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Annual review of genetics最新文献

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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
Transposon Insertion Sequencing, a Global Measure of Gene Function. 转座子插入测序，基因功能的全局测量。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-04 DOI: 10.1146/annurev-genet-112618-043838
Tim van Opijnen, Henry L Levin
{"title":"Transposon Insertion Sequencing, a Global Measure of Gene Function.","authors":"Tim van Opijnen,&nbsp;Henry L Levin","doi":"10.1146/annurev-genet-112618-043838","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043838","url":null,"abstract":"<p><p>The goal of genomics and systems biology is to understand how complex systems of factors assemble into pathways and structures that combine to form living organisms. Great advances in understanding biological processes result from determining the function of individual genes, a process that has classically relied on characterizing single mutations. Advances in DNA sequencing has made available the complete set of genetic instructions for an astonishing and growing number of species. To understand the function of this ever-increasing number of genes, a high-throughput method was developed that in a single experiment can measure the function of genes across the genome of an organism. This occurred approximately 10 years ago, when high-throughput DNA sequencing was combined with advances in transposon-mediated mutagenesis in a method termed transposon insertion sequencing (TIS). In the subsequent years, TIS succeeded in addressing fundamental questions regarding the genes of bacteria, many of which have been shown to play central roles in bacterial infections that result in major human diseases. The field of TIS has matured and resulted in studies of hundreds of species that include significant innovations with a number of transposons. Here, we summarize a number of TIS experiments to provide an understanding of the method and explanation of approaches that are instructive when designing a study. Importantly, we emphasize critical aspects of a TIS experiment and highlight the extension and applicability of TIS into nonbacterial species such as yeast.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"337-365"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043838","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344808","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: 19
Human genetics. 人类遗传学。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-02-02 DOI: 10.1146/annurev.ge.04.120170.000245
V A McKusick
{"title":"Human genetics.","authors":"V A McKusick","doi":"10.1146/annurev.ge.04.120170.000245","DOIUrl":"https://doi.org/10.1146/annurev.ge.04.120170.000245","url":null,"abstract":"Prerequisites A good knowledge of Catalan and Spanish is indispensable, vehicular languages in which the classes will take place. It is advisable that the students have a good knowledge of English, since many of the information sources of this subject are in this language. It is convenient that the student has achieved basic skills in cell biology, biochemistry and molecular biology. It is convenient that the student knows the basic principles of genetics.","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"4 ","pages":""},"PeriodicalIF":11.1,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev.ge.04.120170.000245","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"16043464","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: 2
Behavioral Genetics 行为遗传学
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-02-02 DOI: 10.1002/9780470114735.hawley01624
B. Y C A T H E R I N E B A K
{"title":"Behavioral Genetics","authors":"B. Y C A T H E R I N E B A K","doi":"10.1002/9780470114735.hawley01624","DOIUrl":"https://doi.org/10.1002/9780470114735.hawley01624","url":null,"abstract":"An introduction to how genes and environments interact through development to shape differences in mood, personality, and intelligence A tool to inform public discussion of behavioral genetic research and its broader social implications","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"1 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"51144194","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: 282
Standard Deviations: The Biological Bases of Transmission Ratio Distortion. 标准偏差:传动比失真的生物学基础。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2019-12-03 DOI: 10.1146/annurev-genet-112618-043905
L. Fishman, Mariah McIntosh
{"title":"Standard Deviations: The Biological Bases of Transmission Ratio Distortion.","authors":"L. Fishman, Mariah McIntosh","doi":"10.1146/annurev-genet-112618-043905","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043905","url":null,"abstract":"The rule of Mendelian inheritance is remarkably robust, but deviations from the equal transmission of alternative alleles at a locus [a.k.a. transmission ratio distortion (TRD)] are also commonly observed in genetic mapping populations. Such TRD reveals locus-specific selection acting at some point between the diploid heterozygous parents and progeny genotyping and therefore can provide novel insight into otherwise-hidden genetic and evolutionary processes. Most of the classic selfish genetic elements were discovered through their biasing of transmission, but many unselfish evolutionary and developmental processes can also generate TRD. In this review, we describe methodologies for detecting TRD in mapping populations, detail the arenas and genetic interactions that shape TRD during plant and animal reproduction, and summarize patterns of TRD from across the genetic mapping literature. Finally, we point to new experimental approaches that can accelerate both detection of TRD and characterization of the underlying genetic mechanisms. Expected final online publication date for the Annual Review of Genetics, Volume 53 is November 23, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":""},"PeriodicalIF":11.1,"publicationDate":"2019-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043905","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48291577","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: 36
The Microbiome and Aging. 微生物组与衰老。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2019-12-03 DOI: 10.1146/annurev-genet-112618-043650
Bianca Bana, F. Cabreiro
{"title":"The Microbiome and Aging.","authors":"Bianca Bana, F. Cabreiro","doi":"10.1146/annurev-genet-112618-043650","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043650","url":null,"abstract":"Aging is a natural process of organismal decay that underpins the development of myriad diseases and disorders. Extensive efforts have been made to understand the biology of aging and its regulation, but most studies focus solely on the host organism. Considering the pivotal role of the microbiota in host health and metabolism, we propose viewing the host and its microbiota as a single biological entity whose aging phenotype is influenced by the complex interplay between host and bacterial genetics. In this review we present how the microbiota changes as the host ages, but also how the intricate relationship between host and indigenous bacteria impacts organismal aging and life span. In addition, we highlight other microbiota-dependent mechanisms that potentially regulate aging, and present experimental animal models for addressing these questions. Importantly, we propose microbiome dysbiosis as an additional hallmark and biomarker of aging. Expected final online publication date for the Annual Review of Genetics, Volume 53 is November 23, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":""},"PeriodicalIF":11.1,"publicationDate":"2019-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043650","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41513774","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: 110
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