Pub Date : 2024-09-30DOI: 10.1038/s41576-024-00772-4
Rasmus Nielsen, Andrew H. Vaughn, Yun Deng
Ancestral recombination graphs (ARGs) summarize the complex genealogical relationships between individuals represented in a sample of DNA sequences. Their use is currently revolutionizing the field of population genetics and is leading to the development of powerful new methods to elucidate individual and population genetic processes, including population size history, migration, admixture, recombination, mutation and selection. In this Review, we introduce the readers to the structure of ARGs and discuss how they relate to processes such as recombination and genetic drift. We explore differences and similarities between methods of estimating ARGs and provide concrete illustrative examples of how ARGs can be used to elucidate population-level processes.
祖先重组图（ARGs）概括了 DNA 序列样本中个体之间复杂的系谱关系。目前，ARG 的使用正在给群体遗传学领域带来革命性的变化，并促使人们开发出功能强大的新方法来阐明个体和群体的遗传过程，包括群体规模历史、迁移、混杂、重组、变异和选择。在这篇综述中，我们将向读者介绍ARGs的结构，并讨论它们与重组和遗传漂变等过程的关系。我们探讨了 ARGs 估算方法的异同，并提供了具体的示例，说明如何利用 ARGs 阐明种群水平的过程。
{"title":"Inference and applications of ancestral recombination graphs","authors":"Rasmus Nielsen, Andrew H. Vaughn, Yun Deng","doi":"10.1038/s41576-024-00772-4","DOIUrl":"https://doi.org/10.1038/s41576-024-00772-4","url":null,"abstract":"<p>Ancestral recombination graphs (ARGs) summarize the complex genealogical relationships between individuals represented in a sample of DNA sequences. Their use is currently revolutionizing the field of population genetics and is leading to the development of powerful new methods to elucidate individual and population genetic processes, including population size history, migration, admixture, recombination, mutation and selection. In this Review, we introduce the readers to the structure of ARGs and discuss how they relate to processes such as recombination and genetic drift. We explore differences and similarities between methods of estimating ARGs and provide concrete illustrative examples of how ARGs can be used to elucidate population-level processes.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"3 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142329578","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 : 2024-09-27DOI: 10.1038/s41576-024-00782-2
Kirsty Minton
Bolognini et al. report evidence of positive selection for human amylase gene duplications associated with the agricultural revolution.
Bolognini 等人报告了与农业革命有关的人类淀粉酶基因重复的正选择证据。
{"title":"Selection on structural variation in the amylase locus","authors":"Kirsty Minton","doi":"10.1038/s41576-024-00782-2","DOIUrl":"10.1038/s41576-024-00782-2","url":null,"abstract":"Bolognini et al. report evidence of positive selection for human amylase gene duplications associated with the agricultural revolution.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"748-748"},"PeriodicalIF":39.1,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321963","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 : 2024-09-27DOI: 10.1038/s41576-024-00783-1
Camille L. G. Lambert, Guido van Mierlo, Johannes J. Bues, Orane J. Guillaume-Gentil, Bart Deplancke
The adoption of microfluidics was fundamental to the development of cost-effective, high-throughput DNA sequencing. As the field progresses towards multi-omics, we reflect on the key concepts underlying microfluidics and how resulting engineering advances at the microscale drove the evolution of genomic sequencing. The adoption of microfluidics was fundamental to the development of cost-effective, high-throughput DNA sequencing. As the field progresses towards multi-omics, Lambert et al. reflect on the key concepts underlying microfluidics and how resulting engineering advances at the microscale drove the evolution of genomic sequencing.
