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Tandem repeat variation of human centromeres 人类中心粒的串联重复变异
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-05-08 DOI: 10.1038/s41576-024-00741-x
Kirsty Minton
{"title":"Tandem repeat variation of human centromeres","authors":"Kirsty Minton","doi":"10.1038/s41576-024-00741-x","DOIUrl":"10.1038/s41576-024-00741-x","url":null,"abstract":"Logsdon et al. report the second complete sequence of all centromeres from a single human genome, enabling comparative analyses of the variation in tandemly repeating α-satellite DNA.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 7","pages":"455-455"},"PeriodicalIF":42.7,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140881289","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 emerging role of tandem repeats in complex traits 串联重复序列在复杂性状中的新作用
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-05-07 DOI: 10.1038/s41576-024-00736-8
Michael Lamkin, Melissa Gymrek
{"title":"The emerging role of tandem repeats in complex traits","authors":"Michael Lamkin, Melissa Gymrek","doi":"10.1038/s41576-024-00736-8","DOIUrl":"10.1038/s41576-024-00736-8","url":null,"abstract":"Tandem repeats are a large source of genetic variation but are challenging to analyse and have been missing from most genome-wide studies. Results now suggest that systematic incorporation of tandem repeats into complex trait analyses is likely to yield a rich source of causal variants and new biological insights. In this Comment, Lamkin and Gymrek discuss recent results that suggest that the systematic incorporation of tandem repeats into complex trait analyses will yield a rich source of causal variants and new biological insights.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 7","pages":"452-453"},"PeriodicalIF":42.7,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140845112","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
Prime editing sensors enable multiplexed genome editing 主编辑传感器实现了多路复用基因组编辑
IF 42.7 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-29 DOI: 10.1038/s41576-024-00737-7
Samuel I. Gould
{"title":"Prime editing sensors enable multiplexed genome editing","authors":"Samuel I. Gould","doi":"10.1038/s41576-024-00737-7","DOIUrl":"10.1038/s41576-024-00737-7","url":null,"abstract":"In this Tools of the Trade article, Samuel Gould explains how prime editing sensors can improve experimental efficiency and can be designed using a computational tool he created and named PEGG.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 7","pages":"454-454"},"PeriodicalIF":42.7,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140808422","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
Rapid pathogen surveillance: field-ready sequencing solutions 快速病原体监测：现场就绪的测序解决方案
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-29 DOI: 10.1038/s41576-024-00734-w
Kirstyn Brunker
{"title":"Rapid pathogen surveillance: field-ready sequencing solutions","authors":"Kirstyn Brunker","doi":"10.1038/s41576-024-00734-w","DOIUrl":"10.1038/s41576-024-00734-w","url":null,"abstract":"In this Journal Club, Kirstyn Brunker highlights two papers published in 2017 that showcase how the emergence of portable sequencing capabilities improved the real-time response to infectious disease outbreaks on a global scale.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 8","pages":"532-532"},"PeriodicalIF":39.1,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140808411","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 world of transient enhancers 瞬态增强器的隐秘世界
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-29 DOI: 10.1038/s41576-024-00735-9
Renée Beekman
{"title":"The hidden world of transient enhancers","authors":"Renée Beekman","doi":"10.1038/s41576-024-00735-9","DOIUrl":"10.1038/s41576-024-00735-9","url":null,"abstract":"Renée Beekman discusses the possibilities for research into transient enhancers by highlighting a recent paper by Vermunt et al. that identifies how they can modulate gene silencing dynamics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 8","pages":"533-533"},"PeriodicalIF":39.1,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140808468","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
What tubulin can teach us about gene regulation 微管蛋白对基因调控的启示
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-24 DOI: 10.1038/s41576-024-00733-x
Olivia S. Rissland
{"title":"What tubulin can teach us about gene regulation","authors":"Olivia S. Rissland","doi":"10.1038/s41576-024-00733-x","DOIUrl":"10.1038/s41576-024-00733-x","url":null,"abstract":"In this Journal Club article, Olivia Rissland describes how a 1987 paper by Don Cleveland and colleagues provided insight into co-translational gene regulation of tubulin.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 8","pages":"531-531"},"PeriodicalIF":39.1,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140639802","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
Targeted genome-modification tools and their advanced applications in crop breeding 定向基因组改造工具及其在作物育种中的先进应用
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-24 DOI: 10.1038/s41576-024-00720-2
Boshu Li, Chao Sun, Jiayang Li, Caixia Gao
