Nature Reviews Genetics最新文献

More than a decade of genetic research on the Denisovans 十多年来对丹尼索瓦人的基因研究。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-18 DOI: 10.1038/s41576-023-00643-4

Stéphane Peyrégne, Viviane Slon, Janet Kelso

{"title":"More than a decade of genetic research on the Denisovans","authors":"Stéphane Peyrégne, Viviane Slon, Janet Kelso","doi":"10.1038/s41576-023-00643-4","DOIUrl":"10.1038/s41576-023-00643-4","url":null,"abstract":"Denisovans, a group of now extinct humans who lived in Eastern Eurasia in the Middle and Late Pleistocene, were first identified from DNA sequences just over a decade ago. Only ten fragmentary remains from two sites have been attributed to Denisovans based entirely on molecular information. Nevertheless, there has been great interest in using genetic data to understand Denisovans and their place in human history. From the reconstruction of a single high-quality genome, it has been possible to infer their population history, including events of admixture with other human groups. Additionally, the identification of Denisovan DNA in the genomes of present-day individuals has provided insights into the timing and routes of dispersal of ancient modern humans into Asia and Oceania, as well as the contributions of archaic DNA to the physiology of present-day people. In this Review, we synthesize more than a decade of research on Denisovans, reconcile controversies and summarize insights into their population history and phenotype. We also highlight how our growing knowledge about Denisovans has provided insights into our own evolutionary history. Ancient DNA studies over the past decade have yielded a plethora of insights into the Denisovan archaic hominin group. The authors review our understanding of Denisovan population history and their interactions with other human groups, insights from studies of Denisovan ancestry in modern humans, what we know about the Denisovan phenotype and their impact on our own evolutionary history.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 2","pages":"83-103"},"PeriodicalIF":42.7,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10308551","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

Unequal global implementation of genomic newborn screening 全球新生儿基因组筛查实施不平等。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-18 DOI: 10.1038/s41576-023-00654-1

Ahmad N. Abou Tayoun

引用次数: 0

Transposable elements: McClintock’s legacy revisited 可转换元素：重新审视麦克林托克的遗产。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-18 DOI: 10.1038/s41576-023-00652-3

Cédric Feschotte

引用次数: 0

Illuminating the human yolk sac through single-cell omics 通过单细胞组学照亮人类卵黄囊。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-15 DOI: 10.1038/s41576-023-00658-x

Kirsty Minton

引用次数: 0

Imprinted genes and the manipulation of parenting in mammals 哺乳动物的印记基因和养育子女的操作。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-15 DOI: 10.1038/s41576-023-00644-3

Rosalind M. John, Matthew J. Higgs, Anthony R. Isles

{"title":"Imprinted genes and the manipulation of parenting in mammals","authors":"Rosalind M. John, Matthew J. Higgs, Anthony R. Isles","doi":"10.1038/s41576-023-00644-3","DOIUrl":"10.1038/s41576-023-00644-3","url":null,"abstract":"Genomic imprinting refers to the parent-of-origin expression of genes, which originates from epigenetic events in the mammalian germ line. The evolution of imprinting may reflect a conflict over resource allocation early in life, with silencing of paternal genes in offspring soliciting increased maternal provision and silencing of maternal genes limiting demands on the mother. Parental caregiving has been identified as an area of potential conflict, with several imprinted genes serendipitously found to directly influence the quality of maternal care. Recent systems biology approaches, based on single-cell RNA sequencing data, support a more deliberate relationship, which is reinforced by the finding that imprinted genes expressed in the offspring influence the quality of maternal caregiving. These bidirectional, reiterative relationships between parents and their offspring are critical both for short-term survival and for lifelong wellbeing, with clear implications for human health. Genomic imprinting — the monoallelic expression of genes based on their parent of origin — may have evolved due to an intragenomic conflict between maternal and paternal genomes within an individual, with differential interests regarding the level of parental caregiving. Here, the authors review the influence of genomic imprinting on parenting behaviour in mammals, with a focus on studies in mice.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"24 11","pages":"783-796"},"PeriodicalIF":42.7,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10262164","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

RNA modifications in physiology and disease: towards clinical applications 生理学和疾病中的 RNA 修饰：走向临床应用。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-15 DOI: 10.1038/s41576-023-00645-2

