首页 > 最新文献

Seminars in cell & developmental biology最新文献

英文 中文
Zebrafish tailfin as an in vivo model for capturing tissue-scale cell dynamics. 斑马鱼尾鳍作为捕获组织尺度细胞动力学的体内模型。
IF 6.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-12-25 DOI: 10.1016/j.semcdb.2024.12.005
Yue Rong Tan, Hsiao-Yuh Roan, Chen-Hui Chen

The intricate control of collective cell dynamics is crucial for enabling organismic development and tissue regeneration. Despite the availability of various in vitro and in vivo models, studies on tissue-scale cell dynamics and associated emergent properties in living systems remain methodically challenging. Here, we describe key advantages of using the adult zebrafish tailfin (caudal fin) as a robust in vivo model for dissecting millimeter-scale collective cell dynamics during regeneration and wound healing in a complex tissue. For researchers considering this model system, we briefly introduce the tailfin anatomy, as well as available transgenic reporter tools and live-imaging setups that may be utilized to study epidermal cell behaviors. To highlight the unique strengths of the zebrafish tailfin model, we present an example project that was made possible by techniques for tracking cell dynamics at a millimeter scale with single-cell resolution in live animals. Finally, we discuss the research directions at the interface of collective cell dynamics and regenerative biology that most excite us and can be examined using the tailfin model.

复杂的控制集体细胞动力学是至关重要的,使有机体的发展和组织再生。尽管存在各种体外和体内模型,但对生命系统中组织尺度细胞动力学和相关涌现特性的研究仍然具有系统性的挑战性。在这里,我们描述了使用成年斑马鱼尾鳍作为一个强大的体内模型来解剖复杂组织中再生和伤口愈合过程中毫米尺度的集体细胞动力学的主要优点。对于考虑该模型系统的研究人员,我们简要介绍了尾鳍解剖,以及可用的转基因报告工具和可用于研究表皮细胞行为的实时成像设置。为了突出斑马鱼尾鳍模型的独特优势,我们提出了一个示例项目,该项目通过在活体动物中以单细胞分辨率在毫米尺度上跟踪细胞动力学的技术成为可能。最后,我们讨论了在集体细胞动力学和再生生物学的界面上,最令人兴奋的研究方向,可以用尾翼模型来检验。
{"title":"Zebrafish tailfin as an in vivo model for capturing tissue-scale cell dynamics.","authors":"Yue Rong Tan, Hsiao-Yuh Roan, Chen-Hui Chen","doi":"10.1016/j.semcdb.2024.12.005","DOIUrl":"10.1016/j.semcdb.2024.12.005","url":null,"abstract":"<p><p>The intricate control of collective cell dynamics is crucial for enabling organismic development and tissue regeneration. Despite the availability of various in vitro and in vivo models, studies on tissue-scale cell dynamics and associated emergent properties in living systems remain methodically challenging. Here, we describe key advantages of using the adult zebrafish tailfin (caudal fin) as a robust in vivo model for dissecting millimeter-scale collective cell dynamics during regeneration and wound healing in a complex tissue. For researchers considering this model system, we briefly introduce the tailfin anatomy, as well as available transgenic reporter tools and live-imaging setups that may be utilized to study epidermal cell behaviors. To highlight the unique strengths of the zebrafish tailfin model, we present an example project that was made possible by techniques for tracking cell dynamics at a millimeter scale with single-cell resolution in live animals. Finally, we discuss the research directions at the interface of collective cell dynamics and regenerative biology that most excite us and can be examined using the tailfin model.</p>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"29-35"},"PeriodicalIF":6.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142897122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent advancement in the spatial immuno-oncology. 空间免疫肿瘤学的最新进展。
IF 6.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-12-19 DOI: 10.1016/j.semcdb.2024.12.003
Alex To, Zou Yu, Ryohichi Sugimura

Recent advancements in spatial transcriptomics and spatial proteomics enabled the high-throughput profiling of single or multi-cell types and cell states with spatial information. They transformed our understanding of the higher-order architectures and paired cell-cell interactions within a tumor microenvironment (TME). Within less than a decade, this rapidly emerging field has discovered much crucial fundamental knowledge and significantly improved clinical diagnosis in the field of immuno-oncology. This review summarizes the conceptual frameworks to understand spatial omics data and highlights the updated knowledge of spatial immuno-oncology.

