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Annual review of genetics最新文献

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Genotype-Phenotype Relationships in the Context of Transcriptional Adaptation and Genetic Robustness. 转录适应和遗传稳健性背景下的基因型-表型关系。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-07-27 DOI: 10.1146/annurev-genet-071719-020342
Gabrielius Jakutis, Didier Y R Stainier
{"title":"Genotype-Phenotype Relationships in the Context of Transcriptional Adaptation and Genetic Robustness.","authors":"Gabrielius Jakutis,&nbsp;Didier Y R Stainier","doi":"10.1146/annurev-genet-071719-020342","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020342","url":null,"abstract":"<p><p>Genetic manipulations with a robust and predictable outcome are critical to investigate gene function, as well as for therapeutic genome engineering. For many years, knockdown approaches and reagents including RNA interference and antisense oligonucleotides dominated functional studies; however, with the advent of precise genome editing technologies, CRISPR-based knockout systems have become the state-of-the-art tools for such studies. These technologies have helped decipher the role of thousands of genes in development and disease. Their use has also revealed how limited our understanding of genotype-phenotype relationships is. The recent discovery that certain mutations can trigger the transcriptional modulation of other genes, a phenomenon called transcriptional adaptation, has provided an additional explanation for the contradicting phenotypes observed in knockdown versus knockout models and increased awareness about the use of each of these approaches. In this review, we first cover the strengths and limitations of different gene perturbation strategies. Then we highlight the diverse ways in which the genotype-phenotype relationship can be discordant between these different strategies. Finally, we review the genetic robustness mechanisms that can lead to such discrepancies, paying special attention to the recently discovered phenomenon of transcriptional adaptation.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"71-91"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39226048","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
DNA End Resection: Mechanism and Control. DNA末端切除:机制和控制。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 DOI: 10.1146/annurev-genet-071719-020312
Petr Cejka, Lorraine S Symington
{"title":"DNA End Resection: Mechanism and Control.","authors":"Petr Cejka,&nbsp;Lorraine S Symington","doi":"10.1146/annurev-genet-071719-020312","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020312","url":null,"abstract":"<p><p>DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genome integrity and cell viability. Typically, cells repair DSBs by either nonhomologous end joining (NHEJ) or homologous recombination (HR). The relative use of these two pathways depends on many factors, including cell cycle stage and the nature of the DNA ends. A critical determinant of repair pathway selection is the initiation of 5'→3' nucleolytic degradation of DNA ends, a process referred to as DNA end resection. End resection is essential to create single-stranded DNA overhangs, which serve as the substrate for the Rad51 recombinase to initiate HR and are refractory to NHEJ repair. Here, we review recent insights into the mechanisms of end resection, how it is regulated, and the pathological consequences of its dysregulation.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"285-307"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39651662","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: 73
How to Switch from Mitosis to Meiosis: Regulation of Germline Entry in Plants. 如何从有丝分裂转向减数分裂:植物种系进入的调控。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-16 DOI: 10.1146/annurev-genet-112618-043553
Franziska Böwer, Arp Schnittger
{"title":"How to Switch from Mitosis to Meiosis: Regulation of Germline Entry in Plants.","authors":"Franziska Böwer,&nbsp;Arp Schnittger","doi":"10.1146/annurev-genet-112618-043553","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043553","url":null,"abstract":"<p><p>One of the major cell fate transitions in eukaryotes is entry into meiosis. While in single-celled yeast this decision is triggered by nutrient starvation, in multicellular eukaryotes, such as plants, it is under developmental control. In contrast to animals, plants have only a short germline and instruct cells to become meiocytes in reproductive organs late in development. This situation argues for a fundamentally different mechanism of how plants recruit meiocytes, and consistently, none of the regulators known to control meiotic entry in yeast and animals are present in plants. In recent years, several factors involved in meiotic entry have been identified, especially in the model plant <i>Arabidopsis</i>, and pieces of a regulatory network of germline control in plants are emerging. However, the corresponding studies also show that the mechanisms of meiotic entry control are diversified in flowering plants, calling for further analyses in different plant species.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"427-452"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39422784","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: 7
Drosophila sechellia: A Genetic Model for Behavioral Evolution and Neuroecology. 果蝇:行为进化和神经生态学的遗传模型。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-16 DOI: 10.1146/annurev-genet-071719-020719
