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Mapping trait-associated cells with spatial transcriptomics. 利用空间转录组学定位性状相关细胞。
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-07-15 DOI: 10.1038/s41576-025-00877-4
Liyang Song
{"title":"Mapping trait-associated cells with spatial transcriptomics.","authors":"Liyang Song","doi":"10.1038/s41576-025-00877-4","DOIUrl":"https://doi.org/10.1038/s41576-025-00877-4","url":null,"abstract":"","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"11 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144640200","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
The evolutionary foundations of transcriptional regulation in animals 动物转录调控的进化基础
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-07-09 DOI: 10.1038/s41576-025-00864-9
Maxwell C. Coyle, Nicole King
{"title":"The evolutionary foundations of transcriptional regulation in animals","authors":"Maxwell C. Coyle, Nicole King","doi":"10.1038/s41576-025-00864-9","DOIUrl":"https://doi.org/10.1038/s41576-025-00864-9","url":null,"abstract":"<p>The development of a single-celled zygote into a complex, multicellular animal is directed by transcription factors and regulatory RNAs that coordinate spatio-temporal gene expression patterns. Given the morphological complexity of animals, some prior work has hypothesized that the origin of animals required the evolution of unique and markedly complex transcriptional regulatory mechanisms. Such postulated animal innovations include the evolution of greater numbers of transcription factors, new transcription factor families, distal enhancers and the emergence of long non-coding RNAs. Here, we revisit these explanations in light of new genomic and functional data from diverse early-branching animals and close relatives of animals, which provide essential phylogenetic context for reconstructing the origin of animals. These experimental models also offer examples of how some animal developmental pathways were built from core mechanisms inherited from their protistan ancestors. These new data provide fresh perspectives on whether animal origins entailed fundamental innovations in transcriptional regulation or whether, alternatively, a gradual accumulation of smaller changes sufficed to generate the complex developmental and cell differentiation mechanisms of early animals.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"3 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144586308","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
Author Correction: Evolution and regulation of animal sex chromosomes 作者更正：动物性染色体的进化与调控
IF 52 1区 生物学
Nature Reviews Genetics Pub Date : 2025-07-08 DOI: 10.1038/s41576-025-00876-5
Zexian Zhu, Lubna Younas, Qi Zhou
{"title":"Author Correction: Evolution and regulation of animal sex chromosomes","authors":"Zexian Zhu,&nbsp;Lubna Younas,&nbsp;Qi Zhou","doi":"10.1038/s41576-025-00876-5","DOIUrl":"10.1038/s41576-025-00876-5","url":null,"abstract":"","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 9","pages":"650-650"},"PeriodicalIF":52.0,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41576-025-00876-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144578396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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
Non-retroviral RNA viruses in eukaryotic genomes 真核生物基因组中的非逆转录病毒RNA病毒
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-07-07 DOI: 10.1038/s41576-025-00874-7
Mariangela Bonizzoni
{"title":"Non-retroviral RNA viruses in eukaryotic genomes","authors":"Mariangela Bonizzoni","doi":"10.1038/s41576-025-00874-7","DOIUrl":"https://doi.org/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":"2 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
Harnessing lateral gene transfer and endosymbiosis for adaptation 利用横向基因转移和内共生来适应
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-07-01 DOI: 10.1038/s41576-025-00872-9
Nina Wedell
{"title":"Harnessing lateral gene transfer and endosymbiosis for adaptation","authors":"Nina Wedell","doi":"10.1038/s41576-025-00872-9","DOIUrl":"https://doi.org/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":"13 1","pages":""},"PeriodicalIF":42.7,"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}
引用次数: 0
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 52 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":"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}
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 52 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":"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}
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 52 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,&nbsp;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}
引用次数: 0
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