Pub Date : 2024-11-06DOI: 10.1038/s41576-024-00802-1
Abderrahman Khila
Abderrahman Khila highlights an important 2015 paper by Barson et al. that demonstrated how sexual conflict in Atlantic salmon affects genetic evolution.
{"title":"Genetic conflict and its resolution between the sexes","authors":"Abderrahman Khila","doi":"10.1038/s41576-024-00802-1","DOIUrl":"10.1038/s41576-024-00802-1","url":null,"abstract":"Abderrahman Khila highlights an important 2015 paper by Barson et al. that demonstrated how sexual conflict in Atlantic salmon affects genetic evolution.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 3","pages":"154-154"},"PeriodicalIF":39.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588683","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 : 2024-11-06DOI: 10.1038/s41576-024-00801-2
Charles C. Davis, Sandra Knapp
Natural history collections are unparalleled resources for studying biodiversity across multiple dimensions. As multi-omic tools are being applied to museum specimens, the emerging field of museomics is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies. In this Comment, the authors showcase how the emerging field of museomics — the application of multi-omic tools to natural history collections — is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies.
{"title":"Exploring biodiversity through museomics","authors":"Charles C. Davis, Sandra Knapp","doi":"10.1038/s41576-024-00801-2","DOIUrl":"10.1038/s41576-024-00801-2","url":null,"abstract":"Natural history collections are unparalleled resources for studying biodiversity across multiple dimensions. As multi-omic tools are being applied to museum specimens, the emerging field of museomics is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies. In this Comment, the authors showcase how the emerging field of museomics — the application of multi-omic tools to natural history collections — is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 3","pages":"149-150"},"PeriodicalIF":39.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588684","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 : 2024-11-06DOI: 10.1038/s41576-024-00786-y
Joshua S. James, Junbiao Dai, Wei Leong Chew, Yizhi Cai
Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction. However, translating synthetic genome-scale projects from idea to implementation remains highly complex. Here, we aim to streamline this implementation process by comprehensively reviewing the strategies for design, construction, delivery, debugging and tailoring of synthetic genomes as well as their potential applications.
{"title":"The design and engineering of synthetic genomes","authors":"Joshua S. James, Junbiao Dai, Wei Leong Chew, Yizhi Cai","doi":"10.1038/s41576-024-00786-y","DOIUrl":"https://doi.org/10.1038/s41576-024-00786-y","url":null,"abstract":"<p>Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction. However, translating synthetic genome-scale projects from idea to implementation remains highly complex. Here, we aim to streamline this implementation process by comprehensively reviewing the strategies for design, construction, delivery, debugging and tailoring of synthetic genomes as well as their potential applications.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"36 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588685","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":"Slide-tags enables spatial single-nucleus sequencing","authors":"Andrew J. C. Russell","doi":"10.1038/s41576-024-00797-9","DOIUrl":"10.1038/s41576-024-00797-9","url":null,"abstract":"In this Tools of the Trade article, Andrew Russell describes Slide-tags, a method for scalable, spatially resolved single-nucleus sequencing.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"78-78"},"PeriodicalIF":39.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574463","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 : 2024-10-29DOI: 10.1038/s41576-024-00800-3
Julie Jung, Thomas King
In this Journal Club, Julie Jung and Thomas King recount a paper by Chan et al. that identified the regulatory changes underlying recurrent phenotypic evolution in stickleback fish.
{"title":"The phenotypic consequences of enhancer evolution","authors":"Julie Jung, Thomas King","doi":"10.1038/s41576-024-00800-3","DOIUrl":"10.1038/s41576-024-00800-3","url":null,"abstract":"In this Journal Club, Julie Jung and Thomas King recount a paper by Chan et al. that identified the regulatory changes underlying recurrent phenotypic evolution in stickleback fish.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"79-79"},"PeriodicalIF":39.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520169","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 : 2024-10-29DOI: 10.1038/s41576-024-00798-8
Lingzhao Fang
Lingzhao Fang recalls how a 2002 paper by Brem et al., which investigated the genetic basis of natural variation in gene expression in budding yeast, and the GTEx atlas of genetic regulatory effects across human tissues inspired the FarmGTEx project to accelerate precision agriculture.
{"title":"Context-specific regulatory variants in precision medicine and agriculture","authors":"Lingzhao Fang","doi":"10.1038/s41576-024-00798-8","DOIUrl":"10.1038/s41576-024-00798-8","url":null,"abstract":"Lingzhao Fang recalls how a 2002 paper by Brem et al., which investigated the genetic basis of natural variation in gene expression in budding yeast, and the GTEx atlas of genetic regulatory effects across human tissues inspired the FarmGTEx project to accelerate precision agriculture.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"81-81"},"PeriodicalIF":39.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536895","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 : 2024-10-29DOI: 10.1038/s41576-024-00799-7
Kejun Ying
In this Tools of the Trade article, Kejun Ying describes epigenome-wide Mendelian randomization, which integrates Mendelian randomization into a DNA-methylation-based epigenetic clock to identify CpG sites with potential causal links to lifespan and healthspan.