Thomas O Auer, Michael P Shahandeh, Richard Benton
{"title":"<i>Drosophila sechellia</i>: A Genetic Model for Behavioral Evolution and Neuroecology.","authors":"Thomas O Auer,&nbsp;Michael P Shahandeh,&nbsp;Richard Benton","doi":"10.1146/annurev-genet-071719-020719","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020719","url":null,"abstract":"<p><p>Defining the mechanisms by which animals adapt to their ecological niche is an important problem bridging evolution, genetics, and neurobiology. We review the establishment of a powerful genetic model for comparative behavioral analysis and neuroecology, <i>Drosophila sechellia</i>. This island-endemic fly species is closely related to several cosmopolitan generalists, including <i>Drosophila melanogaster</i>, but has evolved extreme specialism, feeding and reproducing exclusively on the noni fruit of the tropical shrub <i>Morinda citrifolia</i>. We first describe the development and use of genetic approaches to facilitate genotype/phenotype associations in these drosophilids. Next, we survey the behavioral, physiological, and morphological adaptations of <i>D. sechellia</i> throughout its life cycle and outline our current understanding of the genetic and cellular basis of these traits. Finally, we discuss the principles this knowledge begins to establish in the context of host specialization, speciation, and the neurobiology of behavioral evolution and consider open questions and challenges in the field.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"527-554"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39422782","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
Cellular and Molecular Mechanisms Linking Human Cortical Development and Evolution. 连接人类皮质发育和进化的细胞和分子机制。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-17 DOI: 10.1146/annurev-genet-071719-020705
Baptiste Libé-Philippot, Pierre Vanderhaeghen
{"title":"Cellular and Molecular Mechanisms Linking Human Cortical Development and Evolution.","authors":"Baptiste Libé-Philippot,&nbsp;Pierre Vanderhaeghen","doi":"10.1146/annurev-genet-071719-020705","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020705","url":null,"abstract":"<p><p>The cerebral cortex is at the core of brain functions that are thought to be particularly developed in the human species. Human cortex specificities stem from divergent features of corticogenesis, leading to increased cortical size and complexity. Underlying cellular mechanisms include prolonged patterns of neuronal generation and maturation, as well as the amplification of specific types of stem/progenitor cells. While the gene regulatory networks of corticogenesis appear to be largely conserved among all mammals including humans, they have evolved in primates, particularly in the human species, through the emergence of rapidly divergent transcriptional regulatory elements, as well as recently duplicated novel genes. These human-specific molecular features together control key cellular milestones of human corticogenesis and are often affected in neurodevelopmental disorders, thus linking human neural development, evolution, and diseases.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"555-581"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39426585","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: 24
Genetics of Shoot Meristem and Shoot Regeneration. 嫩枝分生组织的遗传与嫩枝再生。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-21 DOI: 10.1146/annurev-genet-071719-020439
Leor Eshed Williams
{"title":"Genetics of Shoot Meristem and Shoot Regeneration.","authors":"Leor Eshed Williams","doi":"10.1146/annurev-genet-071719-020439","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020439","url":null,"abstract":"<p><p>Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"661-681"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39435406","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: 19
The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth. 酵母假菌丝生长的复杂遗传基础和多层调控。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-07-19 DOI: 10.1146/annurev-genet-071719-020249
Anuj Kumar
{"title":"The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth.","authors":"Anuj Kumar","doi":"10.1146/annurev-genet-071719-020249","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020249","url":null,"abstract":"<p><p>Eukaryotic cells are exquisitely responsive to external and internal cues, achieving precise control of seemingly diverse growth processes through a complex interplay of regulatory mechanisms. The budding yeast <i>Saccharomyces cerevisiae</i> provides a fascinating model of cell growth in its stress-responsive transition from planktonic single cells to a filamentous pseudohyphal growth form. During pseudohyphal growth, yeast cells undergo changes in morphology, polarity, and adhesion to form extended and invasive multicellular filaments. This pseudohyphal transition has been studied extensively as a model of conserved signaling pathways regulating cell growth and for its relevance in understanding the pathogenicity of the related opportunistic fungus <i>Candida albicans</i>, wherein filamentous growth is required for virulence. This review highlights the broad gene set enabling yeast pseudohyphal growth, signaling pathways that regulate this process, the role and regulation of proteins conferring cell adhesion, and interesting regulatory mechanisms enabling the pseudohyphal transition.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"1-21"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39202336","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
