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}
Pub Date : 2025-06-04DOI: 10.1038/s41576-025-00849-8
Pamela Ferretti, Kelsey Johnson, Sambhawa Priya, Ran Blekhman
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. In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.
{"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":"10.1038/s41576-025-00849-8","url":null,"abstract":"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. In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome on host gene regulation.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 1","pages":"62-80"},"PeriodicalIF":52.0,"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}
Pub Date : 2025-05-28DOI: 10.1038/s41576-025-00858-7
Delilah Hendriks, Benedetta Artegiani
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.
{"title":"Searching for the origin of human brain tumours","authors":"Delilah Hendriks, Benedetta Artegiani","doi":"10.1038/s41576-025-00858-7","DOIUrl":"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":"26 8","pages":"511-512"},"PeriodicalIF":52.0,"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}
Pub Date : 2025-05-28DOI: 10.1038/s41576-025-00860-z
Jun Kim, Zhe J. Liu
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.
{"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":"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":"26 9","pages":"581-581"},"PeriodicalIF":52.0,"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}
Pub Date : 2025-05-28DOI: 10.1038/s41576-025-00861-y
Jianheng Fox Liu
In this Tools of the Trade article, Jianheng Fox Liu describes CROWN-seq, a method for mapping Am (2′-O-methyladenosine), m6Am (N6,2′-O-dimethyladenosine) and transcription start sites.
在这篇贸易工具文章中，Jianheng Fox Liu介绍了CROWN-seq，这是一种绘制Am （2 ' - o -甲基腺苷），m6Am （n6,2 ' - o -二甲基腺苷）和转录起始位点的方法。
{"title":"CROWN-seq reveals m6Am landscapes and transcription start site diversity","authors":"Jianheng Fox Liu","doi":"10.1038/s41576-025-00861-y","DOIUrl":"10.1038/s41576-025-00861-y","url":null,"abstract":"In this Tools of the Trade article, Jianheng Fox Liu describes CROWN-seq, a method for mapping Am (2′-O-methyladenosine), m6Am (N6,2′-O-dimethyladenosine) and transcription start sites.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 8","pages":"509-509"},"PeriodicalIF":52.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153650","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 : 2025-05-22DOI: 10.1038/s41576-025-00855-w
Diyendo Massilani
In this Journal Club, Diyendo Massilani recalls two studies by Meyer et al. that reported a mitochondrial genome and nuclear DNA sequences from mid-Ice Age Sima de los Huesos hominins.
在这个Journal Club中，Diyendo Massilani回顾了Meyer等人的两项研究，这两项研究报道了冰河时代中期人类Sima de los Huesos的线粒体基因组和核DNA序列。
{"title":"A crossroads in the timeline of human evolution","authors":"Diyendo Massilani","doi":"10.1038/s41576-025-00855-w","DOIUrl":"10.1038/s41576-025-00855-w","url":null,"abstract":"In this Journal Club, Diyendo Massilani recalls two studies by Meyer et al. that reported a mitochondrial genome and nuclear DNA sequences from mid-Ice Age Sima de los Huesos hominins.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 8","pages":"510-510"},"PeriodicalIF":52.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144113684","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 : 2025-05-21DOI: 10.1038/s41576-025-00846-x
Technological and computational advances in recent years, from cryo-electron microscopy to sequencing technologies and machine learning, have substantially deepened our understanding of RNA splicing. Nature Reviews Genetics and Nature Reviews Molecular Cell Biology present an online collection that showcases the biological insights facilitated by these advances. Technological and computational advances in recent years, from cryo-electron microscopy to sequencing technologies and machine learning, have substantially deepened our understanding of RNA splicing. Nature Reviews Genetics and Nature Reviews Molecular Cell Biology present an online collection that showcases the novel biological insights facilitated by these advances.
{"title":"RNA splicing — a central layer of gene regulation","authors":"","doi":"10.1038/s41576-025-00846-x","DOIUrl":"10.1038/s41576-025-00846-x","url":null,"abstract":"Technological and computational advances in recent years, from cryo-electron microscopy to sequencing technologies and machine learning, have substantially deepened our understanding of RNA splicing. Nature Reviews Genetics and Nature Reviews Molecular Cell Biology present an online collection that showcases the biological insights facilitated by these advances. Technological and computational advances in recent years, from cryo-electron microscopy to sequencing technologies and machine learning, have substantially deepened our understanding of RNA splicing. Nature Reviews Genetics and Nature Reviews Molecular Cell Biology present an online collection that showcases the novel biological insights facilitated by these advances.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 6","pages":"369-370"},"PeriodicalIF":52.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41576-025-00846-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103980","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}
Pub Date : 2025-05-20DOI: 10.1038/s41576-025-00857-8
Loïc Binan
In this Tools of the Trade article, Loic Binan explains Perturb-FISH, which measures genetic perturbations and gene expression in situ at high throughput to map gene regulatory networks at cellular and tissue scale.
{"title":"Investigating spatial gene circuits and gene–phenotype mechanisms with Perturb-FISH","authors":"Loïc Binan","doi":"10.1038/s41576-025-00857-8","DOIUrl":"10.1038/s41576-025-00857-8","url":null,"abstract":"In this Tools of the Trade article, Loic Binan explains Perturb-FISH, which measures genetic perturbations and gene expression in situ at high throughput to map gene regulatory networks at cellular and tissue scale.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 8","pages":"507-508"},"PeriodicalIF":52.0,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103599","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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