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Tracking protein binding to cis-regulatory elements with PRINT 用PRINT跟踪蛋白质与顺式调控元件的结合
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 内在无序区域作为转录因子靶标搜索的促进因子
IF 52 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":"10.1038/s41576-025-00816-3","url":null,"abstract":"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. Intrinsically disordered domains (IDRs) are increasingly appreciated as important components of protein function. This Perspective discusses the emerging evidence for IDRs from transcription factors as contributors to the transcription factor target search process, as well as the challenges associated with studying these regions.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 6","pages":"424-435"},"PeriodicalIF":52.0,"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 利用空间转录组学解码细胞间通讯
IF 52 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":"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":"26 5","pages":"295-295"},"PeriodicalIF":52.0,"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
Genomic data sharing: you don’t know what you’ve got (till it’s gone) 基因组数据共享：你不知道你得到了什么（直到它消失）
IF 52 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":"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":"26 5","pages":"293-294"},"PeriodicalIF":52.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41576-025-00820-7.pdf","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":"OA","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 空间miromics：迈向microrna在空间生物学中的整合
IF 52 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":"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":"26 5","pages":"291-292"},"PeriodicalIF":52.0,"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 将ELSI研究团队整合到儿科基因组研究工作中
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 空间代谢组学揭示细胞代谢
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 早期的转录组测序和功能基因组学
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 真核生物细胞质mRNA衰变和质量控制机制
IF 52 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":"10.1038/s41576-024-00810-1","url":null,"abstract":"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. In this Review, Dowdle and Lykke-Andersen discuss advances in our understanding of the machinery and mechanisms involved in the control of cytoplasmic mRNA decay and comment on implications for the design of therapeutic mRNAs.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 7","pages":"463-478"},"PeriodicalIF":52.0,"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 肿瘤隐藏的多样性
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
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