new questions. This review discusses emerging views from these approaches and others, including recent <em>in vitro</em> single-molecule studies of cohesin and condensin motor activities, providing insights into physical and material aspects of chromatin, its plasticity in the context of functional processes, its nonequilibrium or ‘active matter’ properties, and the importance of factors such as chromatin fiber tension and stiffness. This growing field offers exciting opportunities to better understand the interplay between interphase chromosome structure, dynamics, mechanics, and functions.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102296"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900150","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
Rethinking chromatin accessibility: from compaction to dynamic interactions 重新思考染色质可及性：从压实到动态相互作用。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-12-19 DOI: 10.1016/j.gde.2024.102299
Tom Fillot , Davide Mazza
{"title":"Rethinking chromatin accessibility: from compaction to dynamic interactions","authors":"Tom Fillot ,&nbsp;Davide Mazza","doi":"10.1016/j.gde.2024.102299","DOIUrl":"10.1016/j.gde.2024.102299","url":null,"abstract":"<div><div>The genome is traditionally divided into condensed heterochromatin and open euchromatin. However, recent findings challenge this binary classification and the notion that chromatin condensation solely governs the accessibility of transcription factors (TFs) and, consequently, gene expression. Instead, chromatin accessibility is emerging as a factor-specific property that is influenced by multiple determinants. These include the mobility of the chromatin fiber, the capacity of TFs to engage repeatedly with it through multivalent interactions, and the four-dimensional organization of its surrounding diffusible space. Unraveling the molecular and biophysical principles that render a genomic target truly accessible remains a significant challenge, but innovative methods for locally perturbing chromatin, coupled with microscopy techniques that offer single-molecule sensitivity, provide an exciting experimental playground to test new hypotheses.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102299"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873354","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
Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion 超越基因组编织：内聚环挤出外CTCF的分子作用。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 Epub Date: 2024-12-21 DOI: 10.1016/j.gde.2024.102298
Aaron Corin , Elphège P Nora , Vijay Ramani
{"title":"Beyond genomic weaving: molecular roles for CTCF outside cohesin loop extrusion","authors":"Aaron Corin ,&nbsp;Elphège P Nora ,&nbsp;Vijay Ramani","doi":"10.1016/j.gde.2024.102298","DOIUrl":"10.1016/j.gde.2024.102298","url":null,"abstract":"<div><div>CCCTC-binding factor (CTCF) is a key regulator of 3D genome organization and transcriptional activity. Beyond its well-characterized role in facilitating cohesin-mediated loop extrusion, CTCF exhibits several cohesin-independent activities relevant to chromatin structure and various nuclear processes. These functions include patterning of nucleosome arrangement and chromatin accessibility through interactions with ATP-dependent chromatin remodelers. In addition to influencing transcription, DNA replication, and DNA repair in ways that are separable from its role in loop extrusion, CTCF also interacts with RNA and contributes to RNA splicing and condensation of transcriptional activators. Here, we review recent insight into cohesin-independent activities of CTCF, highlighting its multifaceted roles in chromatin biology and transcriptional regulation.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102298"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878372","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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