Abbye E. McEwen, Malvika Tejura, Shawn Fayer, Lea M. Starita, Douglas M. Fowler
{"title":"Multiplexed assays of variant effect for clinical variant interpretation","authors":"Abbye E. McEwen, Malvika Tejura, Shawn Fayer, Lea M. Starita, Douglas M. Fowler","doi":"10.1038/s41576-025-00870-x","DOIUrl":"https://doi.org/10.1038/s41576-025-00870-x","url":null,"abstract":"<p>The rapid expansion of clinical genetic testing has markedly improved the detection of genetic variants. However, most variants lack the evidence needed to classify them as pathogenic or benign, resulting in the accumulation of variants of uncertain significance that cannot be used to diagnose or guide treatment of disease. Moreover, targeted therapy for cancer treatment increasingly depends on correctly identifying oncogenic driver mutations, but the oncogenicity of many variants identified in tumours remains unclear. To address these challenges, efforts to classify variants are increasingly using multiplexed assays of variant effect (MAVEs), which are massively scaled experiments that can generate functional data for thousands of variants simultaneously. The rise of MAVEs is accompanied by better guidance on the use of MAVE data for classifying germline variants to aid their clinical implementation. Here, we overview MAVE technologies from their inception to their increased use in the clinic, including their roles in uncovering mechanisms for variant pathogenicity and guiding targeted therapy and drug development.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"52 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144669634","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}
{"title":"Experimental evolution in an era of molecular manipulation","authors":"Joao A. Ascensao, Michael M. Desai","doi":"10.1038/s41576-025-00867-6","DOIUrl":"https://doi.org/10.1038/s41576-025-00867-6","url":null,"abstract":"<p>Laboratory evolution experiments in microbial and viral populations have provided great insight into the dynamics and predictability of evolution. The rise of high-throughput sequencing technologies over the past two decades has driven a massive expansion in the scale and power of these experiments. However, until recently our abilities to connect genetic with phenotypic changes and analyse the molecular basis of adaptation have remained limited. Rapid technical advances to measure and manipulate both genotypes and phenotypes are now providing opportunities to investigate the genetic basis of phenotypic evolution and the forces that drive evolutionary dynamics. Here we review how these methodological advances are being used to predict and manipulate the course of laboratory evolution, analyse eco-evolutionary interactions, and how they are beginning to bridge the gap between laboratory and natural evolution.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"14 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144669693","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}
{"title":"When cellular reprogramming meets AI: towards de novo cell design","authors":"Jian Shu","doi":"10.1038/s41576-025-00878-3","DOIUrl":"https://doi.org/10.1038/s41576-025-00878-3","url":null,"abstract":"In this Journal Club, Jian Shu recalls a 2006 publication by Takahashi and Yamanaka as well as a 2021 paper introducing AlphaFold to discuss the fascinating potential of cellular reprogramming in the age of artificial intelligence.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"16 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144640359","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}
{"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}
{"title":"Author Correction: Evolution and regulation of animal sex chromosomes","authors":"Zexian Zhu, Lubna Younas, Qi Zhou","doi":"10.1038/s41576-025-00876-5","DOIUrl":"https://doi.org/10.1038/s41576-025-00876-5","url":null,"abstract":"<p>Correction to: <i>Nature Reviews Genetics</i> https://doi.org/10.1038/s41576-024-00757-3, published on 18 July 2024.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"32 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"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}
{"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}
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}
{"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}