Brain Repair by Cell Replacement via In Situ Neuronal Reprogramming. 通过原位神经元重编程实现细胞替换的脑修复。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-07-26 DOI: 10.1146/annurev-genet-071719-023616
Hao Qian, Xiang-Dong Fu
{"title":"Brain Repair by Cell Replacement via In Situ Neuronal Reprogramming.","authors":"Hao Qian,&nbsp;Xiang-Dong Fu","doi":"10.1146/annurev-genet-071719-023616","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-023616","url":null,"abstract":"<p><p>Neurodegenerative diseases, characterized by progressive neural loss, have been some of the most challenging medical problems in aging societies. Treatment strategies such as symptom management have little impact on disease progression, while intervention with specific disease mechanisms may only slow down disease progression. One therapeutic strategy that has the potential to reverse the disease phenotype is to replenish neurons and rebuild the pathway lost to degeneration. Although it is generally believed that the central nervous system has lost the capability to regenerate, increasing evidence indicates that the brain is more plastic than previously thought, containing perhaps the biggest repertoire of cells with latent neurogenic programs in the body. This review focuses on key advances in generating new neurons through in situ neuronal reprogramming, which is tied to fundamental questions regarding adult neurogenesis, cell source, and mechanisms for neuronal reprogramming, as well as the ability of new neurons to integrate into the existing circuitry.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"45-69"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39223126","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 Regulation of RIPK1 and Necroptosis. RIPK1与坏死下垂的遗传调控。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 DOI: 10.1146/annurev-genet-071719-022748
Daichao Xu, Chengyu Zou, Junying Yuan
{"title":"Genetic Regulation of RIPK1 and Necroptosis.","authors":"Daichao Xu,&nbsp;Chengyu Zou,&nbsp;Junying Yuan","doi":"10.1146/annurev-genet-071719-022748","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-022748","url":null,"abstract":"<p><p>The receptor-interacting protein kinase 1 (RIPK1) is recognized as a master upstream regulator that controls cell survival and inflammatory signaling as well as multiple cell death pathways, including apoptosis and necroptosis. The activation of RIPK1 kinase is extensively modulated by ubiquitination and phosphorylation, which are mediated by multiple factors that also control the activation of the NF-κB pathway. We discuss current findings regarding the genetic modulation of RIPK1 that controls its activation and interaction with downstream mediators, such as caspase-8 and RIPK3, to promote apoptosis and necroptosis. We also address genetic autoinflammatory human conditions that involve abnormal activation of RIPK1. Leveraging these new genetic and mechanistic insights, we postulate how an improved understanding of RIPK1 biology may support the development of therapeutics that target RIPK1 for the treatment of human inflammatory and neurodegenerative diseases.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"235-263"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39904019","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: 20
A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons. 神经元树突和轴突中mRNA和局部合成蛋白群的功能解剖。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-08-30 DOI: 10.1146/annurev-genet-030321-054851
Julio D Perez, Claudia M Fusco, Erin M Schuman
{"title":"A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons.","authors":"Julio D Perez,&nbsp;Claudia M Fusco,&nbsp;Erin M Schuman","doi":"10.1146/annurev-genet-030321-054851","DOIUrl":"https://doi.org/10.1146/annurev-genet-030321-054851","url":null,"abstract":"<p><p>Neurons are characterized by a complex morphology that enables the generation of subcellular compartments with unique biochemical and biophysical properties, such as dendrites, axons, and synapses. To sustain these different compartments and carry a wide array of elaborate operations, neurons express a diverse repertoire of gene products. Extensive regulation at both the messenger RNA (mRNA) and protein levels allows for the differentiation of subcellular compartments as well as numerous forms of plasticity in response to variable stimuli. Among the multiple mechanisms that control cellular functions, mRNA translation is manipulated by neurons to regulate where and when a protein emerges. Interestingly, transcriptomic and translatomic profiles of both dendrites and axons have revealed that the mRNA population only partially predicts the local protein population and that this relation significantly varies between different gene groups. Here, we describe the space that local translation occupies within the large molecular and regulatory complexity of neurons, in contrast to other modes of regulation. We then discuss the specialized organization of mRNAs within different neuronal compartments, as revealed by profiles of the local transcriptome. Finally, we discuss the features and functional implications of both locally correlated-and anticorrelated-mRNA-protein relations both under baseline conditions and during synaptic plasticity.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"183-207"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39367371","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: 20
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