Pub Date : 2025-07-07DOI: 10.1038/s41576-025-00874-7
Mariangela Bonizzoni
Mariangela Bonizzoni recalls a 2004 paper by Crochu et al. that revealed non-retroviral integrations into eukaryotic genomics to be a widespread and complex phenomenon.
{"title":"Non-retroviral RNA viruses in eukaryotic genomes","authors":"Mariangela Bonizzoni","doi":"10.1038/s41576-025-00874-7","DOIUrl":"10.1038/s41576-025-00874-7","url":null,"abstract":"Mariangela Bonizzoni recalls a 2004 paper by Crochu et al. that revealed non-retroviral integrations into eukaryotic genomics to be a widespread and complex phenomenon.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 1","pages":"12-12"},"PeriodicalIF":52.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-01DOI: 10.1038/s41576-025-00872-9
Nina Wedell
Nina Wedell discusses how a study by Dunning Hotopp et al., which found widespread lateral gene transfer (LGT) from the bacterium Wolbachia to a variety of arthropod and nematode hosts, catalysed the debate on the extent and functional relevance of LGT-derived genes.
{"title":"Harnessing lateral gene transfer and endosymbiosis for adaptation","authors":"Nina Wedell","doi":"10.1038/s41576-025-00872-9","DOIUrl":"10.1038/s41576-025-00872-9","url":null,"abstract":"Nina Wedell discusses how a study by Dunning Hotopp et al., which found widespread lateral gene transfer (LGT) from the bacterium Wolbachia to a variety of arthropod and nematode hosts, catalysed the debate on the extent and functional relevance of LGT-derived genes.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 12","pages":"811-811"},"PeriodicalIF":52.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144521056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-30DOI: 10.1038/s41576-025-00862-x
Varun K. A. Sreenivasan, Verónica Yumiceba, Malte Spielmann
The spatial organization of the genome within the nucleus — also known as genome architecture or 3D genome — is important to the regulation of gene expression. Disruption of the 3D genome, for example, by structural variation, can contribute to disease, including developmental disorders and cancer. Structural variants can rearrange higher-order chromatin structures, such as topologically associating domains, and disrupt interactions between cis-regulatory elements, which can lead to altered gene expression, a phenomenon known as position effects. New experimental and computational approaches are revealing the effect of structural variants on the 3D genome and gene expression and can help interpret their pathogenic potential, which has important implications for patients. Here, we review mechanisms of disease caused by position effects owing to disruptions of genome architecture, and more specifically topologically associating domains, as well as their consequences and clinical impact. Disruption of the 3D genome caused by structural variation contributes to developmental disorders and cancer. The authors review the causes and molecular and clinical consequences of position effects arising from disruptions to the genome architecture.
{"title":"Structural variants in the 3D genome as drivers of disease","authors":"Varun K. A. Sreenivasan, Verónica Yumiceba, Malte Spielmann","doi":"10.1038/s41576-025-00862-x","DOIUrl":"10.1038/s41576-025-00862-x","url":null,"abstract":"The spatial organization of the genome within the nucleus — also known as genome architecture or 3D genome — is important to the regulation of gene expression. Disruption of the 3D genome, for example, by structural variation, can contribute to disease, including developmental disorders and cancer. Structural variants can rearrange higher-order chromatin structures, such as topologically associating domains, and disrupt interactions between cis-regulatory elements, which can lead to altered gene expression, a phenomenon known as position effects. New experimental and computational approaches are revealing the effect of structural variants on the 3D genome and gene expression and can help interpret their pathogenic potential, which has important implications for patients. Here, we review mechanisms of disease caused by position effects owing to disruptions of genome architecture, and more specifically topologically associating domains, as well as their consequences and clinical impact. Disruption of the 3D genome caused by structural variation contributes to developmental disorders and cancer. The authors review the causes and molecular and clinical consequences of position effects arising from disruptions to the genome architecture.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 11","pages":"742-760"},"PeriodicalIF":52.0,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144515190","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-25DOI: 10.1038/s41576-025-00868-5
Yodai Takei
In this Tools of the Trade article, Yodai Takei presents two-layer seqFISH+, an imaging method that uses a novel barcoding strategy to simultaneously profile chromatin organization, the transcriptome and subnuclear structures at single-cell resolution.
