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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 52 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":"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}
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 52 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,&nbsp;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}
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 52 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,&nbsp;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}
引用次数: 0
CROWN-seq reveals m6Am landscapes and transcription start site diversity CROWN-seq揭示了m6Am的景观和转录起始位点的多样性
IF 52 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-28 DOI: 10.1038/s41576-025-00861-y
Jianheng Fox Liu
{"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}
引用次数: 0
A crossroads in the timeline of human evolution 人类进化史上的一个十字路口
IF 52 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-22 DOI: 10.1038/s41576-025-00855-w
Diyendo Massilani
{"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}
引用次数: 0
RNA splicing — a central layer of gene regulation RNA剪接——基因调控的中心环节
IF 52 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-21 DOI: 10.1038/s41576-025-00846-x
{"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}
引用次数: 0
Investigating spatial gene circuits and gene–phenotype mechanisms with Perturb-FISH 利用Perturb-FISH研究空间基因回路和基因表型机制。
IF 52 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-20 DOI: 10.1038/s41576-025-00857-8
Loïc Binan
{"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}
引用次数: 0
Functional synonymous mutations and their evolutionary consequences 功能同义突变及其进化后果
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-20 DOI: 10.1038/s41576-025-00850-1
Jianzhi Zhang, Wenfeng Qian
{"title":"Functional synonymous mutations and their evolutionary consequences","authors":"Jianzhi Zhang, Wenfeng Qian","doi":"10.1038/s41576-025-00850-1","DOIUrl":"https://doi.org/10.1038/s41576-025-00850-1","url":null,"abstract":"<p>Synonymous mutations are coding mutations that do not alter protein sequences. Commonly thought to have little to no functional consequence, synonymous mutations have been widely used in evolutionary analyses that require neutral markers, including those foundational for the neutral theory. However, recent studies suggest that synonymous mutations can influence nearly every step in the expression of genetic information and may often be strongly non-neutral. We review the extent and mechanisms of these phenotypic and fitness effects and discuss the implications of the functionality and non-neutrality of synonymous mutations for various analyses and conclusions pertinent to genetics, evolution, conservation and disease.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"121 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144097132","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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