{"title":"Targeted genome-modification tools and their advanced applications in crop breeding","authors":"Boshu Li, Chao Sun, Jiayang Li, Caixia Gao","doi":"10.1038/s41576-024-00720-2","DOIUrl":"10.1038/s41576-024-00720-2","url":null,"abstract":"Crop improvement by genome editing involves the targeted alteration of genes to improve plant traits, such as stress tolerance, disease resistance or nutritional content. Techniques for the targeted modification of genomes have evolved from generating random mutations to precise base substitutions, followed by insertions, substitutions and deletions of small DNA fragments, and are finally starting to achieve precision manipulation of large DNA segments. Recent developments in base editing, prime editing and other CRISPR-associated systems have laid a solid technological foundation to enable plant basic research and precise molecular breeding. In this Review, we systematically outline the technological principles underlying precise and targeted genome-modification methods. We also review methods for the delivery of genome-editing reagents in plants and outline emerging crop-breeding strategies based on targeted genome modification. Finally, we consider potential future developments in precise genome-editing technologies, delivery methods and crop-breeding approaches, as well as regulatory policies for genome-editing products. Targeted genome modification using CRISPR–Cas genome editing, base editing or prime editing is driving base research in plants and precise molecular breeding. The authors review the technological principles underlying these methods, approaches for their delivery in plants, and emerging crop-breeding strategies based on targeted genome modification.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 9","pages":"603-622"},"PeriodicalIF":39.1,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140642317","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
Genome assembly in the telomere-to-telomere era 端粒到端粒时代的基因组组装
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-22 DOI: 10.1038/s41576-024-00718-w
Heng Li, Richard Durbin
{"title":"Genome assembly in the telomere-to-telomere era","authors":"Heng Li, Richard Durbin","doi":"10.1038/s41576-024-00718-w","DOIUrl":"10.1038/s41576-024-00718-w","url":null,"abstract":"Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly — the process of reconstructing the genome sequence of an organism from sequencing reads — has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome — also known as telomere-to-telomere assembly — for many organisms. Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes. In this Review, Li and Durbin discuss how to generate telomere-to-telomere assemblies for large haploid or diploid genomes using currently available data types and algorithms, and outline remaining challenges in resolving highly repetitive sequences and polyploid genomes.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 9","pages":"658-670"},"PeriodicalIF":39.1,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140632363","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
Nuclear mRNA decay: regulatory networks that control gene expression 核 mRNA 衰减：控制基因表达的调控网络
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-18 DOI: 10.1038/s41576-024-00712-2
Xavier Rambout, Lynne E. Maquat
{"title":"Nuclear mRNA decay: regulatory networks that control gene expression","authors":"Xavier Rambout, Lynne E. Maquat","doi":"10.1038/s41576-024-00712-2","DOIUrl":"10.1038/s41576-024-00712-2","url":null,"abstract":"Proper regulation of mRNA production in the nucleus is critical for the maintenance of cellular homoeostasis during adaptation to internal and environmental cues. Over the past 25 years, it has become clear that the nuclear machineries governing gene transcription, pre-mRNA processing, pre-mRNA and mRNA decay, and mRNA export to the cytoplasm are inextricably linked to control the quality and quantity of mRNAs available for translation. More recently, an ever-expanding diversity of new mechanisms by which nuclear RNA decay factors finely tune the expression of protein-encoding genes have been uncovered. Here, we review the current understanding of how mammalian cells shape their protein-encoding potential by regulating the decay of pre-mRNAs and mRNAs in the nucleus. In this Review, the authors summarize our current understanding of nuclear pre-mRNA and mRNA decay pathways. They describe how aberrantly processed mRNAs are targeted for decay in the nucleus and how this process is regulated to finely control gene expression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 10","pages":"679-697"},"PeriodicalIF":39.1,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140620238","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
Natural antisense transcripts as versatile regulators of gene expression 作为基因表达多功能调节器的天然反义转录本
IF 39.1 1区 生物学
Nature Reviews Genetics Pub Date : 2024-04-17 DOI: 10.1038/s41576-024-00723-z
Andreas Werner, Aditi Kanhere, Claes Wahlestedt, John S. Mattick
{"title":"Natural antisense transcripts as versatile regulators of gene expression","authors":"Andreas Werner, Aditi Kanhere, Claes Wahlestedt, John S. Mattick","doi":"10.1038/s41576-024-00723-z","DOIUrl":"10.1038/s41576-024-00723-z","url":null,"abstract":"Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense–antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions. In this Perspective, Werner and colleagues discuss the many potential mechanisms by which natural antisense transcripts (NATs) can regulate expression of their complementary sense transcripts, the biological implications of their regulatory effects and the potential of NATs for therapeutic applications.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 10","pages":"730-744"},"PeriodicalIF":39.1,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140608105","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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