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Identifying off-target effects of genome editing with Tracking-seq 利用跟踪-测序技术识别基因组编辑的脱靶效应
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-17 DOI: 10.1038/s41576-024-00775-1
Ming Zhu
{"title":"Identifying off-target effects of genome editing with Tracking-seq","authors":"Ming Zhu","doi":"10.1038/s41576-024-00775-1","DOIUrl":"10.1038/s41576-024-00775-1","url":null,"abstract":"In this Tools of the Trade article, Ming Zhu describes Tracking-seq, a versatile method for detecting off-target effects of genome-editing tools across a range of experimental conditions.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"825-825"},"PeriodicalIF":39.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235253","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
Reshaping Waddington’s developmental landscape 重塑瓦丁顿的发展格局
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-17 DOI: 10.1038/s41576-024-00777-z
Yimiao Qu, Kyle M. Loh
{"title":"Reshaping Waddington’s developmental landscape","authors":"Yimiao Qu, Kyle M. Loh","doi":"10.1038/s41576-024-00777-z","DOIUrl":"10.1038/s41576-024-00777-z","url":null,"abstract":"Yimiao Qu and Kyle Loh discuss a 2004 paper by Xie et al., who demonstrated that B cells can be reprogrammed into macrophages through the enforced expression of a single transcription factor, providing insights into cellular plasticity and lineage conversion.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 11","pages":"749-749"},"PeriodicalIF":39.1,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235255","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
Why geneticists should care about male infertility 遗传学家为何要关注男性不育问题
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-16 DOI: 10.1038/s41576-024-00773-3
Joris A. Veltman, Frank Tüttelmann
{"title":"Why geneticists should care about male infertility","authors":"Joris A. Veltman, Frank Tüttelmann","doi":"10.1038/s41576-024-00773-3","DOIUrl":"10.1038/s41576-024-00773-3","url":null,"abstract":"The widespread use of medically assisted reproduction fosters the false impression that the underlying causes of male infertility are not important to know. However, to improve men’s reproductive and long-term health, as well as the health of their offspring, large-scale genetic studies are essential. Thus, reproductive genomics should be implemented in diagnostics as soon as possible. In this Comment, Veltman and Tüttelmann call on geneticists to further study male infertility and help to develop diagnostic strategies using state-of-the-art genomic approaches.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"823-824"},"PeriodicalIF":39.1,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236232","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 toxicogenomics to protect human health 毒物基因组学在保护人类健康方面的进展
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-09-02 DOI: 10.1038/s41576-024-00767-1
Matthew J. Meier, Joshua Harrill, Kamin Johnson, Russell S. Thomas, Weida Tong, Julia E. Rager, Carole L. Yauk
{"title":"Progress in toxicogenomics to protect human health","authors":"Matthew J. Meier, Joshua Harrill, Kamin Johnson, Russell S. Thomas, Weida Tong, Julia E. Rager, Carole L. Yauk","doi":"10.1038/s41576-024-00767-1","DOIUrl":"https://doi.org/10.1038/s41576-024-00767-1","url":null,"abstract":"<p>Toxicogenomics measures molecular features, such as transcripts, proteins, metabolites and epigenomic modifications, to understand and predict the toxicological effects of environmental and pharmaceutical exposures. Transcriptomics has become an integral tool in contemporary toxicology research owing to innovations in gene expression profiling that can provide mechanistic and quantitative information at scale. These data can be used to predict toxicological hazards through the use of transcriptomic biomarkers, network inference analyses, pattern-matching approaches and artificial intelligence. Furthermore, emerging approaches, such as high-throughput dose–response modelling, can leverage toxicogenomic data for human health protection even in the absence of predicting specific hazards. Finally, single-cell transcriptomics and multi-omics provide detailed insights into toxicological mechanisms. Here, we review the progress since the inception of toxicogenomics in applying transcriptomics towards toxicology testing and highlight advances that are transforming risk assessment.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"14 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118117","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 complex non-genetic inheritance of complex traits 复杂性状的非遗传复杂性
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-08-29 DOI: 10.1038/s41576-024-00770-6
Merly C. Vogt
{"title":"The complex non-genetic inheritance of complex traits","authors":"Merly C. Vogt","doi":"10.1038/s41576-024-00770-6","DOIUrl":"10.1038/s41576-024-00770-6","url":null,"abstract":"Merly C. Vogt recalls a seminal paper by Greer et al., who demonstrated the transgenerational inheritance of longevity, a complex trait, in Caenorhabditis elegans by manipulating the trimethylation of histone H3 lysine 4 (H3K4me3) in the parental generation.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 10","pages":"678-678"},"PeriodicalIF":39.1,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142090006","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
Convergent evolution of prickles across crops 作物皮刺的趋同进化。
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-08-22 DOI: 10.1038/s41576-024-00771-5
Henry Ertl