空间转录组学和空间蛋白质组学的最新进展使得利用空间信息对单个或多个细胞类型和细胞状态进行高通量分析成为可能。他们改变了我们对肿瘤微环境(TME)中高阶结构和配对细胞-细胞相互作用的理解。在不到十年的时间里,这个快速发展的领域已经发现了许多重要的基础知识,并显著改善了免疫肿瘤学领域的临床诊断。本文综述了理解空间组学数据的概念框架,并重点介绍了空间免疫肿瘤学的最新知识。
{"title":"Recent advancement in the spatial immuno-oncology.","authors":"Alex To, Zou Yu, Ryohichi Sugimura","doi":"10.1016/j.semcdb.2024.12.003","DOIUrl":"10.1016/j.semcdb.2024.12.003","url":null,"abstract":"<p><p>Recent advancements in spatial transcriptomics and spatial proteomics enabled the high-throughput profiling of single or multi-cell types and cell states with spatial information. They transformed our understanding of the higher-order architectures and paired cell-cell interactions within a tumor microenvironment (TME). Within less than a decade, this rapidly emerging field has discovered much crucial fundamental knowledge and significantly improved clinical diagnosis in the field of immuno-oncology. This review summarizes the conceptual frameworks to understand spatial omics data and highlights the updated knowledge of spatial immuno-oncology.</p>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"22-28"},"PeriodicalIF":6.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872922","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
Collective sperm movement in mammalian reproductive tracts. 哺乳动物生殖道中精子的集体运动。
IF 6.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-12-14 DOI: 10.1016/j.semcdb.2024.12.002
Tsuyoshi Hirashima, Sound W P, Taichi Noda

Mammalian sperm cells travel from their origin in the male reproductive tract to fertilization in the female tract through a complex process driven by coordinated mechanical and biochemical mechanisms. Recent experimental and theoretical advances have illuminated the collective behaviors of sperm both in vivo and in vitro. However, our understanding of the underlying mechano-chemical processes remains incomplete. This review integrates current insights into sperm group movement, examining both immotile and motile states, which are essential for passive transport and active swimming through the reproductive tracts. We provide an overview of the current understanding of collective sperm movement, focusing on the experimental and theoretical mechanisms behind these behaviors. We also explore how sperm motility is regulated through the coordination of mechanical and chemical processes. Emerging evidence highlights the mechanosensitive properties of a sperm flagellum, suggesting that mechanical stimuli regulate flagellar beating at both individual and collective levels. This self-regulatory, mechano-chemical system reflects a broader principle observed in multicellular systems, offering a system-level insight into the regulation of motility and collective dynamics in biological systems.

{"title":"Collective sperm movement in mammalian reproductive tracts.","authors":"Tsuyoshi Hirashima, Sound W P, Taichi Noda","doi":"10.1016/j.semcdb.2024.12.002","DOIUrl":"10.1016/j.semcdb.2024.12.002","url":null,"abstract":"<p><p>Mammalian sperm cells travel from their origin in the male reproductive tract to fertilization in the female tract through a complex process driven by coordinated mechanical and biochemical mechanisms. Recent experimental and theoretical advances have illuminated the collective behaviors of sperm both in vivo and in vitro. However, our understanding of the underlying mechano-chemical processes remains incomplete. This review integrates current insights into sperm group movement, examining both immotile and motile states, which are essential for passive transport and active swimming through the reproductive tracts. We provide an overview of the current understanding of collective sperm movement, focusing on the experimental and theoretical mechanisms behind these behaviors. We also explore how sperm motility is regulated through the coordination of mechanical and chemical processes. Emerging evidence highlights the mechanosensitive properties of a sperm flagellum, suggesting that mechanical stimuli regulate flagellar beating at both individual and collective levels. This self-regulatory, mechano-chemical system reflects a broader principle observed in multicellular systems, offering a system-level insight into the regulation of motility and collective dynamics in biological systems.</p>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"13-21"},"PeriodicalIF":6.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142829809","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
Collective mechanics of small migrating cell groups.
IF 6.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-12-07 DOI: 10.1016/j.semcdb.2024.12.001
Wenzheng Shi, Selena Gupta, Calina Copos, Alex Mogilner

