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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 Q1 GENETICS & HEREDITY Pub Date : 2024-04-22 DOI: 10.1038/s41576-024-00718-w
Heng Li, Richard Durbin
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.
基因组序列在很大程度上决定了生物体的生物学特性并编码了生物体的历史,而从头组装--根据测序读数重建生物体基因组序列的过程--四十年来一直是生物信息学的核心问题。直到最近,基因组通常最多只能组装成几个兆字节的片段,但现在长读数测序技术的进步使许多生物的每条染色体都能进行近乎完整的组装--也称为端粒到端粒组装(telomere-to-telomere assembly)。在这里,我们回顾了最近在组装算法和协议方面取得的进展,重点是如何获得近端粒到端粒的组装。我们还讨论了解决剩余的组装差距和组装非二倍体基因组所需的其他发展。
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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 Q1 GENETICS & HEREDITY Pub Date : 2024-04-18 DOI: 10.1038/s41576-024-00712-2
Xavier Rambout, Lynne E. Maquat
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.
适当调节细胞核中 mRNA 的产生对于在适应内部和环境线索的过程中维持细胞的平衡至关重要。在过去的 25 年中,人们已经清楚地认识到,管理基因转录、前 mRNA 处理、前 mRNA 和 mRNA 衰减以及向细胞质输出 mRNA 的核机制密不可分,它们控制着可用于翻译的 mRNA 的质量和数量。最近,人们发现了核 RNA 衰变因子精细调节编码蛋白质基因表达的新机制,其多样性不断扩大。在这里,我们回顾了目前对哺乳动物细胞如何通过调节细胞核中前 mRNA 和 mRNA 的衰变来塑造其编码蛋白质潜能的理解。
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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 Q1 GENETICS & HEREDITY Pub Date : 2024-04-17 DOI: 10.1038/s41576-024-00723-z
Andreas Werner, Aditi Kanhere, Claes Wahlestedt, John S. Mattick
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.
长非编码 RNA(lncRNA)正在成为一类重要的基因产物,在细胞和发育生物学中发挥着核心作用。天然反义转录本(NATs)是lncRNAs的一个重要子集,从编码蛋白质和非编码基因的反向链表达,是真核生物和原核生物中的一种全基因组现象。在真核生物中,无数 NATs 参与调控途径,影响其同源感应基因的表达。对 NATs 和 lncRNAs 的研究以及大规模测序和生物信息学项目的最新进展表明,NATs 是否调控有义转录本的表达、剪接、稳定性或翻译受有义-反义配对之间的重叠模式和程度的影响。此外,体细胞中普遍存在表观遗传基因调控机制,而生殖细胞中则普遍存在依赖于双链 RNA 中间体形成的机制。NATs 对有义转录本表达的调节作用使 NATs 成为治疗干预的合理靶点。
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引用次数: 0
Understanding human uniqueness in the pre-genomic era 了解前基因组时代人类的独特性
IF 42.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-04-15 DOI: 10.1038/s41576-024-00732-y
Jenny Tung
In this Journal Club article, Jenny Tung reflects on a 1975 paper from King and Wilson that emphasized the importance of gene regulatory changes in human evolution.
在这篇期刊俱乐部文章中,Jenny Tung 回顾了 King 和 Wilson 1975 年发表的一篇论文,该论文强调了基因调控变化在人类进化中的重要性。
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引用次数: 0
SIMPLE-seq to decode DNA methylation dynamics in single cells 用 SIMPLE-seq 技术解码单细胞中 DNA 甲基化的动态变化
IF 42.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-04-12 DOI: 10.1038/s41576-024-00729-7
Dongsheng Bai, Chenxu Zhu
In this Tools of the Trade article, Dongsheng Bai and Chenxu Zhu describe SIMPLE-seq, a scalable single-cell sequencing method that simultaneously decodes the cytosine modifications 5mC and 5hmC.
在这篇 "贸易工具"(Tools of the Trade)文章中,白东升(Dongsheng Bai)和朱晨旭(Chenxu Zhu)介绍了一种可扩展的单细胞测序方法 SIMPLE-seq,该方法可同时解码胞嘧啶修饰 5mC 和 5hmC。
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引用次数: 0
A developmental exit from totipotency 脱离全能性的发育
IF 42.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-04-12 DOI: 10.1038/s41576-024-00730-0
Henry Ertl
A paper in Nature Genetics identifies a mechanism involving the transcription factor DUXBL that controls the development of early embryonic mouse cells past stages marked by totipotency.
自然-遗传学》(Nature Genetics)杂志上的一篇论文确定了一种涉及转录因子 DUXBL 的机制,该转录因子控制着早期胚胎小鼠细胞的发育,使其度过以全能性为标志的阶段。
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引用次数: 0
Human embryonic genetic mosaicism and its effects on development and disease 人类胚胎基因嵌合及其对发育和疾病的影响
IF 39.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-04-11 DOI: 10.1038/s41576-024-00715-z
Sarah M. Waldvogel, Jennifer E. Posey, Margaret A. Goodell
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease. Genetic variants acquired early during embryogenesis can affect numerous tissues. The authors review the phenomenon of embryonic mosaicism, with a focus on small variants, and discuss mechanisms of cell competition that allow mosaic clones to expand, as well as the functional consequences of mosaicism for embryo viability and the health of the organism.
