首页 > 最新文献

Current Opinion in Genetics & Development最新文献

英文 中文
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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-04 DOI: 10.1016/j.gde.2025.102311
Lei Yang , Mingli Ma , Yawei Gao , Jun Liu
N6-methyladenosine (m6A), a reversible and dynamic RNA modification, plays pivotal roles in regulating stem cell pluripotency and early embryogenesis. Disruptions in m6A 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 m6A’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 m6A, highlighting its critical interplay with chromatin modifications, and explores its broader implications in stem cell biology and early embryonic development.
n6 -甲基腺苷（n6 - methylladenosine, m6A）是一种可逆的、动态的RNA修饰，在干细胞多能性和早期胚胎发生调控中起着关键作用。m6A稳态的破坏会导致严重的发育缺陷，损害诸如干细胞自我更新、谱系规范、卵母细胞成熟、合子基因组激活和受精后母体RNA降解等过程。除了在mRNA转运、稳定性和翻译中众所周知的作用外，最近的研究强调了m6A通过复杂的rna -染色质相互作用在转录调控中的关键作用，特别是涉及染色质相关调控rna （carrna）和反转录转座子rna。这篇综述深入研究了m6A的动态调控格局，强调了它与染色质修饰的关键相互作用，并探讨了其在干细胞生物学和早期胚胎发育中的广泛意义。
{"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":"2025-02-04","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
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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102297
Nicolò Caporale , Oliviero Leonardi , Carlo Emanuele Villa , Alessandro Vitriolo , Cedric Boeckx , Giuseppe Testa
The collection of Homo sapiens 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.
支持“人类状况”的智人解剖学特征的集合并不是在一个特定的时间和地点出现的，而是逐渐形成了一个网状的进化轨迹。最近对不同人类物种和种群之间的迁移模式和基因流动的重建绘制了一个马赛克，我们认为可以通过基因组比较和特定实验来阐明。在这里，我们首先回顾了可以通过描述各种领域的最新进展来实现这一实验努力的关键发现，强调了绘制当前人类神经多样性作为进化变化的解释性基础的重要性。然后，我们确定关键的细胞和分子观察。最后，考虑到大量可能的变异，我们将讨论的重点放在能够以一种与当代基因组和表型特征的惊人数量相兼容的方式对它们进行询问的技术上。
{"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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102287
Xinyi Liu, Xiaoru Ling, Qi Tian, Zibin Huang, Junjun Ding
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.
全能干细胞是胚胎发育过程中最早的细胞，可以分化成完整的胚胎和胚胎外组织，这对理解发育和再生医学至关重要。本文综述了在多能性和全能性转变过程中核结构的动态重塑以及其他细胞命运转变过程的最新进展。此外，我们强调创新的实验和计算方法，阐明核结构和细胞命运决定之间的关系。通过整合这些见解，我们的目标是增强我们对核重塑如何影响全能性和其他细胞命运转变的理解，为未来在这一关键领域的研究铺平道路。
{"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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102286
Runhua Yang, Fen Ji, Jianwei Jiao
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.
神经系统是人体最复杂的系统，中枢神经系统（CNS）的正常发育对于维持个体健康的生命活动至关重要。中枢神经系统的发育需要多种内部或外部或直接或间接因素的协同作用来调节神经干细胞的命运规范。在这里，我们提供了神经细胞命运决定的调控系统的广泛概述，并讨论了实现神经再生的最新技术方法。了解中枢神经系统的发育和再生机制已经将传统的实验模式转变为高通量测序。
{"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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102296
Antoine Coulon
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 in cellulo open new avenues for research, as well as new questions. This review discusses emerging views from these approaches and others, including recent in vitro 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.
间期细胞核内染色质的物理组织和性质与一系列基于dna的功能过程密切相关。在这种背景下，间期染色质力学-即染色质如何在物理上对力作出反应-正在获得越来越多的关注。近年来研究细胞中染色质力响应的方法学进展为研究开辟了新的途径，同时也提出了新的问题。这篇综述讨论了来自这些方法和其他方法的新观点，包括最近的内聚蛋白和凝聚蛋白运动活性的体外单分子研究，提供了对染色质的物理和物质方面的见解，它在功能过程中的可塑性，它的非平衡或“活性物质”特性，以及染色质纤维张力和刚度等因素的重要性。这一不断发展的领域为更好地理解间期染色体结构、动力学、力学和功能之间的相互作用提供了令人兴奋的机会。
{"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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102299
Tom Fillot , Davide Mazza
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.