{"title":"Spatial multi-omics of nuclear architecture with two-layer seqFISH+","authors":"Yodai Takei","doi":"10.1038/s41576-025-00868-5","DOIUrl":"10.1038/s41576-025-00868-5","url":null,"abstract":"In this Tools of the Trade article, Yodai Takei presents two-layer seqFISH+, an imaging method that uses a novel barcoding strategy to simultaneously profile chromatin organization, the transcriptome and subnuclear structures at single-cell resolution.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 9","pages":"582-583"},"PeriodicalIF":52.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-19DOI: 10.1038/s41576-025-00859-6
Karsten Rippe, Argyris Papantonis
Transcription by RNA polymerase II is a fundamental step in gene regulation that mainly occurs in discrete nuclear foci, or transcription compartments, characterized by a high local concentration of polymerases and nascent RNA. Early studies referred to these foci as transcription factories, proposing that they harbour most transcriptional activity and all relevant protein machinery to produce mature RNAs. However, this model of transcriptional organization has long remained controversial owing to its mechanistic uncertainties. Recently, new insights into how these foci may form are being provided by studies of phase-separated transcriptional condensates that encompass RNA polymerases, transcription factors and RNA. Advances in 3D genomics and chromatin imaging are also deepening our understanding of how transcription compartments might facilitate communication between cis-regulatory elements in 3D nuclear space. In this Review, we contrast historical work on transcription factories with recent findings on transcriptional condensates to better understand the architecture and functional relevance of transcription compartments. In this Review, Rippe and Papantonis describe advances in understanding the role of transcription compartments in gene regulation, specifically by collating and contrasting historical work on transcription factories with more recent work on transcriptional condensates.
{"title":"RNA polymerase II transcription compartments — from factories to condensates","authors":"Karsten Rippe, Argyris Papantonis","doi":"10.1038/s41576-025-00859-6","DOIUrl":"10.1038/s41576-025-00859-6","url":null,"abstract":"Transcription by RNA polymerase II is a fundamental step in gene regulation that mainly occurs in discrete nuclear foci, or transcription compartments, characterized by a high local concentration of polymerases and nascent RNA. Early studies referred to these foci as transcription factories, proposing that they harbour most transcriptional activity and all relevant protein machinery to produce mature RNAs. However, this model of transcriptional organization has long remained controversial owing to its mechanistic uncertainties. Recently, new insights into how these foci may form are being provided by studies of phase-separated transcriptional condensates that encompass RNA polymerases, transcription factors and RNA. Advances in 3D genomics and chromatin imaging are also deepening our understanding of how transcription compartments might facilitate communication between cis-regulatory elements in 3D nuclear space. In this Review, we contrast historical work on transcription factories with recent findings on transcriptional condensates to better understand the architecture and functional relevance of transcription compartments. In this Review, Rippe and Papantonis describe advances in understanding the role of transcription compartments in gene regulation, specifically by collating and contrasting historical work on transcription factories with more recent work on transcriptional condensates.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 11","pages":"775-788"},"PeriodicalIF":52.0,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144319502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-16DOI: 10.1038/s41576-025-00866-7
Hakhamanesh Mostafavi
Hakhamanesh Mostafavi recalls a landmark paper by Boyle et al. on the omnigenic model, which proposed that complex traits are influenced by thousands of genes across the genome, including many that are only indirectly related to a trait through regulatory networks.
{"title":"Making sense of the polygenicity of complex traits","authors":"Hakhamanesh Mostafavi","doi":"10.1038/s41576-025-00866-7","DOIUrl":"10.1038/s41576-025-00866-7","url":null,"abstract":"Hakhamanesh Mostafavi recalls a landmark paper by Boyle et al. on the omnigenic model, which proposed that complex traits are influenced by thousands of genes across the genome, including many that are only indirectly related to a trait through regulatory networks.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 8","pages":"513-513"},"PeriodicalIF":52.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144296057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-16DOI: 10.1038/s41576-025-00865-8
Christina M. Kajba, Michael Herger
In this Tools of the Trade article, Christina Kajba and Michael Herger describe their screening platform, based on pooled prime editing, for large-scale functional characterization of genetic variants.
