Nature Reviews Genetics最新文献

The genetic basis of human height

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2025-04-07 DOI: 10.1038/s41576-025-00834-1

Louise S. Bicknell, Joel N. Hirschhorn, Ravi Savarirayan

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Epigenome dynamics in early mammalian embryogenesis

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Nature Reviews Genetics Pub Date : 2025-04-03 DOI: 10.1038/s41576-025-00831-4

Adam Burton, Maria-Elena Torres-Padilla

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Reactivation of retrotransposable elements is associated with environmental stress and ageing 逆转录转座元件的重新激活与环境压力和老化有关

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2025-04-02 DOI: 10.1038/s41576-025-00829-y

Francesco Della Valle, Pradeep Reddy, Alain Aguirre Vazquez, Juan Carlos Izpisua Belmonte

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Computational analysis of DNA methylation from long-read sequencing

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Nature Reviews Genetics Pub Date : 2025-03-28 DOI: 10.1038/s41576-025-00822-5

Yilei Fu, Winston Timp, Fritz J. Sedlazeck

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Transcriptomics in the era of long-read sequencing

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Nature Reviews Genetics Pub Date : 2025-03-28 DOI: 10.1038/s41576-025-00828-z

Carolina Monzó, Tianyuan Liu, Ana Conesa

{"title":"Transcriptomics in the era of long-read sequencing","authors":"Carolina Monzó, Tianyuan Liu, Ana Conesa","doi":"10.1038/s41576-025-00828-z","DOIUrl":"https://doi.org/10.1038/s41576-025-00828-z","url":null,"abstract":"Transcriptome sequencing revolutionized the analysis of gene expression, providing an unbiased approach to gene detection and quantification that enabled the discovery of novel isoforms, alternative splicing events and fusion transcripts. However, although short-read sequencing technologies have surpassed the limited dynamic range of previous technologies such as microarrays, they have limitations, for example, in resolving full-length transcripts and complex isoforms. Over the past 5 years, long-read sequencing technologies have matured considerably, with improvements in instrumentation and analytical methods, enabling their application to RNA sequencing (RNA-seq). Benchmarking studies are beginning to identify the strengths and limitations of long-read RNA-seq, although there remains a need for comprehensive resources to guide newcomers through the intricacies of this approach. In this Review, we provide a comprehensive overview of the long-read RNA-seq workflow, from library preparation and sequencing challenges to core data processing, downstream analyses and emerging developments. We present an extensive inventory of experimental and analytical methods and discuss current challenges and prospects.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"61 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143723240","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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The genesis of paleogenetics

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Nature Reviews Genetics Pub Date : 2025-03-27 DOI: 10.1038/s41576-025-00835-0

Maanasa Raghavan

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From genome to drug: the hidden story of diversity

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Nature Reviews Genetics Pub Date : 2025-03-20 DOI: 10.1038/s41576-025-00833-2

Minoli Perera

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Challenges and solutions to the sustainability of gene and cell therapies

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Nature Reviews Genetics Pub Date : 2025-03-10 DOI: 10.1038/s41576-025-00827-0

Celeste Scotti, Alessandro Aiuti, Luigi Naldini

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Adapting systems biology to address the complexity of human disease in the single-cell era

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2025-03-10 DOI: 10.1038/s41576-025-00821-6

David S. Fischer, Martin A. Villanueva, Peter S. Winter, Alex K. Shalek

{"title":"Adapting systems biology to address the complexity of human disease in the single-cell era","authors":"David S. Fischer, Martin A. Villanueva, Peter S. Winter, Alex K. Shalek","doi":"10.1038/s41576-025-00821-6","DOIUrl":"https://doi.org/10.1038/s41576-025-00821-6","url":null,"abstract":"Systems biology aims to achieve holistic insights into the molecular workings of cellular systems through iterative loops of measurement, analysis and perturbation. This framework has had remarkable success in unicellular model organisms, and recent experimental and computational advances — from single-cell and spatial profiling to CRISPR genome editing and machine learning — have raised the exciting possibility of leveraging such strategies to prevent, diagnose and treat human diseases. However, adapting systems-inspired approaches to dissect human disease complexity is challenging, given that discrepancies between the biological features of human tissues and the experimental models typically used to probe function (which we term ‘translational distance’) can confound insight. Here we review how samples, measurements and analyses can be contextualized within overall multiscale human disease processes to mitigate data and representation gaps. We then examine ways to bridge the translational distance between systems-inspired human discovery loops and model system validation loops to empower precision interventions in the era of single-cell genomics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"19 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582917","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

Integrating model systems and genomic insights to decipher mechanisms of cancer metastasis

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2025-03-10 DOI: 10.1038/s41576-025-00825-2

Michelle M. Leung, Charles Swanton, Nicholas McGranahan

{"title":"Integrating model systems and genomic insights to decipher mechanisms of cancer metastasis","authors":"Michelle M. Leung, Charles Swanton, Nicholas McGranahan","doi":"10.1038/s41576-025-00825-2","DOIUrl":"https://doi.org/10.1038/s41576-025-00825-2","url":null,"abstract":"Deciphering metastatic processes is crucial for understanding cancer progression and potential treatment options. Genetic studies of model systems engineered to mimic metastatic disease, including organoids, genetically engineered mice and human cell lines, have had an important role in shaping our understanding of the metastatic cascade and how it can be manipulated. More recently, advances in high-throughput sequencing have enabled human metastases to be studied at single-cell and single-nucleotide resolution, providing insights into metastatic evolution and phenotypes of both cancer cells and immune cells. However, human tissue studies are often correlative and descriptive, whereas experimental models are reductionistic by nature, meaning that individual results should be interpreted with caution. Crucially, these seemingly disparate branches of metastasis research can and should complement each other to strengthen and validate findings. Here we explore the synergies between model systems and sequencing studies and outline key areas that must be explored to improve our understanding of the metastatic process.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"29 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582923","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