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Searching for the origin of human brain tumours 寻找人类脑肿瘤的起源
IF 42.7 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, Benedetta Artegiani","doi":"10.1038/s41576-025-00858-7","DOIUrl":"https://doi.org/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":"7 1","pages":""},"PeriodicalIF":42.7,"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 42.7 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, Zhe J. Liu","doi":"10.1038/s41576-025-00860-z","DOIUrl":"https://doi.org/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":"98 1","pages":""},"PeriodicalIF":42.7,"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 42.7 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":"https://doi.org/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":"49 1","pages":""},"PeriodicalIF":42.7,"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 42.7 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":"https://doi.org/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":"127 1","pages":""},"PeriodicalIF":42.7,"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 42.7 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":"https://doi.org/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":"1 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 42.7 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":"https://doi.org/10.1038/s41576-025-00857-8","url":null,"abstract":"","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"40 1","pages":""},"PeriodicalIF":42.7,"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
SLAM-RT&Tag: spatiotemporal profiling of RNA within nuclear compartments in situ SLAM-RT&Tag：原位核室内RNA的时空分析
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-19 DOI: 10.1038/s41576-025-00856-9
Nadiya Khyzha
{"title":"SLAM-RT&Tag: spatiotemporal profiling of RNA within nuclear compartments in situ","authors":"Nadiya Khyzha","doi":"10.1038/s41576-025-00856-9","DOIUrl":"https://doi.org/10.1038/s41576-025-00856-9","url":null,"abstract":"In this Tools of the Trade article, Nadiya Khyzha describes SLAM-RT&amp;Tag, a method for profiling RNA localization and dynamics within nuclear compartments, such as speckles.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"85 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087866","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
Methodological opportunities in genomic data analysis to advance health equity 基因组数据分析中促进卫生公平的方法学机会
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-15 DOI: 10.1038/s41576-025-00839-w
Brieuc Lehmann, Leandra Bräuninger, Yoonsu Cho, Fabian Falck, Smera Jayadeva, Michael Katell, Thuy Nguyen, Antonella Perini, Sam Tallman, Maxine Mackintosh, Matt Silver, Karoline Kuchenbäcker, David Leslie, Nilanjan Chatterjee, Chris Holmes
{"title":"Methodological opportunities in genomic data analysis to advance health equity","authors":"Brieuc Lehmann, Leandra Bräuninger, Yoonsu Cho, Fabian Falck, Smera Jayadeva, Michael Katell, Thuy Nguyen, Antonella Perini, Sam Tallman, Maxine Mackintosh, Matt Silver, Karoline Kuchenbäcker, David Leslie, Nilanjan Chatterjee, Chris Holmes","doi":"10.1038/s41576-025-00839-w","DOIUrl":"https://doi.org/10.1038/s41576-025-00839-w","url":null,"abstract":"<p>The causes and consequences of inequities in genomic research and medicine are complex and widespread. However, it is widely acknowledged that underrepresentation of diverse populations in human genetics research risks exacerbating existing health disparities. Efforts to improve diversity are ongoing, but an often-overlooked source of inequity is the choice of analytical methods used to process, analyse and interpret genomic data. This choice can influence all areas of genomic research, from genome-wide association studies and polygenic score development to variant prioritization and functional genomics. New statistical and machine learning techniques to understand, quantify and correct for the impact of biases in genomic data are emerging within the wider genomic research and genomic medicine ecosystems. At this crucial time point, it is important to clarify where improvements in methods and practices can, or cannot, have a role in improving equity in genomics. Here, we review existing approaches to promote equity and fairness in statistical analysis for genomics, and propose future methodological developments that are likely to yield the most impact for equity.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"125 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143979479","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
Cell-type deconvolution methods for spatial transcriptomics 空间转录组学的细胞型反褶积方法
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-05-14 DOI: 10.1038/s41576-025-00845-y
Lucie C. Gaspard-Boulinc, Luca Gortana, Thomas Walter, Emmanuel Barillot, Florence M. G. Cavalli
{"title":"Cell-type deconvolution methods for spatial transcriptomics","authors":"Lucie C. Gaspard-Boulinc, Luca Gortana, Thomas Walter, Emmanuel Barillot, Florence M. G. Cavalli","doi":"10.1038/s41576-025-00845-y","DOIUrl":"https://doi.org/10.1038/s41576-025-00845-y","url":null,"abstract":"<p>Spatial transcriptomics is a powerful method for studying the spatial organization of cells, which is a critical feature in the development, function and evolution of multicellular life. However, sequencing-based spatial transcriptomics has not yet achieved cellular-level resolution, so advanced deconvolution methods are needed to infer cell-type contributions at each location in the data. Recent progress has led to diverse tools for cell-type deconvolution that are helping to describe tissue architectures in health and disease. In this Review, we describe the varied types of cell-type deconvolution methods for spatial transcriptomics, contrast their capabilities and summarize them in a web-based, interactive table to enable more efficient method selection.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"2 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143945698","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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