{"title":"Determining variant effects with pooled prime editing","authors":"Christina M. Kajba, Michael Herger","doi":"10.1038/s41576-025-00865-8","DOIUrl":"10.1038/s41576-025-00865-8","url":null,"abstract":"In this Tools of the Trade article, Christina Kajba and Michael Herger describe their screening platform, based on pooled prime editing, for large-scale functional characterization of genetic variants.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 10","pages":"664-664"},"PeriodicalIF":52.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144296055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-11DOI: 10.1038/s41576-025-00863-w
Michael T. Montgomery
In this Tools of the Trade article, Michael Montgomery presents Variant-EFFECTS, a high-throughput and generalizable approach that combines prime editing, flow cytometry, sequencing, and computational analysis to quantify the effects of regulatory variants.
{"title":"Measuring the effects of regulatory variants in an endogenous context","authors":"Michael T. Montgomery","doi":"10.1038/s41576-025-00863-w","DOIUrl":"10.1038/s41576-025-00863-w","url":null,"abstract":"In this Tools of the Trade article, Michael Montgomery presents Variant-EFFECTS, a high-throughput and generalizable approach that combines prime editing, flow cytometry, sequencing, and computational analysis to quantify the effects of regulatory variants.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 10","pages":"663-663"},"PeriodicalIF":52.0,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144260304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-06DOI: 10.1038/s41576-025-00854-x
Verity Hill, Simon Dellicour, Marta Giovanetti, Nathan D. Grubaugh
Arthropod-borne viruses (arboviruses) impose substantial global health and economic burdens, affecting both human and animal populations. These viruses — including dengue, chikungunya, Rift Valley fever, Crimean–Congo haemorrhagic fever and bluetongue viruses — have complex transmission cycles involving vertebrate hosts and arthropod vectors. Their circulation in livestock and wildlife complicate surveillance, as traditional epidemiological approaches rely mainly on human clinical data. Climate change and increasing global interconnectedness are accelerating their emergence and invasion, necessitating a deeper understanding of their ecological and epidemiological dynamics. Advances in genomic surveillance and phylogenetics can provide insights into spatial and temporal patterns of virus transmission that are difficult to obtain through traditional surveillance systems. By integrating phylogenetic models with ecological and epidemiological data, we can better detect and respond to arbovirus introductions, spillovers and outbreaks that are relevant to both human and veterinary health. Arthropod-borne viruses have a substantial impact on global health, with climate change and urbanization exacerbating their emergence. Integrating genomic surveillance and phylogenetic models with ecological and epidemiological data enhances our understanding of virus transmission dynamics, aiding in effective detection and the response to disease outbreaks affecting humans and animals.
{"title":"Phylogenetic insights into the transmission dynamics of arthropod-borne viruses","authors":"Verity Hill, Simon Dellicour, Marta Giovanetti, Nathan D. Grubaugh","doi":"10.1038/s41576-025-00854-x","DOIUrl":"10.1038/s41576-025-00854-x","url":null,"abstract":"Arthropod-borne viruses (arboviruses) impose substantial global health and economic burdens, affecting both human and animal populations. These viruses — including dengue, chikungunya, Rift Valley fever, Crimean–Congo haemorrhagic fever and bluetongue viruses — have complex transmission cycles involving vertebrate hosts and arthropod vectors. Their circulation in livestock and wildlife complicate surveillance, as traditional epidemiological approaches rely mainly on human clinical data. Climate change and increasing global interconnectedness are accelerating their emergence and invasion, necessitating a deeper understanding of their ecological and epidemiological dynamics. Advances in genomic surveillance and phylogenetics can provide insights into spatial and temporal patterns of virus transmission that are difficult to obtain through traditional surveillance systems. By integrating phylogenetic models with ecological and epidemiological data, we can better detect and respond to arbovirus introductions, spillovers and outbreaks that are relevant to both human and veterinary health. Arthropod-borne viruses have a substantial impact on global health, with climate change and urbanization exacerbating their emergence. Integrating genomic surveillance and phylogenetic models with ecological and epidemiological data enhances our understanding of virus transmission dynamics, aiding in effective detection and the response to disease outbreaks affecting humans and animals.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 1","pages":"47-61"},"PeriodicalIF":52.0,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144228847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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