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Genomic data sharing: you don’t know what you’ve got (till it’s gone)
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-02-12 DOI: 10.1038/s41576-025-00820-7
Kathryn E. Holt, Michael Inouye
{"title":"Genomic data sharing: you don’t know what you’ve got (till it’s gone)","authors":"Kathryn E. Holt, Michael Inouye","doi":"10.1038/s41576-025-00820-7","DOIUrl":"https://doi.org/10.1038/s41576-025-00820-7","url":null,"abstract":"Genomics research has thrived under a culture of data sharing, formalized during the genome-project era. As the field’s complexity has increased to the population scale this culture risks being eroded, yet the core principles still apply. The community would benefit from more open discussion and consensus-building around biological data sharing, recognizing that the answer will shape what the practice of science looks like in future. Reflecting on the core values of early data sharing agreements, the Bermuda Principles and the Fort Lauderdale Agreement, Kathryn E. Holt and Michael Inouye emphasize the need to reaffirm our commitment to genomic data sharing to shape the future of science.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"56 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393014","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
Spatial miRNomics: towards the integration of microRNAs in spatial biology
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-02-06 DOI: 10.1038/s41576-025-00819-0
Agustín Robles-Remacho, Mats Nilsson
{"title":"Spatial miRNomics: towards the integration of microRNAs in spatial biology","authors":"Agustín Robles-Remacho, Mats Nilsson","doi":"10.1038/s41576-025-00819-0","DOIUrl":"https://doi.org/10.1038/s41576-025-00819-0","url":null,"abstract":"Spatial transcriptomics tools enable the detection and localization of hundreds to thousands of transcripts in biological tissues. However, most technologies are not designed to detect microRNAs. Existing technologies should be expanded to incorporate these key molecular regulators and enable more-comprehensive transcriptomic studies that will shape the new field of spatial miRNomics. In this Comment, Agustín Robles-Remacho and Mats Nilsson highlight the opportunities and challenges of using spatial transcriptomics to detect and localize microRNAs in biological tissues, and advocate for the increased development of existing spatial transcriptomics methods.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"40 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192058","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 ELSI study teams in paediatric genomic research efforts
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2025-02-03 DOI: 10.1038/s41576-025-00818-1
Raquel G. Hernandez, Simoné Guambaña, Melissa W. VonDran, Patrick M. Van Hoose, Thomas J. Bell, Melissa A. Faith
{"title":"Integrating ELSI study teams in paediatric genomic research efforts","authors":"Raquel G. Hernandez, Simoné Guambaña, Melissa W. VonDran, Patrick M. Van Hoose, Thomas J. Bell, Melissa A. Faith","doi":"10.1038/s41576-025-00818-1","DOIUrl":"10.1038/s41576-025-00818-1","url":null,"abstract":"Addressing ethical, legal and social implications (ELSI) in genomics requires early integration of specialized teams to enhance community engagement, address disparities and promote health equity. Lessons learnt from the human Developmental Genotype-Tissue Expression (dGTEx) project show how implementing a collaborative framework can support genomic discovery. The promise of paediatric genomics depends on proactively addressing complex ethical and equity issues with sustained community engagement. Hernandez et al. advocate for the integration of ELSI scholars into paediatric genomic study teams to catalyse timely discovery in genomics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 4","pages":"223-224"},"PeriodicalIF":39.1,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143077623","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
Spatial metabolomics to unravel cellular metabolism
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2025-01-28 DOI: 10.1038/s41576-025-00817-2
Arafath K. Najumudeen, Johan Vande Voorde
{"title":"Spatial metabolomics to unravel cellular metabolism","authors":"Arafath K. Najumudeen, Johan Vande Voorde","doi":"10.1038/s41576-025-00817-2","DOIUrl":"10.1038/s41576-025-00817-2","url":null,"abstract":"In this Tools of the Trade article, Arafath Najumudeen and Johan Vande Voorde showcase the potential of mass spectrometry imaging for spatial metabolomics by highlighting its application in cancer, revealing metabolic differences between cell populations in the tumour microenvironment.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 4","pages":"228-228"},"PeriodicalIF":39.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143049947","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
The early days of transcriptome sequencing and functional genomics
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2025-01-28 DOI: 10.1038/s41576-025-00814-5
Ayako Suzuki
{"title":"The early days of transcriptome sequencing and functional genomics","authors":"Ayako Suzuki","doi":"10.1038/s41576-025-00814-5","DOIUrl":"10.1038/s41576-025-00814-5","url":null,"abstract":"Ayako Suzuki recalls two papers published in the early 2000s by the Functional Annotation of the Mammalian Genome (FANTOM) consortium and the Full-Length Long Japan (FLJ) project, which provided reference catalogues of full-length transcripts in mice and humans, respectively.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 3","pages":"155-155"},"PeriodicalIF":39.1,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055053","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
