Apoptosis is an essential cellular process corresponding to a programmed cell suicide. It has long been considered as a cell-autonomous process, supposed to have no particular impact on the surrounding tissue. However, it has become clear in the last 15 years that epithelial apoptotic cells interact mechanically and biochemically with their environment. Here, we explore recent literature on apoptotic mechanics from an individual dying cell to the back-and-forth interplay with the neighboring epithelial tissue. Finally, we discuss how caspases, key regulators of apoptosis, appear to have a dual function as a cytoskeleton regulator favoring either cytoskeleton degradation or dynamics independently of their apoptotic or non-apoptotic role.
{"title":"Epithelial apoptosis: A back-and-forth mechanical interplay between the dying cell and its surroundings","authors":"Stéphanie Arnould , Corinne Benassayag , Tatiana Merle , Bruno Monier , Marianne Montemurro , Magali Suzanne","doi":"10.1016/j.semcdb.2025.02.001","DOIUrl":"10.1016/j.semcdb.2025.02.001","url":null,"abstract":"<div><div>Apoptosis is an essential cellular process corresponding to a programmed cell suicide. It has long been considered as a cell-autonomous process, supposed to have no particular impact on the surrounding tissue. However, it has become clear in the last 15 years that epithelial apoptotic cells interact mechanically and biochemically with their environment. Here, we explore recent literature on apoptotic mechanics from an individual dying cell to the back-and-forth interplay with the neighboring epithelial tissue. Finally, we discuss how caspases, key regulators of apoptosis, appear to have a dual function as a cytoskeleton regulator favoring either cytoskeleton degradation or dynamics independently of their apoptotic or non-apoptotic role.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"168 ","pages":"Pages 1-12"},"PeriodicalIF":6.2,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143464971","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}
Pub Date : 2025-02-01DOI: 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.
{"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":"<div><div>The intricate control of collective cell dynamics is crucial for enabling organismic development and tissue regeneration. Despite the availability of various <em>in vitro</em> and <em>in vivo</em> 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 <em>in vivo</em> 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.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"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}
Pub Date : 2025-02-01DOI: 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.
{"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":"<div><div>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.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"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}
Pub Date : 2025-02-01DOI: 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":"<div><div>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 <em>in vivo</em> and <em>in vitro</em>. 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.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"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}
Pub Date : 2025-02-01DOI: 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":"<div><div>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.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"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}
Pub Date : 2025-02-01DOI: 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.
{"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":"<div><div>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 <em>in vivo</em> 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 <em>in vivo</em> and tissue morphogenesis by optogenetics.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"166 ","pages":"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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-31DOI: 10.1016/j.semcdb.2025.01.002
Chang Liu , Xuerong Li , Qinan Hu , Zihan Jia , Qing Ye , Xianzhe Wang , Kaichen Zhao , Longqi Liu , Mingyue Wang
Embryonic development is a complex and intricately regulated process that encompasses precise control over cell differentiation, morphogenesis, and the underlying gene expression changes. Recent years have witnessed a remarkable acceleration in the development of single-cell and spatial omic technologies, enabling high-throughput profiling of transcriptomic and other multi-omic information at the individual cell level. These innovations offer fresh and multifaceted perspectives for investigating the intricate cellular and molecular mechanisms that govern embryonic development. In this review, we provide an in-depth exploration of the latest technical advancements in single-cell and spatial multi-omic methodologies and compile a systematic catalog of their applications in the field of embryonic development. We deconstruct the research strategies employed by recent studies that leverage single-cell sequencing techniques and underscore the unique advantages of spatial transcriptomics. Furthermore, we delve into both the current applications, data analysis algorithms and the untapped potential of these technologies in advancing our understanding of embryonic development. With the continuous evolution of multi-omic technologies, we anticipate their widespread adoption and profound contributions to unraveling the intricate molecular foundations underpinning embryo development in the foreseeable future.
{"title":"Decoding the blueprints of embryo development with single-cell and spatial omics","authors":"Chang Liu , Xuerong Li , Qinan Hu , Zihan Jia , Qing Ye , Xianzhe Wang , Kaichen Zhao , Longqi Liu , Mingyue Wang","doi":"10.1016/j.semcdb.2025.01.002","DOIUrl":"10.1016/j.semcdb.2025.01.002","url":null,"abstract":"<div><div>Embryonic development is a complex and intricately regulated process that encompasses precise control over cell differentiation, morphogenesis, and the underlying gene expression changes. Recent years have witnessed a remarkable acceleration in the development of single-cell and spatial omic technologies, enabling high-throughput profiling of transcriptomic and other multi-omic information at the individual cell level. These innovations offer fresh and multifaceted perspectives for investigating the intricate cellular and molecular mechanisms that govern embryonic development. In this review, we provide an in-depth exploration of the latest technical advancements in single-cell and spatial multi-omic methodologies and compile a systematic catalog of their applications in the field of embryonic development. We deconstruct the research strategies employed by recent studies that leverage single-cell sequencing techniques and underscore the unique advantages of spatial transcriptomics. Furthermore, we delve into both the current applications, data analysis algorithms and the untapped potential of these technologies in advancing our understanding of embryonic development. With the continuous evolution of multi-omic technologies, we anticipate their widespread adoption and profound contributions to unraveling the intricate molecular foundations underpinning embryo development in the foreseeable future.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"167 ","pages":"Pages 22-39"},"PeriodicalIF":6.2,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075371","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}
Pub Date : 2025-01-30DOI: 10.1016/j.semcdb.2025.01.001
Raymond K.H. Yip , Edwin D. Hawkins , Rory Bowden , Kelly L. Rogers
The tissue microenvironment refers to a localised tissue area where a complex combination of cells, structural components, and signalling molecules work together to support specific biological activities. A prime example is the bone marrow microenvironment, particularly the hematopoietic stem cell (HSC) niche, which is of immense interest due to its critical role in supporting lifelong blood cell production and the growth of malignant cells. In this review, we summarise the current understanding of HSC niche biology, highlighting insights gained from advanced imaging and genomic techniques. We also discuss the potential of emerging technologies such as spatial multi-omics to unravel bone marrow architecture in unprecedented detail.
{"title":"Towards deciphering the bone marrow microenvironment with spatial multi-omics","authors":"Raymond K.H. Yip , Edwin D. Hawkins , Rory Bowden , Kelly L. Rogers","doi":"10.1016/j.semcdb.2025.01.001","DOIUrl":"10.1016/j.semcdb.2025.01.001","url":null,"abstract":"<div><div>The tissue microenvironment refers to a localised tissue area where a complex combination of cells, structural components, and signalling molecules work together to support specific biological activities. A prime example is the bone marrow microenvironment, particularly the hematopoietic stem cell (HSC) niche, which is of immense interest due to its critical role in supporting lifelong blood cell production and the growth of malignant cells. In this review, we summarise the current understanding of HSC niche biology, highlighting insights gained from advanced imaging and genomic techniques. We also discuss the potential of emerging technologies such as spatial multi-omics to unravel bone marrow architecture in unprecedented detail.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"167 ","pages":"Pages 10-21"},"PeriodicalIF":6.2,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075374","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}
Pub Date : 2025-01-08DOI: 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.
{"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":"10.1016/j.semcdb.2024.12.006","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":21735,"journal":{"name":"Seminars in cell & developmental biology","volume":"167 ","pages":"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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-29DOI: 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.
{"title":"Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them","authors":"Shelbi L. Russell , Gabriel Penunuri , 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}
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