在这篇 "贸易工具"（Tools of the Trade）文章中，Kejun Ying介绍了全表观基因组孟德尔随机化（epigenome-wide Mendelian randomization），该方法将孟德尔随机化与基于DNA甲基化的表观遗传时钟相结合，以鉴定与寿命和健康寿命有潜在因果关系的CpG位点。
{"title":"Causal inference for epigenetic ageing","authors":"Kejun Ying","doi":"10.1038/s41576-024-00799-7","DOIUrl":"10.1038/s41576-024-00799-7","url":null,"abstract":"In this Tools of the Trade article, Kejun Ying describes epigenome-wide Mendelian randomization, which integrates Mendelian randomization into a DNA-methylation-based epigenetic clock to identify CpG sites with potential causal links to lifespan and healthspan.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":"3-3"},"PeriodicalIF":39.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520168","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 : 2024-10-25DOI: 10.1038/s41576-024-00795-x
Julia Horsfield
In this Journal Club, Julia Horsfield recounts two papers that demonstrated how cohesin and CTCF together organize the genome and regulate gene expression.
{"title":"Cohesin and CTCF emerge as building blocks of 3D genome structure","authors":"Julia Horsfield","doi":"10.1038/s41576-024-00795-x","DOIUrl":"10.1038/s41576-024-00795-x","url":null,"abstract":"In this Journal Club, Julia Horsfield recounts two papers that demonstrated how cohesin and CTCF together organize the genome and regulate gene expression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"80-80"},"PeriodicalIF":39.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489503","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 : 2024-10-21DOI: 10.1038/s41576-024-00791-1
Pleuni S. Pennings
In this Journal Club, Pleuni Pennings recalls two papers that connected the evolutionary dynamics of HIV variants with therapeutic outcomes, illustrating how evolutionary insights can inform public health decisions.
{"title":"How the waxing and waning of a mutation determines HIV treatment success","authors":"Pleuni S. Pennings","doi":"10.1038/s41576-024-00791-1","DOIUrl":"10.1038/s41576-024-00791-1","url":null,"abstract":"In this Journal Club, Pleuni Pennings recalls two papers that connected the evolutionary dynamics of HIV variants with therapeutic outcomes, illustrating how evolutionary insights can inform public health decisions.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":"6-6"},"PeriodicalIF":39.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451794","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 : 2024-10-21DOI: 10.1038/s41576-024-00780-4
Benjamin R. Sabari, Anthony A. Hyman, Denes Hnisz
Biomolecular condensates are thought to create subcellular microenvironments that regulate specific biochemical activities. Extensive in vitro work has helped link condensate formation to a wide range of cellular processes, including gene expression, nuclear transport, signalling and stress responses. However, testing the relationship between condensate formation and function in cells is more challenging. In particular, the extent to which the cellular functions of condensates depend on the nature of the molecular interactions through which the condensates form is a major outstanding question. Here, we review results from recent genetic complementation experiments in cells, and highlight how genetic complementation provides important insights into cellular functions and functional specificity of biomolecular condensates. Combined with observations from human genetic disease, these experiments suggest that diverse condensate-promoting regions within cellular proteins confer different condensate compositions, biophysical properties and functions. Biomolecular condensates are membraneless cellular compartments that concentrate molecules such as proteins and nucleic acids. In this Review, the authors discuss how complementation experiments, a classic genetics approach, have provided valuable insights into the functions of biomolecular condensates.
{"title":"Functional specificity in biomolecular condensates revealed by genetic complementation","authors":"Benjamin R. Sabari, Anthony A. Hyman, Denes Hnisz","doi":"10.1038/s41576-024-00780-4","DOIUrl":"10.1038/s41576-024-00780-4","url":null,"abstract":"Biomolecular condensates are thought to create subcellular microenvironments that regulate specific biochemical activities. Extensive in vitro work has helped link condensate formation to a wide range of cellular processes, including gene expression, nuclear transport, signalling and stress responses. However, testing the relationship between condensate formation and function in cells is more challenging. In particular, the extent to which the cellular functions of condensates depend on the nature of the molecular interactions through which the condensates form is a major outstanding question. Here, we review results from recent genetic complementation experiments in cells, and highlight how genetic complementation provides important insights into cellular functions and functional specificity of biomolecular condensates. Combined with observations from human genetic disease, these experiments suggest that diverse condensate-promoting regions within cellular proteins confer different condensate compositions, biophysical properties and functions. Biomolecular condensates are membraneless cellular compartments that concentrate molecules such as proteins and nucleic acids. In this Review, the authors discuss how complementation experiments, a classic genetics approach, have provided valuable insights into the functions of biomolecular condensates.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 4","pages":"279-290"},"PeriodicalIF":39.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142452395","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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