Migration of adhesive cell groups is a fundamental part of wound healing, development and carcinogenesis. Intense research has been conducted on mechanisms of collective migration of adhesive groups of cells. Here we focus on mechanical and mechanistic lessons from small migrating cell groups. We review forces and locomotory dynamics of two- and three-cell clusters, rotation of cell doublets, self-organization of one-dimensional cell trains, nascent efforts to understand three-dimensional collective migration and border cell clusters in Drosophila embryo.

{"title":"Collective mechanics of small migrating cell groups.","authors":"Wenzheng Shi, Selena Gupta, Calina Copos, Alex Mogilner","doi":"10.1016/j.semcdb.2024.12.001","DOIUrl":"10.1016/j.semcdb.2024.12.001","url":null,"abstract":"<p><p>Migration of adhesive cell groups is a fundamental part of wound healing, development and carcinogenesis. Intense research has been conducted on mechanisms of collective migration of adhesive groups of cells. Here we focus on mechanical and mechanistic lessons from small migrating cell groups. We review forces and locomotory dynamics of two- and three-cell clusters, rotation of cell doublets, self-organization of one-dimensional cell trains, nascent efforts to understand three-dimensional collective migration and border cell clusters in Drosophila embryo.</p>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"1-12"},"PeriodicalIF":6.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142795065","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
Spatiotemporal dissection of collective cell migration and tissue morphogenesis during development by optogenetics. 光遗传学对发育过程中集体细胞迁移和组织形态发生的时空解剖。
IF 6.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-12-26 DOI: 10.1016/j.semcdb.2024.12.004
Sijia Zhou, Bing Liu, Jiaying Liu, Bin Yi, Xiaobo Wang

Collective cell migration and tissue morphogenesis play a variety of important roles in the development of many species. Tissue morphogenesis often generates mechanical forces that alter cell shapes and arrangements, resembling collective cell migration-like behaviors. Genetic methods have been widely used to study collective cell migration and its like behavior, advancing our understanding of these processes during development. However, a growing body of research shows that collective cell migration during development is not a simple behavior but is often combined with other cellular and tissue processes. In addition, different surrounding environments can also influence migrating cells, further complicating collective cell migration during development. Due to the complexity of developmental processes and tissues, traditional genetic approaches often encounter challenges and limitations. Thus, some methods with spatiotemporal control become urgent in dissecting collective cell migration and tissue morphogenesis during development. Optogenetics is a method that combines optics and genetics, providing a perfect strategy for spatiotemporally controlling corresponding protein activity in subcellular, cellular or tissue levels. In this review, we introduce the basic mechanisms underlying different optogenetic tools. Then, we demonstrate how optogenetic methods have been applied in vivo to dissect collective cell migration and tissue morphogenesis during development. Additionally, we describe some promising optogenetic approaches for advancing this field. Together, this review will guide and facilitate future studies of collective cell migration in vivo and tissue morphogenesis by optogenetics.