几乎哺乳动物的每一次细胞分裂都伴随着突变事件,这种突变会在子细胞中固定下来。当这种突变延续到其他细胞后代时,就会出现变异细胞克隆。因此,哺乳动物是由基因不同的克隆组成的复杂镶嵌体。最近的高通量测序研究发现,镶嵌现象很常见,克隆的大小通常会随着年龄的增长而增加,特定的变异会影响组织功能和疾病的发展。在早期胚胎发生过程中获得的变异由多种细胞类型共享,可影响多种组织。在组织内部,变异克隆会相互竞争,从而导致其扩大或消失。胚胎嵌合对遗传病的严重性和传播有临床影响,但这一现象可能未得到充分认识。为了更好地了解其对马赛克个体的影响,必须利用研究工具来阐明胚胎变异扩增对发育和疾病的影响机制。
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引用次数: 0
Pleiotropy, epistasis and the genetic architecture of quantitative traits 多效性、外显性和数量性状的遗传结构
IF 39.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-04-02 DOI: 10.1038/s41576-024-00711-3
Trudy F. C. Mackay, Robert R. H. Anholt
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans. In this Review, Mackay and Anholt discuss how epistasis and pleiotropy contribute to the genetic architecture of quantitative traits and outline factors that might explain observed differences in their prevalence between model organisms and humans.
多效性(一种遗传多态性影响多种性状)和表观性(遗传多态性之间的非线性相互作用影响同一性状)是数量性状遗传结构的基本方面。近来,人类和模式生物种群中多态变异对分子和生物表型影响的表征能力不断进步,揭示了多效性的普遍性以及包括疾病在内的数量性状之间意想不到的共同分子遗传基础。相比之下,在模式生物中,与数量性状相关的多态性位点之间普遍存在表观性,即一个位点上的等位基因在不同的遗传背景下具有不同的效应,但在人类数量性状和常见疾病中却很少观察到这种表观性。在此,我们回顾了有关多效性和表观性的概念和最新推论,并讨论了导致模式生物和人类数量性状遗传结构异同的因素。
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引用次数: 0
Genetic variation across and within individuals 个体间和个体内的遗传变异
IF 39.1 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-03-28 DOI: 10.1038/s41576-024-00709-x
Zhi Yu, Tim H. H. Coorens, Md Mesbah Uddin, Kristin G. Ardlie, Niall Lennon, Pradeep Natarajan
Germline variation and somatic mutation are intricately connected and together shape human traits and disease risks. Germline variants are present from conception, but they vary between individuals and accumulate over generations. By contrast, somatic mutations accumulate throughout life in a mosaic manner within an individual due to intrinsic and extrinsic sources of mutations and selection pressures acting on cells. Recent advancements, such as improved detection methods and increased resources for association studies, have drastically expanded our ability to investigate germline and somatic genetic variation and compare underlying mutational processes. A better understanding of the similarities and differences in the types, rates and patterns of germline and somatic variants, as well as their interplay, will help elucidate the mechanisms underlying their distinct yet interlinked roles in human health and biology. In this Review, the authors compare the characteristics and detection methods of germline and somatic variants. Furthermore, they outline how the interplay between the two types of genetic variation can affect human health.
种系变异和体细胞突变错综复杂地联系在一起,共同塑造了人类的特征和疾病风险。种系变异从受孕开始就存在,但个体之间存在差异,并经过几代人的积累。与此相反,体细胞变异在个体一生中以镶嵌方式积累,这是由于内在和外在的变异来源以及作用于细胞的选择压力。最近的进步,如检测方法的改进和关联研究资源的增加,极大地扩展了我们研究种系和体细胞遗传变异以及比较潜在突变过程的能力。更好地了解种系变异和体细胞变异在类型、发生率和模式上的异同以及它们之间的相互作用,将有助于阐明它们在人类健康和生物学中不同但又相互关联的作用机制。
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引用次数: 0
Building a catalogue of short tandem repeats in diverse populations 建立不同人群的短串联重复序列目录。
IF 42.7 1区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2024-03-27 DOI: 10.1038/s41576-024-00726-w
Ning Xie
Reflecting on the importance of short tandem repeats (STRs) in population genetics, Ning Xie highlights a 2023 publication that characterized genome-wide STR variation in global human genomes to expand our understanding of STR genetic diversity within and across populations.
谢宁在谈到短串联重复序列(STR)在群体遗传学中的重要性时,重点介绍了 2023 年发表的一篇论文,该论文描述了全球人类基因组中全基因组 STR 变异的特征,从而拓展了我们对人群内部和人群之间 STR 遗传多样性的理解。
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引用次数: 0
期刊
Nature Reviews Genetics
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