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Annual review of genetics最新文献

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Moonlighting Proteins. 兼职蛋白质。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-01 DOI: 10.1146/annurev-genet-030620-102906
Nadia Singh, Needhi Bhalla
{"title":"Moonlighting Proteins.","authors":"Nadia Singh,&nbsp;Needhi Bhalla","doi":"10.1146/annurev-genet-030620-102906","DOIUrl":"https://doi.org/10.1146/annurev-genet-030620-102906","url":null,"abstract":"<p><p>The single gene, single protein, single function hypothesis is increasingly becoming obsolete. Numerous studies have demonstrated that individual proteins can moonlight, meaning they can have multiple functions based on their cellular or developmental context. In this review, we discuss moonlighting proteins, highlighting the biological pathways where this phenomenon may be particularly relevant. In addition, we combine genetic, cell biological, and evolutionary perspectives so that we can better understand how, when, and why moonlighting proteins may take on multiple roles.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"265-285"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-030620-102906","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38331788","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: 53
The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. 现代马的进化和历史基础：古代基因组学的教训。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-22 DOI: 10.1146/annurev-genet-021920-011805
Ludovic Orlando
{"title":"The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics.","authors":"Ludovic Orlando","doi":"10.1146/annurev-genet-021920-011805","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-011805","url":null,"abstract":"<p><p>The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"563-581"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-011805","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38503084","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: 15
Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation. 控制翻译的保守上游开放阅读框新生肽。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-01 DOI: 10.1146/annurev-genet-112618-043822
Thomas E Dever, Ivaylo P Ivanov, Matthew S Sachs
{"title":"Conserved Upstream Open Reading Frame Nascent Peptides That Control Translation.","authors":"Thomas E Dever,&nbsp;Ivaylo P Ivanov,&nbsp;Matthew S Sachs","doi":"10.1146/annurev-genet-112618-043822","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043822","url":null,"abstract":"<p><p>Cells utilize transcriptional and posttranscriptional mechanisms to alter gene expression in response to environmental cues. Gene-specific controls, including changing the translation of specific messenger RNAs (mRNAs), provide a rapid means to respond precisely to different conditions. Upstream open reading frames (uORFs) are known to control the translation of mRNAs. Recent studies in bacteria and eukaryotes have revealed the functions of evolutionarily conserved uORF-encoded peptides. Some of these uORF-encoded nascent peptides enable responses to specific metabolites to modulate the translation of their mRNAs by stalling ribosomes and through ribosome stalling may also modulate the level of their mRNAs. In this review, we highlight several examples of conserved uORF nascent peptides that stall ribosomes to regulate gene expression in response to specific metabolites in bacteria, fungi, mammals, and plants.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"237-264"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043822","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38331785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 52
Measuring and Modeling Single-Cell Heterogeneity and Fate Decision in Mouse Embryos. 小鼠胚胎单细胞异质性和命运决定的测量和建模。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-08-31 DOI: 10.1146/annurev-genet-021920-110200
Jonathan Fiorentino, Maria-Elena Torres-Padilla, Antonio Scialdone
{"title":"Measuring and Modeling Single-Cell Heterogeneity and Fate Decision in Mouse Embryos.","authors":"Jonathan Fiorentino,&nbsp;Maria-Elena Torres-Padilla,&nbsp;Antonio Scialdone","doi":"10.1146/annurev-genet-021920-110200","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-110200","url":null,"abstract":"<p><p>Cellular heterogeneity is a property of any living system; however, its relationship with cellular fate decision remains an open question. Recent technological advances have enabled valuable insights, especially in complex systems such as the mouse embryo. In this review, we discuss recent studies that characterize cellular heterogeneity at different levels during mouse development, from the two-cell stage up to gastrulation. In addition to key experimental findings, we review mathematical modeling approaches that help researchers interpret these findings. Disentangling the role of heterogeneity in cell fate decision will likely rely on the refined integration of experiments, large-scale omics data, and mathematical modeling, complemented by the use of synthetic embryos and gastruloids as promising in vitro models.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"167-187"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-110200","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38424060","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: 12
What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? 一个世纪的定量遗传学让我们了解了大自然的基因工具箱吗?