集体细胞迁移和组织形态发生在许多物种的发育中起着各种重要作用。组织形态发生经常产生改变细胞形状和排列的机械力,类似于集体细胞迁移行为。遗传方法已被广泛用于研究细胞集体迁移及其类似行为,促进了我们对这些过程的理解。然而,越来越多的研究表明,在发育过程中,集体细胞迁移不是一种简单的行为,而是经常与其他细胞和组织过程相结合。此外,不同的周围环境也会影响细胞的迁移,使发育过程中的集体细胞迁移进一步复杂化。由于发育过程和组织的复杂性,传统的遗传方法经常遇到挑战和局限性。因此,研究细胞在发育过程中的集体迁移和组织形态发生,迫切需要一些具有时空控制的方法。光遗传学是一种将光学和遗传学相结合的方法,为在亚细胞、细胞或组织水平上对相应的蛋白质活性进行时空控制提供了一种完美的策略。在本文中,我们介绍了不同光遗传学工具的基本机制。然后,我们展示了如何在体内应用光遗传学方法来解剖发育过程中的集体细胞迁移和组织形态发生。此外,我们描述了一些有前途的光遗传学方法来推进这一领域。本文综述将指导和促进光遗传学在体内集体细胞迁移和组织形态发生方面的进一步研究。
{"title":"Spatiotemporal dissection of collective cell migration and tissue morphogenesis during development by optogenetics.","authors":"Sijia Zhou, Bing Liu, Jiaying Liu, Bin Yi, Xiaobo Wang","doi":"10.1016/j.semcdb.2024.12.004","DOIUrl":"10.1016/j.semcdb.2024.12.004","url":null,"abstract":"<p><p>Collective cell migration and tissue morphogenesis play a variety of important roles in the development of many species. Tissue morphogenesis often generates mechanical forces that alter cell shapes and arrangements, resembling collective cell migration-like behaviors. Genetic methods have been widely used to study collective cell migration and its like behavior, advancing our understanding of these processes during development. However, a growing body of research shows that collective cell migration during development is not a simple behavior but is often combined with other cellular and tissue processes. In addition, different surrounding environments can also influence migrating cells, further complicating collective cell migration during development. Due to the complexity of developmental processes and tissues, traditional genetic approaches often encounter challenges and limitations. Thus, some methods with spatiotemporal control become urgent in dissecting collective cell migration and tissue morphogenesis during development. Optogenetics is a method that combines optics and genetics, providing a perfect strategy for spatiotemporally controlling corresponding protein activity in subcellular, cellular or tissue levels. In this review, we introduce the basic mechanisms underlying different optogenetic tools. Then, we demonstrate how optogenetic methods have been applied in vivo to dissect collective cell migration and tissue morphogenesis during development. Additionally, we describe some promising optogenetic approaches for advancing this field. Together, this review will guide and facilitate future studies of collective cell migration in vivo and tissue morphogenesis by optogenetics.</p>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"36-51"},"PeriodicalIF":6.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142897121","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
Spatial omics shed light on the tumour organisation of glioblastoma. 空间组学揭示了胶质母细胞瘤的肿瘤组织。
IF 6.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2025-01-08 DOI: 10.1016/j.semcdb.2024.12.006
James R Whittle, Jurgen Kriel, Oluwaseun E Fatunla, Tianyao Lu, Joel J D Moffet, Montana Spiteri, Sarah A Best, Saskia Freytag

The glioblastoma tumour microenvironment is characterised by immense heterogeneity, with malignant and non-malignant cells that interact in a complex ecosystem. Emerging evidence suggests that the tumour microenvironment is key in facilitating rapid proliferation, invasion, migration and cancer cell survival, crucial for treatment resistance. Spatial omics technologies have enabled the molecular characterisation of regions or individual cells within their spatial context, providing previously unattainable insights into the complex organisation of the glioblastoma tumour microenvironment. Understanding this organisation is crucial for the development of new therapeutics and novel diagnostic tools that guide patient care. This review explores spatial omics technologies and how they have contributed to the development of a model outlining the architecture of the glioblastoma tumour microenvironment.

