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Structural variants in the 3D genome as drivers of disease 三维基因组中的结构变异是疾病的驱动因素
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-30 DOI: 10.1038/s41576-025-00862-x
Varun K. A. Sreenivasan, Verónica Yumiceba, Malte Spielmann
{"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":"https://doi.org/10.1038/s41576-025-00862-x","url":null,"abstract":"<p>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 <i>cis-</i>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.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"2 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
Spatial multi-omics of nuclear architecture with two-layer seqFISH+ 基于双层seqFISH+的核结构空间多组学研究
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-25 DOI: 10.1038/s41576-025-00868-5
Yodai Takei
{"title":"Spatial multi-omics of nuclear architecture with two-layer seqFISH+","authors":"Yodai Takei","doi":"10.1038/s41576-025-00868-5","DOIUrl":"https://doi.org/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":"16 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
RNA polymerase II transcription compartments — from factories to condensates RNA聚合酶II转录室-从工厂到冷凝物
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-19 DOI: 10.1038/s41576-025-00859-6
Karsten Rippe, Argyris Papantonis
{"title":"RNA polymerase II transcription compartments — from factories to condensates","authors":"Karsten Rippe, Argyris Papantonis","doi":"10.1038/s41576-025-00859-6","DOIUrl":"https://doi.org/10.1038/s41576-025-00859-6","url":null,"abstract":"<p>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 <i>cis</i>-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.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"236 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
Making sense of the polygenicity of complex traits 理解复杂性状的多基因性
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-16 DOI: 10.1038/s41576-025-00866-7
Hakhamanesh Mostafavi
{"title":"Making sense of the polygenicity of complex traits","authors":"Hakhamanesh Mostafavi","doi":"10.1038/s41576-025-00866-7","DOIUrl":"https://doi.org/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":"22 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
Determining variant effects with pooled prime editing 用集合质数编辑确定不同的效果
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-16 DOI: 10.1038/s41576-025-00865-8
Christina M. Kajba, Michael Herger
{"title":"Determining variant effects with pooled prime editing","authors":"Christina M. Kajba, Michael Herger","doi":"10.1038/s41576-025-00865-8","DOIUrl":"https://doi.org/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":"10 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
Measuring the effects of regulatory variants in an endogenous context 测量内源性环境中调节变异的影响
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-11 DOI: 10.1038/s41576-025-00863-w
Michael T. Montgomery
{"title":"Measuring the effects of regulatory variants in an endogenous context","authors":"Michael T. Montgomery","doi":"10.1038/s41576-025-00863-w","DOIUrl":"https://doi.org/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":"32 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
Phylogenetic insights into the transmission dynamics of arthropod-borne viruses 节肢动物传播病毒动力学的系统发育研究
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-06 DOI: 10.1038/s41576-025-00854-x
Verity Hill, Simon Dellicour, Marta Giovanetti, Nathan D. Grubaugh
{"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":"https://doi.org/10.1038/s41576-025-00854-x","url":null,"abstract":"<p>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.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"142 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
Genomics of host–microbiome interactions in humans 人类宿主-微生物组相互作用的基因组学
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-06-04 DOI: 10.1038/s41576-025-00849-8
Pamela Ferretti, Kelsey Johnson, Sambhawa Priya, Ran Blekhman
{"title":"Genomics of host–microbiome interactions in humans","authors":"Pamela Ferretti, Kelsey Johnson, Sambhawa Priya, Ran Blekhman","doi":"10.1038/s41576-025-00849-8","DOIUrl":"https://doi.org/10.1038/s41576-025-00849-8","url":null,"abstract":"<p>The human microbiome is a complex ecosystem of microorganisms that inhabit the human body and have a crucial role in human health. Microbiome composition is shaped by its interaction with many factors, including human genetics. Advances in genomic technologies are improving the ability to quantify the effect of human genetics on the microbiome through improved heritability studies and microbiome genome-wide association studies (GWAS). Complementary studies using transcriptomic analyses are providing a more comprehensive view of the bidirectional relationship between host gene expression and the microbiome. The resulting insights into the genetic mechanisms driving host–microbiome interactions will ultimately contribute to the development of personalized medicine and targeted therapies.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"11 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144211026","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}
引用次数: 0
Searching for the origin of human brain tumours 寻找人类脑肿瘤的起源
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-28 DOI: 10.1038/s41576-025-00858-7
Delilah Hendriks, Benedetta Artegiani
{"title":"Searching for the origin of human brain tumours","authors":"Delilah Hendriks, Benedetta Artegiani","doi":"10.1038/s41576-025-00858-7","DOIUrl":"https://doi.org/10.1038/s41576-025-00858-7","url":null,"abstract":"In this Journal Club, Delilah Hendriks and Benedetta Artegiani recall a 2018 paper by Lee et al. that combined data from human patients and experimental model systems to reveal the complexities of how brain tumours originate.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"7 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153678","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}
引用次数: 0
High-resolution imaging of RNA and proteins in thick tissues using cycleHCR 使用cycleHCR对厚组织中的RNA和蛋白质进行高分辨率成像
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-28 DOI: 10.1038/s41576-025-00860-z
Jun Kim, Zhe J. Liu
{"title":"High-resolution imaging of RNA and proteins in thick tissues using cycleHCR","authors":"Jun Kim, Zhe J. Liu","doi":"10.1038/s41576-025-00860-z","DOIUrl":"https://doi.org/10.1038/s41576-025-00860-z","url":null,"abstract":"In this Tools of the Trade article, Jun Kim and Zhe Liu describe cycleHCR, a method that enables researchers to simultaneously detect several different RNA and protein molecules at high-resolution across tissues.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"98 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153649","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}
引用次数: 0
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