{"title":"Convergent evolution of prickles across crops","authors":"Henry Ertl","doi":"10.1038/s41576-024-00771-5","DOIUrl":"10.1038/s41576-024-00771-5","url":null,"abstract":"Satterlee et al. employ several approaches to demonstrate that prickle evolution has a common genetic basis among several plant lineages.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 10","pages":"676-676"},"PeriodicalIF":39.1,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036402","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
Mosaic variegated aneuploidy in development, ageing and cancer 发育、衰老和癌症中的镶嵌变异非整倍体
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-08-21 DOI: 10.1038/s41576-024-00762-6
Marcos Malumbres, Carolina Villarroya-Beltri
{"title":"Mosaic variegated aneuploidy in development, ageing and cancer","authors":"Marcos Malumbres,&nbsp;Carolina Villarroya-Beltri","doi":"10.1038/s41576-024-00762-6","DOIUrl":"10.1038/s41576-024-00762-6","url":null,"abstract":"Mosaic variegated aneuploidy (MVA) is a rare condition in which abnormal chromosome counts (that is, aneuploidies), affecting different chromosomes in each cell (making it variegated) are found only in a certain number of cells (making it mosaic). MVA is characterized by various developmental defects and, despite its rarity, presents a unique clinical scenario to understand the consequences of chromosomal instability and copy number variation in humans. Research from patients with MVA, genetically engineered mouse models and functional cellular studies have found the genetic causes to be mutations in components of the spindle-assembly checkpoint as well as in related proteins involved in centrosome dynamics during mitosis. MVA is accompanied by tumour susceptibility (depending on the genetic basis) as well as cellular and systemic stress, including chronic immune response and the associated clinical implications. Mosaic variegated aneuploidy is a rare condition in which the copy number of different chromosomes varies across some cells within an individual. In this Review, the authors discuss the genetic underpinnings and clinical manifestations of this condition and relate these findings to the consequences of chromosomal instability more broadly.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 12","pages":"864-878"},"PeriodicalIF":39.1,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142013800","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
Multifunctional histone variants in genome function 基因组功能中的多功能组蛋白变体
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-08-13 DOI: 10.1038/s41576-024-00759-1
Lee H. Wong, David J. Tremethick
{"title":"Multifunctional histone variants in genome function","authors":"Lee H. Wong, David J. Tremethick","doi":"10.1038/s41576-024-00759-1","DOIUrl":"https://doi.org/10.1038/s41576-024-00759-1","url":null,"abstract":"<p>Histones are integral components of eukaryotic chromatin that have a pivotal role in the organization and function of the genome. The dynamic regulation of chromatin involves the incorporation of histone variants, which can dramatically alter its structural and functional properties. Contrary to an earlier view that limited individual histone variants to specific genomic functions, new insights have revealed that histone variants exert multifaceted roles involving all aspects of genome function, from governing patterns of gene expression at precise genomic loci to participating in genome replication, repair and maintenance. This conceptual change has led to a new understanding of the intricate interplay between chromatin and DNA-dependent processes and how this connection translates into normal and abnormal cellular functions.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"142 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141973775","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
DNA methylation in mammalian development and disease 哺乳动物发育和疾病中的 DNA 甲基化
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-08-12 DOI: 10.1038/s41576-024-00760-8
Zachary D. Smith, Sara Hetzel, Alexander Meissner
{"title":"DNA methylation in mammalian development and disease","authors":"Zachary D. Smith,&nbsp;Sara Hetzel,&nbsp;Alexander Meissner","doi":"10.1038/s41576-024-00760-8","DOIUrl":"10.1038/s41576-024-00760-8","url":null,"abstract":"The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan&nbsp;and discuss how they interact with other regulatory layers to support diverse genomic functions. We then&nbsp;review the rising interest in alternative patterns found&nbsp;during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype. In this Review, Smith et al. describe DNA methylation landscapes that emerge over&nbsp;mammalian development and within&nbsp;key disease states, as well as how different methyltransferases interface with histone modifications and other proteins to create and maintain them.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":"7-30"},"PeriodicalIF":39.1,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918822","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
Position-dependent effects of transcription factor binding 转录因子结合的位置依赖效应
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-08-12 DOI: 10.1038/s41576-024-00769-z
Kirsty Minton
{"title":"Position-dependent effects of transcription factor binding","authors":"Kirsty Minton","doi":"10.1038/s41576-024-00769-z","DOIUrl":"10.1038/s41576-024-00769-z","url":null,"abstract":"Duttke et al. show that transcription factors have position-dependent effects relative to their distance from the transcription start site, which suggests that a ''spatial grammar'' could be used to encode multiple gene-regulatory programmes.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 10","pages":"675-675"},"PeriodicalIF":39.1,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918819","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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