Cytoplasmic mRNA decay and quality control machineries in eukaryotes
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-01-27 DOI: 10.1038/s41576-024-00810-1
Megan E. Dowdle, Jens Lykke-Andersen
{"title":"Cytoplasmic mRNA decay and quality control machineries in eukaryotes","authors":"Megan E. Dowdle, Jens Lykke-Andersen","doi":"10.1038/s41576-024-00810-1","DOIUrl":"https://doi.org/10.1038/s41576-024-00810-1","url":null,"abstract":"<p>mRNA degradation pathways have key regulatory roles in gene expression. The intrinsic stability of mRNAs in the cytoplasm of eukaryotic cells varies widely in a gene- and isoform-dependent manner and can be regulated by cellular cues, such as kinase signalling, to control mRNA levels and spatiotemporal dynamics of gene expression. Moreover, specialized quality control pathways exist to rid cells of non-functional mRNAs produced by errors in mRNA processing or mRNA damage that negatively impact translation. Recent advances in structural, single-molecule and genome-wide methods have provided new insights into the central machineries that carry out mRNA turnover, the mechanisms by which mRNAs are targeted for degradation and the general principles that govern mRNA stability at a global level. This improved understanding of mRNA degradation in the cytoplasm of eukaryotic cells is finding practical applications in the design of therapeutic mRNAs.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"77 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044066","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
The hidden diversity of tumours
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2025-01-27 DOI: 10.1038/s41576-025-00815-4
Mariana Boroni
{"title":"The hidden diversity of tumours","authors":"Mariana Boroni","doi":"10.1038/s41576-025-00815-4","DOIUrl":"10.1038/s41576-025-00815-4","url":null,"abstract":"In this Journal Club, Mariana Boroni recalls a 2012 study by Gerlinger et al. that revealed the complex and branched evolution of cancer and challenged the prevailing view of linear tumour progression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 4","pages":"229-229"},"PeriodicalIF":39.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044166","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
Diversity and consequences of structural variation in the human genome 人类基因组结构变异的多样性和后果
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2025-01-21 DOI: 10.1038/s41576-024-00808-9
Ryan L. Collins, Michael E. Talkowski
{"title":"Diversity and consequences of structural variation in the human genome","authors":"Ryan L. Collins, Michael E. Talkowski","doi":"10.1038/s41576-024-00808-9","DOIUrl":"https://doi.org/10.1038/s41576-024-00808-9","url":null,"abstract":"<p>The biomedical community is increasingly invested in capturing all genetic variants across human genomes, interpreting their functional consequences and translating these findings to the clinic. A crucial component of this endeavour is the discovery and characterization of structural variants (SVs), which are ubiquitous in the human population, heterogeneous in their mutational processes, key substrates for evolution and adaptation, and profound drivers of human disease. The recent emergence of new technologies and the remarkable scale of sequence-based population studies have begun to crystalize our understanding of SVs as a mutational class and their widespread influence across phenotypes. In this Review, we summarize recent discoveries and new insights into SVs in the human genome in terms of their mutational patterns, population genetics, functional consequences, and impact on human traits and disease. We conclude by outlining three frontiers to be explored by the field over the next decade.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"46 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990632","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
Profiling the total transcriptome of single nuclei in archived samples with snRandom-seq 用snRandom-seq分析存档样本中单个细胞核的总转录组
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2025-01-17 DOI: 10.1038/s41576-025-00812-7
Ziye Xu, Yongcheng Wang
{"title":"Profiling the total transcriptome of single nuclei in archived samples with snRandom-seq","authors":"Ziye Xu,&nbsp;Yongcheng Wang","doi":"10.1038/s41576-025-00812-7","DOIUrl":"10.1038/s41576-025-00812-7","url":null,"abstract":"In this Tools of the Trade article, Ziye Xu and Yongcheng Wang describe snRandom-seq, a high-throughput, high-sensitivity single-nucleus total RNA sequencing technology optimized for archived samples.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 3","pages":"151-152"},"PeriodicalIF":39.1,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987227","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
Indirect recognition of pathogen virulence proteins to activate plant immune receptors 间接识别病原体毒力蛋白，激活植物免疫受体
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2025-01-15 DOI: 10.1038/s41576-025-00811-8
Xiu-Fang Xin  (, )
{"title":"Indirect recognition of pathogen virulence proteins to activate plant immune receptors","authors":"Xiu-Fang Xin \u0000 (,&nbsp;)","doi":"10.1038/s41576-025-00811-8","DOIUrl":"10.1038/s41576-025-00811-8","url":null,"abstract":"Xiu-Fang Xin recalls several papers that described one of the most influential and widely accepted examples of indirect activation of nucleotide-binding, leucine-rich repeat receptors in plants.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 3","pages":"153-153"},"PeriodicalIF":39.1,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981350","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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