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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
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
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