{"title":"How germ granules promote germ cell fate","authors":"Melissa C. Pamula, Ruth Lehmann","doi":"10.1038/s41576-024-00744-8","DOIUrl":"10.1038/s41576-024-00744-8","url":null,"abstract":"Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules. These specialized RNA and protein complexes are hallmarks of germ cells throughout their life cycle: as embryonic germ granules in late oocytes and zygotes, Balbiani bodies in immature oocytes, and nuage in maturing gametes. Decades of developmental, genetic and biochemical studies have identified protein and RNA constituents unique to germ granules and have implicated these in germ cell identity, genome integrity and gamete differentiation. Now, emerging research is defining germ granules as biomolecular condensates that achieve high molecular concentrations by phase separation, and it is assigning distinct roles to germ granules during different stages of germline development. This organization of the germ cell cytoplasm into cellular subcompartments seems to be critical not only for the flawless continuity through the germline life cycle within the developing organism but also for the success of the next generation. In this Review, Pamula and Lehmann describe how distinct membraneless germ granules organize the germ cell cytoplasm at different stages of the germline life cycle to determine germ cell identity, maintain genome integrity and regulate gamete differentiation.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"803-821"},"PeriodicalIF":39.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419992","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}
{"title":"BRCA1 and friends 30 years on","authors":"William D. Foulkes","doi":"10.1038/s41576-024-00754-6","DOIUrl":"10.1038/s41576-024-00754-6","url":null,"abstract":"With the benefit of hindsight, recognition of the cancer susceptibility gene BRCA1 and its later cloning were defining moments for breast and ovarian cancer genetics that should be celebrated. Thirty years after the discovery and cloning of the cancer susceptibility gene BRCA1, William Foulkes reflects on this defining moment for breast and ovarian cancer genetics and how far the field has come.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 10","pages":"671-672"},"PeriodicalIF":39.1,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141334159","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}
{"title":"DNA packaging by molecular motors: from bacteriophage to human chromosomes","authors":"Bram Prevo, William C. Earnshaw","doi":"10.1038/s41576-024-00740-y","DOIUrl":"10.1038/s41576-024-00740-y","url":null,"abstract":"Dense packaging of genomic DNA is crucial for organismal survival, as DNA length always far exceeds the dimensions of the cells that contain it. Organisms, therefore, use sophisticated machineries to package their genomes. These systems range across kingdoms from a single ultra-powerful rotary motor that spools the DNA into a bacteriophage head, to hundreds of thousands of relatively weak molecular motors that coordinate the compaction of mitotic chromosomes in eukaryotic cells. Recent technological advances, such as DNA proximity-based sequencing approaches, polymer modelling and in vitro reconstitution of DNA loop extrusion, have shed light on the biological mechanisms driving DNA organization in different systems. Here, we discuss DNA packaging in bacteriophage, bacteria and eukaryotic cells, which, despite their extreme variation in size, structure and genomic content, all rely on the action of molecular motors to package their genomes. In this Review, the authors summarize DNA packaging in bacteriophage, bacteria and eukaryotic cells. They describe the difficulties each system faces when packaging its DNA, outline the molecular motor components involved, and provide insights from new studies that reveal how DNA organization is achieved.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"785-802"},"PeriodicalIF":39.1,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141333682","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}
William Hemstrom, Jared A. Grummer, Gordon Luikart, Mark R. Christie
{"title":"Next-generation data filtering in the genomics era","authors":"William Hemstrom, Jared A. Grummer, Gordon Luikart, Mark R. Christie","doi":"10.1038/s41576-024-00738-6","DOIUrl":"10.1038/s41576-024-00738-6","url":null,"abstract":"Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology, evolution and human health. However, these datasets often contain noise or errors and are missing information that can affect the accuracy and reliability of subsequent computational analyses and conclusions. A key step in genomic data analysis is filtering — removing sequencing bases, reads, genetic variants and/or individuals from a dataset — to improve data quality for downstream analyses. Researchers are confronted with a multitude of choices when filtering genomic data; they must choose which filters to apply and select appropriate thresholds. To help usher in the next generation of genomic data filtering, we review and suggest best practices to improve the implementation, reproducibility and reporting standards for filter types and thresholds commonly applied to genomic datasets. We focus mainly on filters for minor allele frequency, missing data per individual or per locus, linkage disequilibrium and Hardy–Weinberg deviations. Using simulated and empirical datasets, we illustrate the large effects of different filtering thresholds on common population genetics statistics, such as Tajima’s D value, population differentiation (FST), nucleotide diversity (π) and effective population size (Ne). Filtering genomic data is a crucial step to ensure the quality and reliability of downstream analyses. The authors provide guidance on the choice of filtering strategies and thresholds, including filters that remove sequencing bases or reads, variants, loci, genotypes or individuals from genomic datasets to improve accuracy and reproducibility.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"750-767"},"PeriodicalIF":39.1,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319957","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}
