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Annual review of genetics最新文献

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New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation. 剖析作物数量性状变异上位性的新视野。
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-050720-122916
Sebastian Soyk, Matthias Benoit, Zachary B Lippman
{"title":"New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation.","authors":"Sebastian Soyk,&nbsp;Matthias Benoit,&nbsp;Zachary B Lippman","doi":"10.1146/annurev-genet-050720-122916","DOIUrl":"https://doi.org/10.1146/annurev-genet-050720-122916","url":null,"abstract":"<p><p>Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the cumulative effect of individual gene mutations. This deviation is due to epistasis, in which interactions between alleles are often unpredictable and quantitative in effect. Recent advances in genomics and genome-editing technologies are elevating the study of epistasis in crops. Using the traits and developmental pathways that were major targets in domestication and breeding, we highlight how epistasis is central in guiding the behavior of the genetic variation that shapes quantitative trait variation. We outline new strategies that illuminate how quantitative epistasis from modified gene dosage defines background dependencies. Advancing our understanding of epistasis in crops can reveal new principles and approaches to engineering targeted improvements in agriculture.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"287-307"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-050720-122916","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38331787","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: 18
Regulation and Function of RNA Pseudouridylation in Human Cells. RNA假尿嘧啶化在人细胞中的调控和功能。
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-112618-043830
Erin K Borchardt, Nicole M Martinez, Wendy V Gilbert
{"title":"Regulation and Function of RNA Pseudouridylation in Human Cells.","authors":"Erin K Borchardt,&nbsp;Nicole M Martinez,&nbsp;Wendy V Gilbert","doi":"10.1146/annurev-genet-112618-043830","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043830","url":null,"abstract":"<p><p>Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"309-336"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043830","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38331789","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: 61
Pioneer Transcription Factors Initiating Gene Network Changes. 启动基因网络变化的先锋转录因子。
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-030220-015007
Kenneth S Zaret
{"title":"Pioneer Transcription Factors Initiating Gene Network Changes.","authors":"Kenneth S Zaret","doi":"10.1146/annurev-genet-030220-015007","DOIUrl":"https://doi.org/10.1146/annurev-genet-030220-015007","url":null,"abstract":"<p><p>Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA sequence motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inaccessible to other transcription factors. Pioneer factors subsequently enable other transcription factors, nucleosome remodeling complexes, and histone modifiers to engage chromatin, thereby initiating the formation of an activating or repressive regulatory sequence. Thus, pioneer factors endow the competence for fate changes in embryonic development, are essential for cellular reprogramming, and rewire gene networks in cancer cells. Recent studies with reconstituted nucleosomes in vitro and chromatin binding in vivo reveal that pioneer factors can directly perturb nucleosome structure and chromatin accessibility in different ways. This review focuses on our current understanding of the mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to our ability to control cell fates at will.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"367-385"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-030220-015007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344810","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: 197
The Sins of Our Forefathers: Paternal Impacts on De Novo Mutation Rate and Development. 我们祖先的罪过:父系对新生突变率和发育的影响。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-07-14 DOI: 10.1146/annurev-genet-112618-043617
R John Aitken, Geoffry N De Iuliis, Brett Nixon
{"title":"The Sins of Our Forefathers: Paternal Impacts on De Novo Mutation Rate and Development.","authors":"R John Aitken,&nbsp;Geoffry N De Iuliis,&nbsp;Brett Nixon","doi":"10.1146/annurev-genet-112618-043617","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043617","url":null,"abstract":"Spermatogonial stem cells (SSCs) are generally characterized by excellent DNA surveillance and repair, resulting in one of the lowest spontaneous mutation rates in the body. However, the barriers to mutagenesis can be overwhelmed under two sets of circumstances. First, replication errors may generate age-dependent mutations that provide the mutant cells with a selective advantage, leading to the clonal expansions responsible for dominant genetic diseases such as Apert syndrome and achondroplasia. The second mechanism centers on the vulnerability of the male germline to oxidative stress and the induction of oxidative DNA damage in spermatozoa. Defective repair of such oxidative damage in the fertilized oocyte results in the creation of mutations in the zygote that can influence the health and well-being of the offspring. A particular hot spot for such oxidative attack on chromosome 15 has been found to align with several mutations responsible for paternally mediated disease, including cancer, psychiatric disorders, and infertility. Expected final online publication date for the Annual Review of Genetics, Volume 54 is November 23, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"1-24"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043617","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38157710","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: 23
