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Topological epigenetics: The biophysics of DNA supercoiling and its relation to transcription and genome instability 拓扑表观遗传学：DNA超卷曲的生物物理学及其与转录和基因组不稳定性的关系。
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2025-02-01 DOI: 10.1016/j.ceb.2024.102448
Nick Gilbert , Davide Marenduzzo
{"title":"Topological epigenetics: The biophysics of DNA supercoiling and its relation to transcription and genome instability","authors":"Nick Gilbert ,&nbsp;Davide Marenduzzo","doi":"10.1016/j.ceb.2024.102448","DOIUrl":"10.1016/j.ceb.2024.102448","url":null,"abstract":"<div><div>Whilst DNA encodes our genetic blueprint as individual nucleobases, as well as epigenetic annotations in the form of biochemical marks, it also carries an extra layer of topological information –, the local over or underwinding of the double helix, known as DNA supercoiling. Supercoiling is a fundamental property of DNA that can be viewed as “topological epigenetics”: it stores energy and structural information, and is tightly linked to fundamental processes; however, its quantification and study, by experiments and modelling alike, is challenging. We review experimental and simulation techniques to study supercoiling and its partition into twist and writhe, especially in the context of chromatin. We then discuss the dynamics of transcription-driven supercoiling in vitro and in vivo, and of supercoiling propagation along mammalian genomes. We finally provide evidence from the literature and potential mechanisms linking this ethereal topological mark to gene expression and chromosome instabilities in genetic diseases and cancer.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"92 ","pages":"Article 102448"},"PeriodicalIF":6.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822916","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
Lessons on the force-form-function connection in cell biology from modeling a syncytial germline 从合胞种系建模中汲取细胞生物学中力-形式-功能联系的教训。
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2025-01-31 DOI: 10.1016/j.ceb.2025.102465
John B. Linehan , Michael E. Werner , Amy Shaub Maddox
{"title":"Lessons on the force-form-function connection in cell biology from modeling a syncytial germline","authors":"John B. Linehan ,&nbsp;Michael E. Werner ,&nbsp;Amy Shaub Maddox","doi":"10.1016/j.ceb.2025.102465","DOIUrl":"10.1016/j.ceb.2025.102465","url":null,"abstract":"<div><div>Germline architecture plays a critical role in the production of functional gametes. Across species, oogenesis involves not only the preparation of the genome for sexual reproduction, but also the dramatic enlargement of a cell compartment to reach a volume sufficient to support embryogenesis. Creating exceptionally large cells is accomplished by a syncytial structure, in which many nucleus-containing compartments are interconnected by cytoplasmic bridges. Maintenance and function of the intricate multi-compartment architecture of syncytia requires cortical contractility, cytoplasmic flows, and germline extrinsic forces that deform and displace the germline and its constituent compartments. The dynamic interplay between local and global force production in shaping syncytial architecture makes the germline an excellent model to study the force-form-function connection in cell biology. Here, we highlight work that has combined physical modeling with cell biological measurements to define the force-form-function connection, using the <em>Caenorhabditis elegans</em> oogenic germline as an archetype.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"93 ","pages":"Article 102465"},"PeriodicalIF":6.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076300","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
Sister chromatid cohesion through the lens of biochemical experiments 姐妹染色单体内聚通过镜头进行生化实验。
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2025-01-28 DOI: 10.1016/j.ceb.2025.102464
Yasuto Murayama
{"title":"Sister chromatid cohesion through the lens of biochemical experiments","authors":"Yasuto Murayama","doi":"10.1016/j.ceb.2025.102464","DOIUrl":"10.1016/j.ceb.2025.102464","url":null,"abstract":"<div><div>Faithful chromosome segregation in eukaryotes relies on physical cohesion between newly duplicated sister chromatids. Cohesin is a ring-shaped ATPase assembly that mediates sister chromatid cohesion through its ability to topologically entrap DNA. Cohesin, assisted by several regulatory proteins, binds to DNA prior to DNA replication and then holds two sister DNAs together when it encounters the replication machinery. Cohesion establishment further requires cohesin acetylation, which confers near eternal stability on chromatin-bound cohesin until the onset of chromosome segregation. In addition to a wealth of experimental evidence from cellular studies, recent advances in reconstitution approaches are now beginning to unravel the biochemical properties of cohesin that underlie its function in sister chromatid cohesion. This review summarizes recent insights into the mechanism of cohesion establishment.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"93 ","pages":"Article 102464"},"PeriodicalIF":6.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069381","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
