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The genesis of paleogenetics
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-03-27 DOI: 10.1038/s41576-025-00835-0
Maanasa Raghavan
{"title":"The genesis of paleogenetics","authors":"Maanasa Raghavan","doi":"10.1038/s41576-025-00835-0","DOIUrl":"https://doi.org/10.1038/s41576-025-00835-0","url":null,"abstract":"In this Journal Club, Maanasa Raghavan recalls a 1984 paper by Higuchi et al. that demonstrated how sequencing ancient DNA provides unique evolutionary insights.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"41 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143713070","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
From genome to drug: the hidden story of diversity
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-03-20 DOI: 10.1038/s41576-025-00833-2
Minoli Perera
{"title":"From genome to drug: the hidden story of diversity","authors":"Minoli Perera","doi":"10.1038/s41576-025-00833-2","DOIUrl":"https://doi.org/10.1038/s41576-025-00833-2","url":null,"abstract":"In this Journal Club, Minoli Perera reflects on a 2005 sequencing study by Cohen et al., who discovered two common loss-of-function mutations with large effects on plasma cholesterol levels thanks to the inclusion of African American study participants.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"22 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665918","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
Challenges and solutions to the sustainability of gene and cell therapies
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-03-10 DOI: 10.1038/s41576-025-00827-0
Celeste Scotti, Alessandro Aiuti, Luigi Naldini
{"title":"Challenges and solutions to the sustainability of gene and cell therapies","authors":"Celeste Scotti, Alessandro Aiuti, Luigi Naldini","doi":"10.1038/s41576-025-00827-0","DOIUrl":"https://doi.org/10.1038/s41576-025-00827-0","url":null,"abstract":"The promise of gene and cell therapy has become a clinical reality for several devastating diseases. However, major hurdles constrain their economic sustainability and endanger their survival on the drug market, especially those for rare diseases, which calls for innovative solutions. Despite their immense potential, gene and cell therapies that target rare diseases are at risk of market withdrawal, owing to several challenges. The authors describe these hurdles and call for innovative measures to improve the economic sustainability of gene and cell therapies after regulatory approval.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"2 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582921","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
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":"<p>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.</p>","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":"<p>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.</p>","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
Progress in understanding the vertebrate segmentation clock
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-03-04 DOI: 10.1038/s41576-025-00813-6
Akihiro Isomura, Ryoichiro Kageyama
{"title":"Progress in understanding the vertebrate segmentation clock","authors":"Akihiro Isomura, Ryoichiro Kageyama","doi":"10.1038/s41576-025-00813-6","DOIUrl":"https://doi.org/10.1038/s41576-025-00813-6","url":null,"abstract":"<p>The segmentation clock is a molecular oscillator that regulates the periodic formation of somites from the presomitic mesoderm during vertebrate embryogenesis. Synchronous oscillatory expression of a Hairy homologue or Hairy-related basic helix–loop–helix (bHLH) transcriptional repressor in presomitic mesoderm cells regulates periodic expression of downstream factors that control somite segmentation with a periodicity that varies across species. Although many of the key components of the clock have been identified and characterized, less is known about how the clock is synchronized across cells and how species-specific periodicity is achieved. Advances in live imaging, stem cell and organoid technologies, and synthetic approaches have started to uncover the detailed mechanisms underlying these aspects of somitogenesis, providing insight into how morphogenesis is coordinated in space and time during embryonic development.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"23 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538296","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
Beyond the black box with biologically informed neural networks
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-03-04 DOI: 10.1038/s41576-025-00826-1
David A. Selby, Maximilian Sprang, Jan Ewald, Sebastian J. Vollmer
{"title":"Beyond the black box with biologically informed neural networks","authors":"David A. Selby, Maximilian Sprang, Jan Ewald, Sebastian J. Vollmer","doi":"10.1038/s41576-025-00826-1","DOIUrl":"https://doi.org/10.1038/s41576-025-00826-1","url":null,"abstract":"Machine learning models for multi-omics data often trade off predictive accuracy against biological interpretability. An emerging class of deep learning architectures structurally encode biological knowledge to improve both prediction and explainability. Opportunities and challenges remain for broader adoption. Biologically informed neural networks promise to lead to more explainable, data-driven discoveries in genomics, drug development and precision medicine. Selby et al. highlight emerging opportunities, as well as challenges that will need to be overcome to enable their wider adoption.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"32 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143538429","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
Tracking protein binding to cis-regulatory elements with PRINT
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2025-02-21 DOI: 10.1038/s41576-025-00823-4
Yan Hu
{"title":"Tracking protein binding to cis-regulatory elements with PRINT","authors":"Yan Hu","doi":"10.1038/s41576-025-00823-4","DOIUrl":"10.1038/s41576-025-00823-4","url":null,"abstract":"In this Tools of the Trade article, Yan Hu explains the development and application of PRINT and seq2PRINT, computational tools that together use single-cell ATAC-seq data to predict protein binding dynamics at detailed cellular resolution.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 4","pages":"227-227"},"PeriodicalIF":39.1,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462436","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
Intrinsically disordered regions as facilitators of the transcription factor target search
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-02-21 DOI: 10.1038/s41576-025-00816-3
Felix Jonas, Yoav Navon, Naama Barkai
{"title":"Intrinsically disordered regions as facilitators of the transcription factor target search","authors":"Felix Jonas, Yoav Navon, Naama Barkai","doi":"10.1038/s41576-025-00816-3","DOIUrl":"https://doi.org/10.1038/s41576-025-00816-3","url":null,"abstract":"<p>Transcription factors (TFs) contribute to organismal development and function by regulating gene expression. Despite decades of research, the factors determining the specificity and speed at which eukaryotic TFs detect their target binding sites remain poorly understood. Recent studies have pointed to intrinsically disordered regions (IDRs) within TFs as key regulators of the process by which TFs find their target sites on DNA (the TF target search). However, IDRs are challenging to study because they can confer specificity despite low sequence complexity and can be functionally conserved despite rapid sequence divergence. Nevertheless, emerging computational and experimental approaches are beginning to elucidate the sequence–function relationship within the IDRs of TFs. Additional insights are informing potential mechanisms underlying the IDR-directed search for the DNA targets of TFs, including incorporation into biomolecular condensates, facilitating TF co-localization, and the hypothesis that IDRs recognize and directly interact with specific genomic regions.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"176 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462486","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
Decoding cell–cell communication using spatial transcriptomics
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-02-21 DOI: 10.1038/s41576-025-00824-3
Ankit Agrawal
{"title":"Decoding cell–cell communication using spatial transcriptomics","authors":"Ankit Agrawal","doi":"10.1038/s41576-025-00824-3","DOIUrl":"https://doi.org/10.1038/s41576-025-00824-3","url":null,"abstract":"In this Tools of the Trade article, Ankit Agrawal introduces the computational framework NiCo (Niche Covariation), which integrates spatial transcriptomics with single-cell RNA-sequencing data to study cell–cell communication.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"209 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462487","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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