Toxin-Antidote Elements Across the Tree of Life. 生命之树上的毒素解毒剂元素。
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-112618-043659
Alejandro Burga, Eyal Ben-David, Leonid Kruglyak
{"title":"Toxin-Antidote Elements Across the Tree of Life.","authors":"Alejandro Burga,&nbsp;Eyal Ben-David,&nbsp;Leonid Kruglyak","doi":"10.1146/annurev-genet-112618-043659","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043659","url":null,"abstract":"<p><p>In life's constant battle for survival, it takes one to kill but two to conquer. Toxin-antitoxin or toxin-antidote (TA) elements are genetic dyads that cheat the laws of inheritance to guarantee their transmission to the next generation. This seemingly simple genetic arrangement-a toxin linked to its antidote-is capable of quickly spreading and persisting in natural populations. TA elements were first discovered in bacterial plasmids in the 1980s and have recently been characterized in fungi, plants, and animals, where they underlie genetic incompatibilities and sterility in crosses between wild isolates. In this review, we provide a unified view of TA elements in both prokaryotic and eukaryotic organisms and highlight their similarities and differences at the evolutionary, genetic, and molecular levels. Finally, we propose several scenarios that could explain the paradox of the evolutionary origin of TA elements and argue that these elements may be key evolutionary players and that the full scope of their roles is only beginning to be uncovered.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"387-415"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043659","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344806","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: 22
Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria. 细菌中CRISPR-Cas免疫的分子机制
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-08-28 DOI: 10.1146/annurev-genet-022120-112523
Philip M Nussenzweig, Luciano A Marraffini
{"title":"Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria.","authors":"Philip M Nussenzweig,&nbsp;Luciano A Marraffini","doi":"10.1146/annurev-genet-022120-112523","DOIUrl":"https://doi.org/10.1146/annurev-genet-022120-112523","url":null,"abstract":"<p><p>Prokaryotes have developed numerous defense strategies to combat the constant threat posed by the diverse genetic parasites that endanger them. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas loci guard their hosts with an adaptive immune system against foreign nucleic acids. Protection starts with an immunization phase, in which short pieces of the invader's genome, known as spacers, are captured and integrated into the CRISPR locus after infection. Next, during the targeting phase, spacers are transcribed into CRISPR RNAs (crRNAs) that guide CRISPR-associated (Cas) nucleases to destroy the invader's DNA or RNA. Here we describe the many different molecular mechanisms of CRISPR targeting and how they are interconnected with the immunization phase through a third phase of the CRISPR-Cas immune response: primed spacer acquisition. In this phase, Cas proteins direct the crRNA-guided acquisition of additional spacers to achieve a more rapid and robust immunization of the population.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"93-120"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-022120-112523","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38415311","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: 80
Canary in the Coal Mine? Male Infertility as a Marker of Overall Health. 煤矿里的金丝雀?男性不育是整体健康的标志。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 DOI: 10.1146/annurev-genet-022020-023434
Nahid Punjani, Dolores J Lamb
{"title":"Canary in the Coal Mine? Male Infertility as a Marker of Overall Health.","authors":"Nahid Punjani,&nbsp;Dolores J Lamb","doi":"10.1146/annurev-genet-022020-023434","DOIUrl":"https://doi.org/10.1146/annurev-genet-022020-023434","url":null,"abstract":"<p><p>Male factor infertility is a common problem. Evidence is emerging regarding the spectrum of systemic disease and illness harbored by infertile men who otherwise appear healthy. In this review, we present evidence that infertile men have poor overall health and increased morbidity and mortality, increased rates of both genitourinary and non-genitourinary malignancy, and greater risks of systemic disease. The review also highlights numerous genetic conditions associated with male infertility as well as emerging translational evidence of genitourinary birth defects and their impact on male infertility. Finally, parallels to the overall health of infertile women are presented. This review highlights the importance of a comprehensive health evaluation of men who present for an infertility assessment.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"465-486"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-022020-023434","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38635974","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: 14