Autophagic flux measurement: Cargo degradation versus generation of degradation products 自噬通量测量：货物降解与降解产物的产生。
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2025-01-27 DOI: 10.1016/j.ceb.2025.102463
Noboru Mizushima
{"title":"Autophagic flux measurement: Cargo degradation versus generation of degradation products","authors":"Noboru Mizushima","doi":"10.1016/j.ceb.2025.102463","DOIUrl":"10.1016/j.ceb.2025.102463","url":null,"abstract":"<div><div>Autophagy is the cellular processes that transport cytoplasmic components to lysosomes for degradation. It plays essential physiological roles, including in adaptation to environmental changes such as starvation and maintaining intracellular quality control. Recently, its links to aging and disease have garnered substantial attention. Although various methods to measure autophagic activity (autophagic flux) have been developed, accurate measurement remains challenging and often contentious. This review presents a discussion of techniques to measure the flux of autophagy, particularly macroautophagy, utilizing two contrasting approaches—assaying cargo degradation versus assaying the generation of degradation products—with an emphasis on the advantages of the latter.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"93 ","pages":"Article 102463"},"PeriodicalIF":6.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048552","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
Outside Back Cover 外封底
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2024-12-01 DOI: 10.1016/S0955-0674(24)00135-2
{"title":"Outside Back Cover","authors":"","doi":"10.1016/S0955-0674(24)00135-2","DOIUrl":"10.1016/S0955-0674(24)00135-2","url":null,"abstract":"","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"91 ","pages":"Article 102456"},"PeriodicalIF":6.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143157197","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
Unleashing XIST from X-chromosome inactivation 从 X 染色体失活中释放 XIST
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2024-11-27 DOI: 10.1016/j.ceb.2024.102446
Céline Morey, Claire Rougeulle, Jean-François Ouimette
{"title":"Unleashing XIST from X-chromosome inactivation","authors":"Céline Morey,&nbsp;Claire Rougeulle,&nbsp;Jean-François Ouimette","doi":"10.1016/j.ceb.2024.102446","DOIUrl":"10.1016/j.ceb.2024.102446","url":null,"abstract":"<div><div>Recognition that the most abundant class of genes present in the human genome are those producing long noncoding RNA (lncRNA) has hyped research on this category of transcripts. One such prototypical RNA, <em>Xist</em>, has particularly fueled interest. Initially characterized for its specific expression from the inactive X (Xi), recent studies have uncovered the molecular mechanisms underlying its essential role in the initiation of X-chromosome inactivation, from its exquisitely precise transcriptional regulation to the plethora of protein interactors forming the <em>Xist</em> ribonucleoprotein (RNP) that mediate its gene silencing activity. Here, we will discuss the recent advances that have broadened our knowledge of <em>Xist</em> functions, challenging classical models and revealing unsuspected, unconventional actions of its RNP.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"92 ","pages":"Article 102446"},"PeriodicalIF":6.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721375","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
Interplay between Notch signaling and mechanical forces during developmental patterning processes 发育模式过程中 Notch 信号与机械力之间的相互作用
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2024-11-27 DOI: 10.1016/j.ceb.2024.102444
Shahar Kasirer , David Sprinzak
{"title":"Interplay between Notch signaling and mechanical forces during developmental patterning processes","authors":"Shahar Kasirer ,&nbsp;David Sprinzak","doi":"10.1016/j.ceb.2024.102444","DOIUrl":"10.1016/j.ceb.2024.102444","url":null,"abstract":"<div><div>The coordination between biochemical signals and cell mechanics has emerged in recent years as a crucial mechanism driving developmental patterning processes across a variety of developing and homeostatic systems. An important class of such developmental processes relies on local communication between neighboring cells through Notch signaling. Here, we review how the coordination between Notch-mediated differentiation and cell mechanics can give rise to unique cellular patterns. We discuss how global and local mechanical cues can affect, and be affected by, cellular differentiation and reorganization controlled by Notch signaling. We compare recent studies of such developmental processes, including the mammalian inner ear, Drosophila ommatidia, intestinal organoids, and zebrafish myocardium, to draw shared general concepts and their broader implications in biology.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"91 ","pages":"Article 102444"},"PeriodicalIF":6.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721272","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