微流控技术的采用是开发具有成本效益的高通量 DNA 测序技术的基础。随着多组学领域的发展，我们思考了微流控技术的关键概念，以及由此产生的微尺度工程技术进步如何推动了基因组测序的发展。微流控技术的采用是开发具有成本效益的高通量 DNA 测序技术的基础。随着多组学领域的发展，Lambert 等人反思了微流控技术的关键概念，以及由此产生的微尺度工程技术进步如何推动了基因组测序的发展。
{"title":"The evolution of DNA sequencing with microfluidics","authors":"Camille L. G. Lambert, Guido van Mierlo, Johannes J. Bues, Orane J. Guillaume-Gentil, Bart Deplancke","doi":"10.1038/s41576-024-00783-1","DOIUrl":"https://doi.org/10.1038/s41576-024-00783-1","url":null,"abstract":"The adoption of microfluidics was fundamental to the development of cost-effective, high-throughput DNA sequencing. As the field progresses towards multi-omics, we reflect on the key concepts underlying microfluidics and how resulting engineering advances at the microscale drove the evolution of genomic sequencing. The adoption of microfluidics was fundamental to the development of cost-effective, high-throughput DNA sequencing. As the field progresses towards multi-omics, Lambert et al. reflect on the key concepts underlying microfluidics and how resulting engineering advances at the microscale drove the evolution of genomic sequencing.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"49 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321966","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 : 2024-09-19DOI: 10.1038/s41576-024-00768-0
Adil Mardinoglu, Bernhard Ø. Palsson
Metabologenomics integrates metabolomics with other omics data types to comprehensively study the genetic and environmental factors that influence metabolism. These multi-omics data can be incorporated into genome-scale metabolic models (GEMs), which are highly curated knowledge bases that explicitly account for genes, transcripts, proteins and metabolites. By including all known biochemical reactions catalysed by enzymes and transporters encoded in the human genome, GEMs analyse and predict the behaviour of complex metabolic networks. Continued advancements to the scale and scope of GEMs — from cells and tissues to microbiomes and the whole body — have helped to design effective treatments and develop better diagnostic tools for metabolic diseases. Furthermore, increasing amounts of multi-omics data are incorporated into GEMs to better identify the underlying mechanisms, biomarkers and potential drug targets of metabolic diseases.
{"title":"Genome-scale models in human metabologenomics","authors":"Adil Mardinoglu, Bernhard Ø. Palsson","doi":"10.1038/s41576-024-00768-0","DOIUrl":"https://doi.org/10.1038/s41576-024-00768-0","url":null,"abstract":"<p>Metabologenomics integrates metabolomics with other omics data types to comprehensively study the genetic and environmental factors that influence metabolism. These multi-omics data can be incorporated into genome-scale metabolic models (GEMs), which are highly curated knowledge bases that explicitly account for genes, transcripts, proteins and metabolites. By including all known biochemical reactions catalysed by enzymes and transporters encoded in the human genome, GEMs analyse and predict the behaviour of complex metabolic networks. Continued advancements to the scale and scope of GEMs — from cells and tissues to microbiomes and the whole body — have helped to design effective treatments and develop better diagnostic tools for metabolic diseases. Furthermore, increasing amounts of multi-omics data are incorporated into GEMs to better identify the underlying mechanisms, biomarkers and potential drug targets of metabolic diseases.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"4 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245261","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 : 2024-09-18DOI: 10.1038/s41576-024-00781-3
Linda Koch
A study in Science investigating bacterial defence mechanisms against phages reports a novel mode of gene regulation through reverse transcription of a non-coding RNA template, leading to the formation of a toxic repetitive gene.
{"title":"Gene synthesis from a non-coding RNA","authors":"Linda Koch","doi":"10.1038/s41576-024-00781-3","DOIUrl":"10.1038/s41576-024-00781-3","url":null,"abstract":"A study in Science investigating bacterial defence mechanisms against phages reports a novel mode of gene regulation through reverse transcription of a non-coding RNA template, leading to the formation of a toxic repetitive gene.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"747-747"},"PeriodicalIF":39.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236231","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 : 2024-09-18DOI: 10.1038/s41576-024-00779-x
Alejo E. Rodriguez-Fraticelli
In this Journal Club, Alejo Rodriguez-Fratelli discusses a paper by Spudich and Koshland Jr that characterized non-genetic cell individuality in bacteria, a concept with emerging relevance to cancer progression.
在本期 "期刊俱乐部 "中，Alejo Rodriguez-Fratelli 讨论了 Spudich 和 Koshland Jr 发表的一篇论文，该论文描述了细菌中非遗传细胞个体性的特征，这一概念与癌症进展密切相关。
{"title":"Tumbling bacteria and non-genetic individuality","authors":"Alejo E. Rodriguez-Fraticelli","doi":"10.1038/s41576-024-00779-x","DOIUrl":"10.1038/s41576-024-00779-x","url":null,"abstract":"In this Journal Club, Alejo Rodriguez-Fratelli discusses a paper by Spudich and Koshland Jr that characterized non-genetic cell individuality in bacteria, a concept with emerging relevance to cancer progression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"826-826"},"PeriodicalIF":39.1,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236227","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 : 2024-09-17DOI: 10.1038/s41576-024-00775-1
Ming Zhu
In this Tools of the Trade article, Ming Zhu describes Tracking-seq, a versatile method for detecting off-target effects of genome-editing tools across a range of experimental conditions.