Sylvain Delaunay, Mark Helm, Michaela Frye

{"title":"RNA modifications in physiology and disease: towards clinical applications","authors":"Sylvain Delaunay, Mark Helm, Michaela Frye","doi":"10.1038/s41576-023-00645-2","DOIUrl":"10.1038/s41576-023-00645-2","url":null,"abstract":"The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules — to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches. Native nucleotide modifications regulate RNA function and metabolism, the study of which has revealed disease mechanisms, offers therapeutic potential and enables innovative clinical strategies. Chemical modifications in RNA are harnessed for clinical use in stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 2","pages":"104-122"},"PeriodicalIF":42.7,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10317056","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

Mary Lyon and the birth of X-inactivation research 玛丽-里昂与 X 失活研究的诞生。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-13 DOI: 10.1038/s41576-023-00655-0

Marnie E. Blewitt

引用次数: 0

Computational methods for analysing multiscale 3D genome organization 分析多尺度三维基因组组织的计算方法。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-06 DOI: 10.1038/s41576-023-00638-1

Yang Zhang, Lorenzo Boninsegna, Muyu Yang, Tom Misteli, Frank Alber, Jian Ma

{"title":"Computational methods for analysing multiscale 3D genome organization","authors":"Yang Zhang, Lorenzo Boninsegna, Muyu Yang, Tom Misteli, Frank Alber, Jian Ma","doi":"10.1038/s41576-023-00638-1","DOIUrl":"10.1038/s41576-023-00638-1","url":null,"abstract":"Recent progress in whole-genome mapping and imaging technologies has enabled the characterization of the spatial organization and folding of the genome in the nucleus. In parallel, advanced computational methods have been developed to leverage these mapping data to reveal multiscale three-dimensional (3D) genome features and to provide a more complete view of genome structure and its connections to genome functions such as transcription. Here, we discuss how recently developed computational tools, including machine-learning-based methods and integrative structure-modelling frameworks, have led to a systematic, multiscale delineation of the connections among different scales of 3D genome organization, genomic and epigenomic features, functional nuclear components and genome function. However, approaches that more comprehensively integrate a wide variety of genomic and imaging datasets are still needed to uncover the functional role of 3D genome structure in defining cellular phenotypes in health and disease. In this Review, Zhang et al. discuss how recent advances in computational methods are helping to reveal the multiscale features involved in genome folding within the nucleus and how the resulting 3D genome organization relates to genome function.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 2","pages":"123-141"},"PeriodicalIF":42.7,"publicationDate":"2023-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10226392","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

Harnessing deep learning for population genetic inference 利用深度学习进行群体遗传推断。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-09-04 DOI: 10.1038/s41576-023-00636-3

Xin Huang, Aigerim Rymbekova, Olga Dolgova, Oscar Lao, Martin Kuhlwilm

{"title":"Harnessing deep learning for population genetic inference","authors":"Xin Huang, Aigerim Rymbekova, Olga Dolgova, Oscar Lao, Martin Kuhlwilm","doi":"10.1038/s41576-023-00636-3","DOIUrl":"10.1038/s41576-023-00636-3","url":null,"abstract":"In population genetics, the emergence of large-scale genomic data for various species and populations has provided new opportunities to understand the evolutionary forces that drive genetic diversity using statistical inference. However, the era of population genomics presents new challenges in analysing the massive amounts of genomes and variants. Deep learning has demonstrated state-of-the-art performance for numerous applications involving large-scale data. Recently, deep learning approaches have gained popularity in population genetics; facilitated by the advent of massive genomic data sets, powerful computational hardware and complex deep learning architectures, they have been used to identify population structure, infer demographic history and investigate natural selection. Here, we introduce common deep learning architectures and provide comprehensive guidelines for implementing deep learning models for population genetic inference. We also discuss current challenges and future directions for applying deep learning in population genetics, focusing on efficiency, robustness and interpretability. Applying deep learning to large-scale genomic data of species or populations is providing new opportunities to understand the evolutionary forces that drive genetic diversity. This Review introduces common deep learning architectures and provides comprehensive guidelines to implement deep learning models for population genetic inference. The authors also discuss current opportunities and challenges for deep learning in population genetics.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 1","pages":"61-78"},"PeriodicalIF":42.7,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10151512","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: 1

Enhancing sustainable development through plant genetics 通过植物遗传学促进可持续发展。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2023-08-29 DOI: 10.1038/s41576-023-00651-4

Pamela C. Ronald

引用次数: 0