基因组传统上分为凝聚异染色质和开放常染色质。然而，最近的研究结果挑战了这种二元分类，以及染色质凝聚仅控制转录因子（tf）的可及性和基因表达的概念。相反，染色质可及性正在成为一种受多个决定因素影响的因子特异性特性。这些包括染色质纤维的移动性，tf通过多价相互作用与染色质纤维重复接触的能力，以及染色质纤维周围扩散空间的四维组织。解开分子和生物物理原理，使基因组靶点真正接近仍然是一个重大的挑战，但是局部扰动染色质的创新方法，加上提供单分子灵敏度的显微镜技术，为测试新的假设提供了一个令人兴奋的实验场所。
{"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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102298
Aaron Corin , Elphège P Nora , Vijay Ramani
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.
ccctc结合因子（CTCF）是三维基因组组织和转录活性的关键调控因子。除了在促进黏结蛋白介导的环挤压方面的作用外，CTCF还表现出与染色质结构和各种核过程相关的几种与黏结蛋白无关的活性。这些功能包括核小体排列模式和通过与atp依赖的染色质重塑子相互作用的染色质可及性。除了影响转录、DNA复制和DNA修复之外，CTCF还与RNA相互作用，并有助于RNA剪接和转录激活子的缩合。在这里，我们回顾了最近对CTCF内聚蛋白独立活动的见解，强调了其在染色质生物学和转录调控中的多方面作用。
{"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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102303
Ryan H Kittle , Michal Levo
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.
已知后生动物基因组中的增强子可以在短基因组距离和长基因组距离上激活它们的靶基因。染色体构象捕获测定和单细胞成像的最新进展揭示了潜在的染色质接触和动力学。然而，三维物理增强子-启动子（E-P）相互作用与转录激活之间的关系仍未得到解决。在这篇简短的综述中，我们讨论了最近的研究跨尺度探索这种关系：从发育阶段到转录激活周围的几分钟，从组织水平到单等位基因亚细胞动力学。我们讨论了看似矛盾的观察结果是如何调和的，并有助于E-P相互作用和转录之间的精细因果关系，相互影响。
{"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 Q2 CELL BIOLOGY
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
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.
由于获得患者样本的机会有限，以及缺乏真正反映人类癌症生物学的可靠模型系统，癌症研究在许多领域仍未得到临床满足。患者来源的诱导多能干细胞和工程化人类多能干细胞（hPSCs）的出现帮助克服了这些挑战，为推进癌症研究提供了一个多功能的替代平台。这些hPSCs已经被证明是研究特定癌症驱动突变的有价值的模型，为癌症的起源、发病机制、肿瘤异质性、克隆进化提供了见解，并促进了药物的发现和测试。本文综述了利用hPSCs建立临床相关癌症模型的最新进展，并强调了加深我们对基础癌症生物学的理解的努力。
{"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 Q2 CELL BIOLOGY
Current Opinion in Genetics & Development
Pub Date : 2025-02-01 DOI: 10.1016/j.gde.2024.102300
Ervin Ascic , Carlos-Filipe Pereira
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.
抗原呈递细胞（APCs）是由树突状细胞（dc）和巨噬细胞（mφ）组成的异质免疫细胞群，它们对协调免疫对抗癌症或感染至关重要。已经探索了几种产生APC亚群的策略，包括从外周血富集和从多能或多能细胞分化。在发育过程中，APC亚群的产生是由转录因子（tf）指导的。直接细胞重编程，也称为转分化，提供了一种利用tf组合从不相关的体细胞（包括癌细胞）中产生apc的方法。在这篇综述中，我们总结了DC亚群的转录规范，重点介绍了它们产生的转录网络，并讨论了DC重编程在癌症免疫治疗中的未来应用。
{"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
首页 上一页 下一页 尾页
类型
全部 化学•材料 生命科学 医学 物理 工程技术 环境•农林 材料科学 地球科学 法学 管理学 化学 环境科学与生态学 计算机科学 教育学 经济学 农林科学 人文科学 生物学 数学 物理与天体物理 心理学 综合性期刊 其他 工业工程 理学 历史学 农学 文学 信息工程
数据库
全部 ACS Publications Elsevier ieeexplore Springer The Royal Society of Chemistry Wiley
期刊
Current Opinion in Genetics & Development
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
﹀
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们：info@booksci.cn
Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1