{"title":"Identifying off-target effects of genome editing with Tracking-seq","authors":"Ming Zhu","doi":"10.1038/s41576-024-00775-1","DOIUrl":"10.1038/s41576-024-00775-1","url":null,"abstract":"In this Tools of the Trade article, Ming Zhu describes Tracking-seq, a versatile method for detecting off-target effects of genome-editing tools across a range of experimental conditions.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"825-825"},"PeriodicalIF":39.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235253","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 : 2024-09-17DOI: 10.1038/s41576-024-00777-z
Yimiao Qu, Kyle M. Loh
Yimiao Qu and Kyle Loh discuss a 2004 paper by Xie et al., who demonstrated that B cells can be reprogrammed into macrophages through the enforced expression of a single transcription factor, providing insights into cellular plasticity and lineage conversion.
{"title":"Reshaping Waddington’s developmental landscape","authors":"Yimiao Qu, Kyle M. Loh","doi":"10.1038/s41576-024-00777-z","DOIUrl":"10.1038/s41576-024-00777-z","url":null,"abstract":"Yimiao Qu and Kyle Loh discuss a 2004 paper by Xie et al., who demonstrated that B cells can be reprogrammed into macrophages through the enforced expression of a single transcription factor, providing insights into cellular plasticity and lineage conversion.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"749-749"},"PeriodicalIF":39.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235255","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 : 2024-09-16DOI: 10.1038/s41576-024-00773-3
Joris A. Veltman, Frank Tüttelmann
The widespread use of medically assisted reproduction fosters the false impression that the underlying causes of male infertility are not important to know. However, to improve men’s reproductive and long-term health, as well as the health of their offspring, large-scale genetic studies are essential. Thus, reproductive genomics should be implemented in diagnostics as soon as possible. In this Comment, Veltman and Tüttelmann call on geneticists to further study male infertility and help to develop diagnostic strategies using state-of-the-art genomic approaches.
{"title":"Why geneticists should care about male infertility","authors":"Joris A. Veltman, Frank Tüttelmann","doi":"10.1038/s41576-024-00773-3","DOIUrl":"10.1038/s41576-024-00773-3","url":null,"abstract":"The widespread use of medically assisted reproduction fosters the false impression that the underlying causes of male infertility are not important to know. However, to improve men’s reproductive and long-term health, as well as the health of their offspring, large-scale genetic studies are essential. Thus, reproductive genomics should be implemented in diagnostics as soon as possible. In this Comment, Veltman and Tüttelmann call on geneticists to further study male infertility and help to develop diagnostic strategies using state-of-the-art genomic approaches.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"823-824"},"PeriodicalIF":39.1,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236232","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 : 2024-09-02DOI: 10.1038/s41576-024-00767-1
Matthew J. Meier, Joshua Harrill, Kamin Johnson, Russell S. Thomas, Weida Tong, Julia E. Rager, Carole L. Yauk
Toxicogenomics measures molecular features, such as transcripts, proteins, metabolites and epigenomic modifications, to understand and predict the toxicological effects of environmental and pharmaceutical exposures. Transcriptomics has become an integral tool in contemporary toxicology research owing to innovations in gene expression profiling that can provide mechanistic and quantitative information at scale. These data can be used to predict toxicological hazards through the use of transcriptomic biomarkers, network inference analyses, pattern-matching approaches and artificial intelligence. Furthermore, emerging approaches, such as high-throughput dose–response modelling, can leverage toxicogenomic data for human health protection even in the absence of predicting specific hazards. Finally, single-cell transcriptomics and multi-omics provide detailed insights into toxicological mechanisms. Here, we review the progress since the inception of toxicogenomics in applying transcriptomics towards toxicology testing and highlight advances that are transforming risk assessment.
{"title":"Progress in toxicogenomics to protect human health","authors":"Matthew J. Meier, Joshua Harrill, Kamin Johnson, Russell S. Thomas, Weida Tong, Julia E. Rager, Carole L. Yauk","doi":"10.1038/s41576-024-00767-1","DOIUrl":"https://doi.org/10.1038/s41576-024-00767-1","url":null,"abstract":"<p>Toxicogenomics measures molecular features, such as transcripts, proteins, metabolites and epigenomic modifications, to understand and predict the toxicological effects of environmental and pharmaceutical exposures. Transcriptomics has become an integral tool in contemporary toxicology research owing to innovations in gene expression profiling that can provide mechanistic and quantitative information at scale. These data can be used to predict toxicological hazards through the use of transcriptomic biomarkers, network inference analyses, pattern-matching approaches and artificial intelligence. Furthermore, emerging approaches, such as high-throughput dose–response modelling, can leverage toxicogenomic data for human health protection even in the absence of predicting specific hazards. Finally, single-cell transcriptomics and multi-omics provide detailed insights into toxicological mechanisms. Here, we review the progress since the inception of toxicogenomics in applying transcriptomics towards toxicology testing and highlight advances that are transforming risk assessment.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"14 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118117","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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