胶质母细胞瘤肿瘤微环境的特点是巨大的异质性,恶性和非恶性细胞在一个复杂的生态系统中相互作用。新出现的证据表明,肿瘤微环境是促进癌细胞快速增殖、侵袭、迁移和存活的关键,对治疗耐药性至关重要。空间组学技术使区域或单个细胞在其空间背景下的分子特征成为可能,为胶质母细胞瘤肿瘤微环境的复杂组织提供了以前无法实现的见解。了解这种组织对于开发指导患者护理的新疗法和新诊断工具至关重要。这篇综述探讨了空间组学技术,以及它们如何促进了胶质母细胞瘤肿瘤微环境结构模型的发展。
{"title":"Spatial omics shed light on the tumour organisation of glioblastoma.","authors":"James R Whittle, Jurgen Kriel, Oluwaseun E Fatunla, Tianyao Lu, Joel J D Moffet, Montana Spiteri, Sarah A Best, Saskia Freytag","doi":"10.1016/j.semcdb.2024.12.006","DOIUrl":"https://doi.org/10.1016/j.semcdb.2024.12.006","url":null,"abstract":"<p><p>The glioblastoma tumour microenvironment is characterised by immense heterogeneity, with malignant and non-malignant cells that interact in a complex ecosystem. Emerging evidence suggests that the tumour microenvironment is key in facilitating rapid proliferation, invasion, migration and cancer cell survival, crucial for treatment resistance. Spatial omics technologies have enabled the molecular characterisation of regions or individual cells within their spatial context, providing previously unattainable insights into the complex organisation of the glioblastoma tumour microenvironment. Understanding this organisation is crucial for the development of new therapeutics and novel diagnostic tools that guide patient care. This review explores spatial omics technologies and how they have contributed to the development of a model outlining the architecture of the glioblastoma tumour microenvironment.</p>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"167 ","pages":"1-9"},"PeriodicalIF":6.2,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142954505","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
Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them 分子拟态介导的多种基因冲突以及检测这些冲突的计算方法。
IF 6.2 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-29 DOI: 10.1016/j.semcdb.2024.07.001
Shelbi L. Russell , Gabriel Penunuri , Christopher Condon

In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.

在基因组间和自私元素之间的遗传冲突中,驱动元素和杀手元素通过各种分子机制(包括拟态),在敏感元素和目标元素之上实现有偏向的生存、复制或传播。驱动机制体现在生物体的各个层面,从单个基因的偏向传播(如转座元件)到基因组的偏向传播(如病毒),再到细胞系的偏向传播(如癌症)。靶向基因组通过自身信号传递和调控所使用的保守基序,很容易受到分子模仿的影响。模仿这些基调可使基因组间或自私的元素控制核心目标过程,并可发生在序列、结构或功能水平上。分子模拟在二十多年前首次被视为一种重要现象。现代基因组学技术、数据库和机器学习方法为研究分子拟态在自然界遗传冲突中的分布提供了巨大的潜力。在此,我们将探讨冲突基因组间分子拟态的理论预期、已知基因冲突中分子拟态机制的趋势,并概述如何从群体基因组数据集中收集新的实例。我们讨论了涉及短序列图案或基因重复的拟态如何从新突变中趋同进化。而涉及不同结构域或完全折叠结构的过程则是通过水平基因转移在基因组之间发生的。这些趋势主要基于少数生物,应该在一个普遍的、独立于系统发育的框架内重新评估。目前,可从公开数据库中挖掘驱动非孟德尔遗传模式、表观相互作用和趋同蛋白质结构的基因型。这些冲突元素的一个子集可能是分子模拟物。我们提出了从这些数据集中检测遗传冲突和分子模仿的方法。
{"title":"Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them","authors":"Shelbi L. Russell ,&nbsp;Gabriel Penunuri ,&nbsp;Christopher Condon","doi":"10.1016/j.semcdb.2024.07.001","DOIUrl":"10.1016/j.semcdb.2024.07.001","url":null,"abstract":"<div><p>In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations<em>.</em> Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.</p></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"165 ","pages":"Pages 1-12"},"PeriodicalIF":6.2,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1084952124000557/pdfft?md5=d2592468bfb577ff0aef406716dc2946&pid=1-s2.0-S1084952124000557-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856430","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
From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements 来自冲突的大锅:piRNA 的内源基因调控以及自私的转座元件促成的其他适应模式。
IF 7.3 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-05-31 DOI: 10.1016/j.semcdb.2024.05.001
Justin P. Blumenstiel

Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.

