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Current Opinion in Genetics & Development最新文献

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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 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
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 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 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 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
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 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
Decoding cancer etiology with cellular reprogramming 用细胞重编程解码癌症病因学。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102301
Mo-Fan Huang , Megan E. Fisher , Trinh T.T. Phan , Ruiying Zhao , Dung-Fang Lee
{"title":"Decoding cancer etiology with cellular reprogramming","authors":"Mo-Fan Huang ,&nbsp;Megan E. Fisher ,&nbsp;Trinh T.T. Phan ,&nbsp;Ruiying Zhao ,&nbsp;Dung-Fang Lee","doi":"10.1016/j.gde.2024.102301","DOIUrl":"10.1016/j.gde.2024.102301","url":null,"abstract":"<div><div>Cancer research remains clinically unmet in many areas due to limited access to patient samples and the lack of reliable model systems that truly reflect human cancer biology. The emergence of patient-derived induced pluripotent stem cells and engineered human pluripotent stem cells (hPSCs) has helped overcome these challenges, offering a versatile alternative platform for advancing cancer research. These hPSCs are already proving to be valuable models for studying specific cancer driver mutations, offering insights into cancer origins, pathogenesis, tumor heterogeneity, clonal evolution, and facilitating drug discovery and testing. This article reviews recent progress in utilizing hPSCs for clinically relevant cancer models and highlights efforts to deepen our understanding of fundamental cancer biology.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102301"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900149","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
Transcription factor–mediated reprogramming to antigen-presenting cells 转录因子介导的抗原呈递细胞重编程。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102300
Ervin Ascic , Carlos-Filipe Pereira
{"title":"Transcription factor–mediated reprogramming to antigen-presenting cells","authors":"Ervin Ascic ,&nbsp;Carlos-Filipe Pereira","doi":"10.1016/j.gde.2024.102300","DOIUrl":"10.1016/j.gde.2024.102300","url":null,"abstract":"<div><div>Antigen-presenting cells (APCs) are a heterogenous group of immune cells composed by dendritic cells (DCs) and macrophages (Mϕ), which are critical for orchestrating immunity against cancer or infections. Several strategies have been explored to generate APC subsets, including enrichment from peripheral blood and differentiation from pluripotent or multipotent cells. During development, the generation of APC subsets is instructed by transcription factors (TFs). Direct cell reprogramming, also known as transdifferentiation, offers an approach to harness combinations of TFs to generate APCs from unrelated somatic cells, including cancer cells. In this review, we summarize the transcriptional specification of DC subsets, highlight transcriptional networks for their generation, and discuss future applications of DC reprogramming in cancer immunotherapy.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102300"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900151","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
Roles of intrinsically disordered protein regions in transcriptional regulation and genome organization 内在无序的蛋白质区域在转录调控和基因组组织中的作用。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102285
Jiapei Miao, Shasha Chong
{"title":"Roles of intrinsically disordered protein regions in transcriptional regulation and genome organization","authors":"Jiapei Miao,&nbsp;Shasha Chong","doi":"10.1016/j.gde.2024.102285","DOIUrl":"10.1016/j.gde.2024.102285","url":null,"abstract":"<div><div>Eukaryotic transcription is a complex process regulated by transcription factors (TFs), coactivators, and RNA polymerase machineries, many of which contain sizable intrinsically disordered regions (IDRs). Many TFs activate transcription through multivalent IDR–IDR interactions. Optimal levels of such multivalent interactions associated with appropriate IDR concentrations, interaction strengths, or interaction valencies are required for effective transcriptional activation. The interaction selectivity of IDRs is crucial for the precise regulation of transcription, and this selectivity is dependent on the IDR sequences. Furthermore, IDRs modulate gene expression by bringing chromatin sites together to form transcriptionally active chromatin hubs. Mutations in IDRs may cause dysregulation of their multivalent interactions, contributing to diseases, including cancers and neurodegenerative disorders. Understanding the effects of IDR-related mutations on transcription control and genome organization opens new opportunities for developing targeted therapeutic strategies. In this review, we discuss recent reports documenting important functions of IDRs in transcriptional regulation and their implications for human health and disease.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"90 ","pages":"Article 102285"},"PeriodicalIF":3.7,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781760","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 : 2025-01-24 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
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