{"title":"From Mendel’s laws to non-Mendelian inheritance","authors":"Laura Ross","doi":"10.1038/s41576-024-00753-7","DOIUrl":"10.1038/s41576-024-00753-7","url":null,"abstract":"In this Journal Club article, Laura Ross discusses several seminal papers that describe the discovery of germline-specific chromosomes and paternal genome elimination, striking examples of non-Mendelian genetics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 10","pages":"677-677"},"PeriodicalIF":39.1,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141309126","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}
{"title":"Mini-colons unlock tumour development outside the body","authors":"L. Francisco Lorenzo-Martín, Matthias P. Lutolf","doi":"10.1038/s41576-024-00752-8","DOIUrl":"10.1038/s41576-024-00752-8","url":null,"abstract":"In this Tools of the Trade article, Francisco Lorenzo-Martín and Matthias Lutolf present mini-colons as a new ex vivo cancer model that incorporates microfabrication, tissue engineering and optogenetics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 9","pages":"598-598"},"PeriodicalIF":39.1,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141251570","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}
{"title":"SCENT defines non-coding disease mechanisms using single-cell multi-omics","authors":"Saori Sakaue","doi":"10.1038/s41576-024-00747-5","DOIUrl":"10.1038/s41576-024-00747-5","url":null,"abstract":"In this Tools of the Trade article, Saori Sakaue describes SCENT, a tool to generate cell-type-specific enhancer–gene maps using single-cell multi-omics data, which can help identify disease-causal, non-coding variants and genes from GWAS-defined loci.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 9","pages":"597-597"},"PeriodicalIF":39.1,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180126","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}
Esther Herrera-Luis, Kelly Benke, Heather Volk, Christine Ladd-Acosta, Genevieve L. Wojcik
{"title":"Gene–environment interactions in human health","authors":"Esther Herrera-Luis, Kelly Benke, Heather Volk, Christine Ladd-Acosta, Genevieve L. Wojcik","doi":"10.1038/s41576-024-00731-z","DOIUrl":"10.1038/s41576-024-00731-z","url":null,"abstract":"Gene–environment interactions (G × E), the interplay of genetic variation with environmental factors, have a pivotal impact on human complex traits and diseases. Statistically, G × E can be assessed by determining the deviation from expectation of predictive models based solely on the phenotypic effects of genetics or environmental exposures. Despite the unprecedented, widespread and diverse use of G × E analytical frameworks, heterogeneity in their application and reporting hinders their applicability in public health. In this Review, we discuss study design considerations as well as G × E analytical frameworks to assess polygenic liability dependent on the environment, to identify specific genetic variants exhibiting G × E, and to characterize environmental context for these dynamics. We conclude with recommendations to address the most common challenges and pitfalls in the conceptualization, methodology and reporting of G × E studies, as well as future directions. Despite their impact on human complex traits and diseases, gene–environment interactions (G × E) remain challenging to assess statistically. The authors review considerations for the conceptualization, methodology, interpretation and reporting of G × E studies, and provide recommendations on how to avoid common pitfalls.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"768-784"},"PeriodicalIF":39.1,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141162442","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}
{"title":"Nuclear receptors — studying genes to understand hormones","authors":"Jessica Tollkuhn","doi":"10.1038/s41576-024-00745-7","DOIUrl":"10.1038/s41576-024-00745-7","url":null,"abstract":"In this Journal Club, Jessica Tollkuhn discusses how a paper describing genome-wide application of chromatin immunoprecipitation (ChIP)-on-chip inspired her own research into oestrogen-based gene regulation in the brain.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 9","pages":"602-602"},"PeriodicalIF":39.1,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141079268","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}
{"title":"BANKSY: scalable cell typing and domain segmentation for spatial omics","authors":"Vipul Singhal, Nigel Chou","doi":"10.1038/s41576-024-00743-9","DOIUrl":"10.1038/s41576-024-00743-9","url":null,"abstract":"In this Tools of the Trade article, Vipul Singhal and Nigel Chou describe BANKSY, a machine learning tool that harnesses gene expression gradients from the neighbourhood of a cell for cell typing and domain segmentation.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 8","pages":"527-528"},"PeriodicalIF":39.1,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140944429","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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