可转座元件(Transposable elements,TEs)是遗传冲突的一个典型例子,因为它们即使对宿主有害,也能在基因组和种群中大量繁殖。然而,大量研究表明,可转座元件虽然通常有害,但也能为适应性提供动力。这是因为它们编码的功能序列对宿主有用。在这篇综述中,我将总结 TE 与宿主之间的遗传冲突是如何和为什么促成适应的。此外,我将重点放在小 piwi-interacting RNAs(piRNAs)控制 TE 的机制上,强调冲突带来的一种间接适应形式。在这种情况下,调控 TE 的宿主防御机制被重新用于内源基因调控。我提出,早期真核生物减数分裂释放的遗传冲突之所以重要,除其他原因外,可能还因为它刺激了多种交织轨迹上的进化创新--既有宿主方面的,也有嵌入的遗传寄生虫方面的。这种进化形式可能是真核生物进化过程中产生复杂性的一个关键引擎。
{"title":"From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements","authors":"Justin P. Blumenstiel","doi":"10.1016/j.semcdb.2024.05.001","DOIUrl":"10.1016/j.semcdb.2024.05.001","url":null,"abstract":"<div><p>Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the \"how\" and \"why\" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.</p></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"164 ","pages":"Pages 1-12"},"PeriodicalIF":7.3,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186135","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
WHO elements – A new category of selfish genetic elements at the borderline between homing elements and transposable elements 世卫组织元件--介于同源元件和转座元件之间的一类新的自私遗传元件。
IF 7.3 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-04-25 DOI: 10.1016/j.semcdb.2024.04.001
Matthieu Osborne, Athaliah Fubara, Eoin Ó Cinnéide, Aisling Y. Coughlan, Kenneth H. Wolfe

Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an ‘arms race’ between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.

同源遗传因子是一种自私的 DNA,它插入基因组中的特定目标位点,并通过偏向遗传的过程在群体中传播。几十年前,人们就发现了两种众所周知的归巢元件,分别称为内含子和归巢内含子。在这篇综述中,我们将介绍一种新发现的同源元件--WHO元件,它构成了独特的第三类同源元件,但非常罕见,迄今只在少数酵母物种中发现过。据推断,WHO 元子与内含子和内含子一样,都是利用分子归巢机制进行传播的:它们编码一种位点特异性内切酶,能在目标位点裂解基因组,造成 DNA 断裂,随后通过复制元件进行修复。对于大多数 WHO 基因元件来说,目标位点位于糖酵解基因 FBA1 中。世卫组织元件与内含子和归巢内含子有两个根本区别:它们不会中断宿主基因(FBA1),而且是成簇出现。这些基因簇是由不同的WHO元件连续整合到FBA1基因座中形成的,是内切酶与其目标位点之间 "军备竞赛 "的结果。我们还描述了一个世卫组织元件家族(WHO10),它不再与 FBA1 基因座有特异性关联,而似乎已成为可转座元件,插入到球花藻(Torulaspora globosa)的随机基因组位点,每个菌株多达 26 个拷贝。因此,世卫组织元件家族处于同源遗传元件和转座元件的交界处。
{"title":"WHO elements – A new category of selfish genetic elements at the borderline between homing elements and transposable elements","authors":"Matthieu Osborne,&nbsp;Athaliah Fubara,&nbsp;Eoin Ó Cinnéide,&nbsp;Aisling Y. Coughlan,&nbsp;Kenneth H. Wolfe","doi":"10.1016/j.semcdb.2024.04.001","DOIUrl":"10.1016/j.semcdb.2024.04.001","url":null,"abstract":"<div><p>Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene <em>FBA1</em>. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (<em>FBA1</em>), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the <em>FBA1</em> locus, the result of an ‘arms race’ between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the <em>FBA1</em> locus and instead appears to have become transposable, inserting at random genomic sites in <em>Torulaspora globosa</em> with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.</p></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"163 ","pages":"Pages 2-13"},"PeriodicalIF":7.3,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1084952124000326/pdfft?md5=ca5197c79a4967a06b53c679ce8a49e9&pid=1-s2.0-S1084952124000326-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140774912","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
Out with the old, in with the new: Meiotic driving of sex chromosome evolution 旧的不去,新的不来:性染色体进化的减数分裂驱动力。
IF 7.3 2区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-04-24 DOI: 10.1016/j.semcdb.2024.04.004
Callie M. Swanepoel, Jacob L. Mueller