Design principles of regulatory networks underlying epithelial mesenchymal plasticity in cancer cells 癌细胞上皮间充质可塑性基础调控网络的设计原则
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2024-11-27 DOI: 10.1016/j.ceb.2024.102445
Sarthak Sahoo, Kishore Hari , Mohit Kumar Jolly
{"title":"Design principles of regulatory networks underlying epithelial mesenchymal plasticity in cancer cells","authors":"Sarthak Sahoo,&nbsp;Kishore Hari ,&nbsp;Mohit Kumar Jolly","doi":"10.1016/j.ceb.2024.102445","DOIUrl":"10.1016/j.ceb.2024.102445","url":null,"abstract":"<div><div>Phenotypic plasticity is a hallmark of cancer and drives metastatic disease and drug resistance. The dynamics of epithelial mesenchymal plasticity is driven by complex interactions involving multiple feedback loops in underlying networks operating at multiple regulatory levels such as transcriptional and epigenetic. The past decade has witnessed a surge in systems level analysis of structural and dynamical traits of these networks. Here, we highlight the key insights elucidated from such efforts—a) multistability in gene regulatory networks and the co-existence of many hybrid phenotypes, thus enabling a landscape with multiple ‘attractors’, b) mutually antagonistic ‘teams’ of genes in these networks, shaping the rates of cell state transition in this landscape, and c) chromatin level changes that can alter the landscape, thus controlling reversibility of cell state transitions, allowing cellular memory in the context of epithelial mesenchymal plasticity in cancer cells. Such approaches, in close integration with high-throughput longitudinal data, have improved our understanding of the dynamics of cell state transitions implicated in tumor cell plasticity.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"92 ","pages":"Article 102445"},"PeriodicalIF":6.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721374","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
SMC-mediated chromosome organization: Does loop extrusion explain it all? SMC 介导的染色体组织：环状挤压能解释这一切吗？
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2024-11-26 DOI: 10.1016/j.ceb.2024.102447
Tatsuya Hirano, Kazuhisa Kinoshita
{"title":"SMC-mediated chromosome organization: Does loop extrusion explain it all?","authors":"Tatsuya Hirano,&nbsp;Kazuhisa Kinoshita","doi":"10.1016/j.ceb.2024.102447","DOIUrl":"10.1016/j.ceb.2024.102447","url":null,"abstract":"<div><div>In recent years, loop extrusion has attracted much attention as a general mechanism of chromosome organization mediated by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin. Despite accumulating evidence in support of this mechanism, it is not fully established whether or how loop extrusion operates under physiological conditions, or whether any alternative or additional SMC-mediated mechanisms operate in the cell. In this review, we summarize non-loop extrusion mechanisms proposed in the literature and clarify unresolved issues to further enrich our understanding of how SMC protein complexes work.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"92 ","pages":"Article 102447"},"PeriodicalIF":6.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721373","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
Mechanochemical control systems regulating animal cell size 调节动物细胞大小的机械化学控制系统
IF 6 2区 生物学
Current Opinion in Cell Biology Pub Date : 2024-11-06 DOI: 10.1016/j.ceb.2024.102443
Heather E. Rizzo , Andy L. Zhang , Margaret L. Gardel
{"title":"Mechanochemical control systems regulating animal cell size","authors":"Heather E. Rizzo ,&nbsp;Andy L. Zhang ,&nbsp;Margaret L. Gardel","doi":"10.1016/j.ceb.2024.102443","DOIUrl":"10.1016/j.ceb.2024.102443","url":null,"abstract":"<div><div>Cell size regulation arises from physical manifestations of cell proliferation and metabolic pathways. On one hand, coordination between these systems yields a constant cell size over generations to maintain cell size homeostasis. However, active regulation of cell size is crucial to physiology and to establish broad variation of cell sizes within an individual organism, and is accomplished via physical and biochemical pathways modulated by myriad intrinsic and extrinsic cues. In this review, we explore recent data elucidating the mechanobiological regulation of the volume of animal cells and its coordination with metabolic and proliferative pathways.</div></div>","PeriodicalId":50608,"journal":{"name":"Current Opinion in Cell Biology","volume":"91 ","pages":"Article 102443"},"PeriodicalIF":6.0,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592009","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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