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Annual review of genetics最新文献

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Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. 利用单细胞群体揭示复杂性状的遗传基础。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-08-10 DOI: 10.1146/annurev-genet-022123-110824
Mark A A Minow, Alexandre P Marand, Robert J Schmitz
{"title":"Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits.","authors":"Mark A A Minow, Alexandre P Marand, Robert J Schmitz","doi":"10.1146/annurev-genet-022123-110824","DOIUrl":"10.1146/annurev-genet-022123-110824","url":null,"abstract":"<p><p>The ease and throughput of single-cell genomics have steadily improved, and its current trajectory suggests that surveying single-cell populations will become routine. We discuss the merger of quantitative genetics with single-cell genomics and emphasize how this synergizes with advantages intrinsic to plants. Single-cell population genomics provides increased detection resolution when mapping variants that control molecular traits, including gene expression or chromatin accessibility. Additionally, single-cell population genomics reveals the cell types in which variants act and, when combined with organism-level phenotype measurements, unveils which cellular contexts impact higher-order traits. Emerging technologies, notably multiomics, can facilitate the measurement of both genetic changes and genomic traits in single cells, enabling single-cell genetic experiments. The implementation of single-cell genetics will advance the investigation of the genetic architecture of complex molecular traits and provide new experimental paradigms to study eukaryotic genetics.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"297-319"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10775913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9974614","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
Integrating Complex Life Cycles in Comparative Developmental Biology. 比较发育生物学中复杂生命周期的整合。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-08-16 DOI: 10.1146/annurev-genet-071719-020641
Laurent Formery, Christopher J Lowe
{"title":"Integrating Complex Life Cycles in Comparative Developmental Biology.","authors":"Laurent Formery, Christopher J Lowe","doi":"10.1146/annurev-genet-071719-020641","DOIUrl":"10.1146/annurev-genet-071719-020641","url":null,"abstract":"<p><p>The goal of comparative developmental biology is identifying mechanistic differences in embryonic development between different taxa and how these evolutionary changes have led to morphological and organizational differences in adult body plans. Much of this work has focused on direct-developing species in which the adult forms straight from the embryo and embryonic modifications have direct effects on the adult. However, most animal lineages are defined by indirect development, in which the embryo gives rise to a larval body plan and the adult forms by transformation of the larva. Historically, much of our understanding of complex life cycles is viewed through the lenses of ecology and zoology. In this review, we discuss the importance of establishing developmental rather than morphological or ecological criteria for defining developmental mode and explicitly considering the evolutionary implications of incorporating complex life cycles into broad developmental comparisons of embryos across metazoans.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"321-339"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10004512","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: 0
RNA Repair: Hiding in Plain Sight. RNA修复:隐藏在视线之中。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-09-18 DOI: 10.1146/annurev-genet-071719-021856
Stewart Shuman
{"title":"RNA Repair: Hiding in Plain Sight.","authors":"Stewart Shuman","doi":"10.1146/annurev-genet-071719-021856","DOIUrl":"10.1146/annurev-genet-071719-021856","url":null,"abstract":"<p><p>Enzymes that phosphorylate, dephosphorylate, and ligate RNA 5' and 3' ends were discovered more than half a century ago and were eventually shown to repair purposeful site-specific endonucleolytic breaks in the RNA phosphodiester backbone. The pace of discovery and characterization of new candidate RNA repair activities in taxa from all phylogenetic domains greatly exceeds our understanding of the biological pathways in which they act. The key questions anent RNA break repair in vivo are (<i>a</i>) identifying the triggers, agents, and targets of RNA cleavage and (<i>b</i>) determining whether RNA repair results in restoration of the original RNA, modification of the RNA (by loss or gain at the ends), or rearrangements of the broken RNA segments (i.e., RNA recombination). This review provides a perspective on the discovery, mechanisms, and physiology of purposeful RNA break repair, highlighting exemplary repair pathways (e.g., tRNA restriction-repair and tRNA splicing) for which genetics has figured prominently in their elucidation.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"461-489"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10301472","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: 0
Pooled Genome-Scale CRISPR Screens in Single Cells. 单个细胞的基因组级CRISPR筛选。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-08-10 DOI: 10.1146/annurev-genet-072920-013842
Daniel Schraivogel, Lars M Steinmetz, Leopold Parts
{"title":"Pooled Genome-Scale CRISPR Screens in Single Cells.","authors":"Daniel Schraivogel, Lars M Steinmetz, Leopold Parts","doi":"10.1146/annurev-genet-072920-013842","DOIUrl":"10.1146/annurev-genet-072920-013842","url":null,"abstract":"<p><p>Assigning functions to genes and learning how to control their expression are part of the foundation of cell biology and therapeutic development. An efficient and unbiased method to accomplish this is genetic screening, which historically required laborious clone generation and phenotyping and is still limited by scale today. The rapid technological progress on modulating gene function with CRISPR-Cas and measuring it in individual cells has now relaxed the major experimental constraints and enabled pooled screening with complex readouts from single cells. Here, we review the principles and practical considerations for pooled single-cell CRISPR screening. We discuss perturbation strategies, experimental model systems, matching the perturbation to the individual cells, reading out cell phenotypes, and data analysis. Our focus is on single-cell RNA sequencing and cell sorting-based readouts, including image-enabled cell sorting. We expect this transformative approach to fuel biomedical research for the next several decades.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"223-244"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9974608","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: 0
Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach. 解开珊瑚-鞭毛藻共生的复杂细胞生物学:模型系统方法。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-09-18 DOI: 10.1146/annurev-genet-072320-125436
Marie R Jacobovitz, Elizabeth A Hambleton, Annika Guse
{"title":"Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach.","authors":"Marie R Jacobovitz, Elizabeth A Hambleton, Annika Guse","doi":"10.1146/annurev-genet-072320-125436","DOIUrl":"10.1146/annurev-genet-072320-125436","url":null,"abstract":"<p><p>Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"411-434"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10301475","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: 0
Interplay Between Antimicrobial Resistance and Global Environmental Change. 抗菌素耐药性与全球环境变化的相互作用。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-09-14 DOI: 10.1146/annurev-genet-022123-113904
María Mercedes Zambrano
{"title":"Interplay Between Antimicrobial Resistance and Global Environmental Change.","authors":"María Mercedes Zambrano","doi":"10.1146/annurev-genet-022123-113904","DOIUrl":"10.1146/annurev-genet-022123-113904","url":null,"abstract":"<p><p>Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"275-296"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233151","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: 0
Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility. 诱导多能干细胞在疾病生物学中的应用及其体外应用证据。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-09-14 DOI: 10.1146/annurev-genet-022123-090319
Ayodeji Adegunsoye, Natalia M Gonzales, Yoav Gilad
{"title":"Induced Pluripotent Stem Cells in Disease Biology and the Evidence for Their In Vitro Utility.","authors":"Ayodeji Adegunsoye, Natalia M Gonzales, Yoav Gilad","doi":"10.1146/annurev-genet-022123-090319","DOIUrl":"10.1146/annurev-genet-022123-090319","url":null,"abstract":"<p><p>Many human phenotypes are impossible to recapitulate in model organisms or immortalized human cell lines. Induced pluripotent stem cells (iPSCs) offer a way to study disease mechanisms in a variety of differentiated cell types while circumventing ethical and practical issues associated with finite tissue sources and postmortem states. Here, we discuss the broad utility of iPSCs in genetic medicine and describe how they are being used to study musculoskeletal, pulmonary, neurologic, and cardiac phenotypes. We summarize the particular challenges presented by each organ system and describe how iPSC models are being used to address them. Finally, we discuss emerging iPSC-derived organoid models and the potential value that they can bring to studies of human disease.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"341-360"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10240258","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: 0
Asymmetric Stem Cell Division and Germline Immortality. 不对称干细胞分裂和生殖系不朽。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-08-08 DOI: 10.1146/annurev-genet-022123-040039
Yukiko M Yamashita
{"title":"Asymmetric Stem Cell Division and Germline Immortality.","authors":"Yukiko M Yamashita","doi":"10.1146/annurev-genet-022123-040039","DOIUrl":"10.1146/annurev-genet-022123-040039","url":null,"abstract":"<p><p>Germ cells are the only cell type that is capable of transmitting genetic information to the next generation, which has enabled the continuation of multicellular life for the last 1.5 billion years. Surprisingly little is known about the mechanisms supporting the germline's remarkable ability to continue in this eternal cycle, termed germline immortality. Even unicellular organisms age at a cellular level, demonstrating that cellular aging is inevitable. Extensive studies in yeast have established the framework of how asymmetric cell division and gametogenesis may contribute to the resetting of cellular age. This review examines the mechanisms of germline immortality-how germline cells reset the aging of cells-drawing a parallel between yeast and multicellular organisms.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"181-199"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9959866","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: 0
Meiosis: Dances Between Homologs. 减数分裂：同性恋之间的舞蹈。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 Epub Date: 2023-10-03 DOI: 10.1146/annurev-genet-061323-044915
Denise Zickler, Nancy Kleckner
{"title":"Meiosis: Dances Between Homologs.","authors":"Denise Zickler, Nancy Kleckner","doi":"10.1146/annurev-genet-061323-044915","DOIUrl":"10.1146/annurev-genet-061323-044915","url":null,"abstract":"<p><p>The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"1-63"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41103352","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: 0
The Clockwork Embryo: Mechanisms Regulating Developmental Rate. 发条胚胎:调节发育速率的机制。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2023-11-27 DOI: 10.1146/annurev-genet-022123-104503
Margarete Diaz-Cuadros, Olivier Pourquié
{"title":"The Clockwork Embryo: Mechanisms Regulating Developmental Rate.","authors":"Margarete Diaz-Cuadros, Olivier Pourquié","doi":"10.1146/annurev-genet-022123-104503","DOIUrl":"10.1146/annurev-genet-022123-104503","url":null,"abstract":"<p><p>Organismal development requires the reproducible unfolding of an ordered sequence of discrete steps (cell fate determination, migration, tissue folding, etc.) in both time and space. Here, we review the mechanisms that grant temporal specificity to developmental steps, including molecular clocks and timers. Individual timing mechanisms must be coordinated with each other to maintain the overall developmental sequence. However, phenotypic novelties can also arise through the modification of temporal patterns over the course of evolution. Two main types of variation in temporal patterning characterize interspecies differences in developmental time: allochrony, where the overall developmental sequence is either accelerated or slowed down while maintaining the relative duration of individual steps, and heterochrony, where the duration of specific developmental steps is altered relative to the rest. New advances in in vitro modeling of mammalian development using stem cells have recently enabled the revival of mechanistic studies of allochrony and heterochrony. In both cases, differences in the rate of basic cellular functions such as splicing, translation, protein degradation, and metabolism seem to underlie differences in developmental time. In the coming years, these studies should identify the genetic differences that drive divergence in developmental time between species.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"57 ","pages":"117-134"},"PeriodicalIF":11.1,"publicationDate":"2023-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138443647","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: 0
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