Brown Algal Model Organisms. 褐藻模式生物
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 DOI: 10.1146/annurev-genet-030620-093031
Susana M Coelho, J Mark Cock
{"title":"Brown Algal Model Organisms.","authors":"Susana M Coelho, J Mark Cock","doi":"10.1146/annurev-genet-030620-093031","DOIUrl":"10.1146/annurev-genet-030620-093031","url":null,"abstract":"<p><p>Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga <i>Ectocarpus</i> has led to it emerging as a general model system for this group, but additional models, such as <i>Fucus</i> or <i>Dictyota dichotoma</i>, remain of interest for specific biological questions. In addition, <i>Saccharina japonica</i> has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"71-92"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-030620-093031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38635975","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: 13
Histone Variants: The Nexus of Developmental Decisions and Epigenetic Memory. 组蛋白变异:发育决定和表观遗传记忆的关系。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-08-28 DOI: 10.1146/annurev-genet-022620-100039
Benjamin Loppin, Frédéric Berger
{"title":"Histone Variants: The Nexus of Developmental Decisions and Epigenetic Memory.","authors":"Benjamin Loppin,&nbsp;Frédéric Berger","doi":"10.1146/annurev-genet-022620-100039","DOIUrl":"https://doi.org/10.1146/annurev-genet-022620-100039","url":null,"abstract":"<p><p>Nucleosome dynamics and properties are central to all forms of genomic activities. Among the core histones, H3 variants play a pivotal role in modulating nucleosome structure and function. Here, we focus on the impact of H3 variants on various facets of development. The deposition of the replicative H3 variant following DNA replication is essential for the transmission of the epigenomic information encoded in posttranscriptional modifications. Through this process, replicative H3 maintains cell fate while, in contrast, the replacement H3.3 variant opposes cell differentiation during early embryogenesis. In later steps of development, H3.3 and specialized H3 variants are emerging as new, important regulators of terminal cell differentiation, including neurons and gametes. The specific pathways that regulate the dynamics of the deposition of H3.3 are paramount during reprogramming events that drive zygotic activation and the initiation of a new cycle of development.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"121-149"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-022620-100039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38319654","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: 28
Evolutionary Genomics of High Fecundity. 高繁殖力进化基因组学。
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-021920-095932
Bjarki Eldon
{"title":"Evolutionary Genomics of High Fecundity.","authors":"Bjarki Eldon","doi":"10.1146/annurev-genet-021920-095932","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-095932","url":null,"abstract":"<p><p>Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations provide an important contrast to the low-fecundity organisms that have traditionally been applied in evolutionary studies. A key question regarding high fecundity is whether large numbers of offspring are produced on a regular basis, by few individuals each time, in a sweepstakes mode of reproduction. Such reproduction characteristics are not incorporated into the classical Wright-Fisher model, the standard reference model of population genetics, or similar types of models, in which each individual can produce only small numbers of offspring relative to the population size. The expected genomic footprints of population genetic models of sweepstakes reproduction are very different from those of the Wright-Fisher model. A key, immediate issue involves identifying the footprints of sweepstakes reproduction in genomic data. Whole-genome sequencing data can be used to distinguish the patterns made by sweepstakes reproduction from the patterns made by population growth in a population evolving according to the Wright-Fisher model (or similar models). If the hypothesis of sweepstakes reproduction cannot be rejected, then models of sweepstakes reproduction and associated multiple-merger coalescents will become at least as relevant as the Wright-Fisher model (or similar models) and the Kingman coalescent, the cornerstones of mathematical population genetics, in further discussions of evolutionary genomics of highly fecund populations.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"213-236"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-095932","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38330889","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: 9
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