Chromosomal regions with meiotic drivers exhibit biased transmission (> 50 %) over their competing homologous chromosomal region. These regions often have two prominent genetic features: suppressed meiotic crossing over and rapidly evolving multicopy gene families. Heteromorphic sex chromosomes (e.g., XY) often share these two genetic features with chromosomal regions exhibiting meiotic drive. Here, we discuss parallels between meiotic drive and sex chromosome evolution, how the divergence of heteromorphic sex chromosomes can be influenced by meiotic drive, experimental approaches to study meiotic drive on sex chromosomes, and meiotic drive in traditional and non-traditional model organisms with high-quality genome assemblies. The newly available diversity of high-quality sex chromosome sequences allows us to revisit conventional models of sex chromosome evolution through the lens of meiotic drive.

具有减数分裂驱动力的染色体区域比与其竞争的同源染色体区域表现出偏向传递(50%)。这些区域通常有两个突出的遗传特征:减数分裂交叉抑制和快速进化的多拷贝基因家族。异形性染色体(如 XY)与表现出减数分裂驱动力的染色体区域通常具有这两个遗传特征。在此,我们将讨论减数分裂驱动与性染色体进化之间的相似之处、减数分裂驱动如何影响异形性染色体的分化、研究性染色体减数分裂驱动的实验方法,以及具有高质量基因组组装的传统和非传统模式生物的减数分裂驱动。新近获得的高质量性染色体序列的多样性使我们能够通过减数分裂驱动的视角重新审视性染色体进化的传统模型。
{"title":"Out with the old, in with the new: Meiotic driving of sex chromosome evolution","authors":"Callie M. Swanepoel,&nbsp;Jacob L. Mueller","doi":"10.1016/j.semcdb.2024.04.004","DOIUrl":"10.1016/j.semcdb.2024.04.004","url":null,"abstract":"<div><p>Chromosomal regions with meiotic drivers exhibit biased transmission (&gt; 50 %) over their competing homologous chromosomal region. These regions often have two prominent genetic features: suppressed meiotic crossing over and rapidly evolving multicopy gene families. Heteromorphic sex chromosomes (e.g., XY) often share these two genetic features with chromosomal regions exhibiting meiotic drive. Here, we discuss parallels between meiotic drive and sex chromosome evolution, how the divergence of heteromorphic sex chromosomes can be influenced by meiotic drive, experimental approaches to study meiotic drive on sex chromosomes, and meiotic drive in traditional and non-traditional model organisms with high-quality genome assemblies. The newly available diversity of high-quality sex chromosome sequences allows us to revisit conventional models of sex chromosome evolution through the lens of meiotic drive.</p></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"163 ","pages":"Pages 14-21"},"PeriodicalIF":7.3,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140759524","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
期刊
Seminars in cell & developmental biology
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:481959085
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