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-08 DOI: 10.1146/annurev-genet-021920-102037
Christopher M Jakobson, Daniel F Jarosz
{"title":"What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit?","authors":"Christopher M Jakobson,&nbsp;Daniel F Jarosz","doi":"10.1146/annurev-genet-021920-102037","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-102037","url":null,"abstract":"<p><p>The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"439-464"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-102037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38354520","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: 6
Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. 结核分枝杆菌临床分离株的遗传多样性及结核感染和疾病的结果。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-14 DOI: 10.1146/annurev-genet-022820-085940
Julian S Peters, Nabila Ismail, Anzaan Dippenaar, Shuyi Ma, David R Sherman, Robin M Warren, Bavesh D Kana
{"title":"Genetic Diversity in <i>Mycobacterium tuberculosis</i> Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease.","authors":"Julian S Peters,&nbsp;Nabila Ismail,&nbsp;Anzaan Dippenaar,&nbsp;Shuyi Ma,&nbsp;David R Sherman,&nbsp;Robin M Warren,&nbsp;Bavesh D Kana","doi":"10.1146/annurev-genet-022820-085940","DOIUrl":"https://doi.org/10.1146/annurev-genet-022820-085940","url":null,"abstract":"<p><p>Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, <i>Mycobacterium tuberculosis</i>, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of <i>M. tuberculosis</i> isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"511-537"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-022820-085940","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38380003","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: 16
Canalization and Robustness in Human Genetics and Disease. 人类遗传和疾病的管化和稳健性。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-08-31 DOI: 10.1146/annurev-genet-022020-022327
Greg Gibson, Kristine A Lacek
{"title":"Canalization and Robustness in Human Genetics and Disease.","authors":"Greg Gibson,&nbsp;Kristine A Lacek","doi":"10.1146/annurev-genet-022020-022327","DOIUrl":"https://doi.org/10.1146/annurev-genet-022020-022327","url":null,"abstract":"<p><p>Canalization refers to the evolution of populations such that the number of individuals who deviate from the optimum trait, or experience disease, is minimized. In the presence of rapid cultural, environmental, or genetic change, the reverse process of decanalization may contribute to observed increases in disease prevalence. This review starts by defining relevant concepts, drawing distinctions between the canalization of populations and robustness of individuals. It then considers evidence pertaining to three continuous traits and six domains of disease. In each case, existing genetic evidence for genotype-by-environment interactions is insufficient to support a strong inference of decanalization, but we argue that the advent of genome-wide polygenic risk assessment now makes an empirical evaluation of the role of canalization in preventing disease possible. Finally, the contributions of both rare and common variants to congenital abnormality and adult onset disease are considered in light of a new kerplunk model of genetic effects.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"189-211"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-022020-022327","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38424059","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: 17
Noncanonical Roles of tRNAs: tRNA Fragments and Beyond. tRNA 的非规范作用：tRNA 片段及其他。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-08-25 DOI: 10.1146/annurev-genet-022620-101840
Zhangli Su, Briana Wilson, Pankaj Kumar, Anindya Dutta
{"title":"Noncanonical Roles of tRNAs: tRNA Fragments and Beyond.","authors":"Zhangli Su, Briana Wilson, Pankaj Kumar, Anindya Dutta","doi":"10.1146/annurev-genet-022620-101840","DOIUrl":"10.1146/annurev-genet-022620-101840","url":null,"abstract":"<p><p>As one of the most abundant and conserved RNA species, transfer RNAs (tRNAs) are well known for their role in reading the codons on messenger RNAs and translating them into proteins. In this review, we discuss the noncanonical functions of tRNAs. These include tRNAs as precursors to novel small RNA molecules derived from tRNAs, also called tRNA-derived fragments, that are abundant across species and have diverse functions in different biological processes, including regulating protein translation, Argonaute-dependent gene silencing, and more. Furthermore, the role of tRNAs in biosynthesis and other regulatory pathways, including nutrient sensing, splicing, transcription, retroelement regulation, immune response, and apoptosis, is reviewed. Genome organization and sequence variation of tRNA genes are also discussed in light of their noncanonical functions. Lastly, we discuss the recent applications of tRNAs in genome editing and microbiome sequencing.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"47-69"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7686126/pdf/nihms-1625447.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38305799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mosaicism in Human Health and Disease. 人类健康与疾病中的镶嵌现象。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-11 DOI: 10.1146/annurev-genet-041720-093403
Jeremy Thorpe, Ikeoluwa A Osei-Owusu, Bracha Erlanger Avigdor, Rossella Tupler, Jonathan Pevsner
{"title":"Mosaicism in Human Health and Disease.","authors":"Jeremy Thorpe,&nbsp;Ikeoluwa A Osei-Owusu,&nbsp;Bracha Erlanger Avigdor,&nbsp;Rossella Tupler,&nbsp;Jonathan Pevsner","doi":"10.1146/annurev-genet-041720-093403","DOIUrl":"https://doi.org/10.1146/annurev-genet-041720-093403","url":null,"abstract":"<p><p>Mosaicism refers to the occurrence of two or more genomes in an individual derived from a single zygote. Germline mosaicism is a mutation that is limited to the gonads and can be transmitted to offspring. Somatic mosaicism is a postzygotic mutation that occurs in the soma, and it may occur at any developmental stage or in adult tissues. Mosaic variation may be classified in six ways: (<i>a</i>) germline or somatic origin, (<i>b</i>) class of DNA mutation (ranging in scale from single base pairs to multiple chromosomes), (<i>c</i>) developmental context, (<i>d</i>) body location(s), (<i>e</i>) functional consequence (including deleterious, neutral, or advantageous), and (<i>f</i>) additional sources of mosaicism, including mitochondrial heteroplasmy, exogenous DNA sources such as vectors, and epigenetic changes such as imprinting and X-chromosome inactivation. Technological advances, including single-cell and other next-generation sequencing, have facilitated improved sensitivity and specificity to detect mosaicism in a variety of biological contexts.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"487-510"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-041720-093403","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38370630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 42
A Field Guide to Eukaryotic Transposable Elements. 真核生物可转座元件实地指南》。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-21 DOI: 10.1146/annurev-genet-040620-022145
Jonathan N Wells, Cédric Feschotte
{"title":"A Field Guide to Eukaryotic Transposable Elements.","authors":"Jonathan N Wells, Cédric Feschotte","doi":"10.1146/annurev-genet-040620-022145","DOIUrl":"10.1146/annurev-genet-040620-022145","url":null,"abstract":"<p><p>Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"539-561"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293684/pdf/nihms-1723479.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38405024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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