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Annual review of genetics最新文献

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The Genetics of Autophagy in Multicellular Organisms. 多细胞生物自噬的遗传学。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 DOI: 10.1146/annurev-genet-022422-095608
Hong Zhang
{"title":"The Genetics of Autophagy in Multicellular Organisms.","authors":"Hong Zhang","doi":"10.1146/annurev-genet-022422-095608","DOIUrl":"https://doi.org/10.1146/annurev-genet-022422-095608","url":null,"abstract":"<p><p>Autophagy, a lysosome-mediated degradation process evolutionarily conserved from yeast to mammals, is essential for maintaining cellular homeostasis and combating diverse cellular stresses. Autophagy involves de novo synthesis of a double-membrane autophagosome, sequestration of selected cellular contents, and subsequent delivery of sequestrated contents to the vacuole (in yeasts and plants) or to lysosomes (in animal cells) for degradation and recycling. Genetic studies in unicellular and multicellular model organisms have systematically revealed the molecular machinery, regulation, and function of autophagy in physiological settings. I review genetic studies in model organisms-from yeast to worm to fly-that enable us to not only identify autophagy genes, including <i>ATG</i> genes and the metazoan-specific <i>EPG</i> genes, but also uncover variants of autophagy in developmental contexts, novel regulatory mechanisms, and signaling events involved in mediating systemic autophagy response. Genetic analysis also helps us understand the liquid-liquid phase separation and transition that control autophagic degradation of protein aggregates. The emerging role of autophagy in zebrafish tissue regeneration is also discussed.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"17-39"},"PeriodicalIF":11.1,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10732099","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: 3
Genome Maintenance in Mammalian Stem Cells. 哺乳动物干细胞的基因组维持。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 DOI: 10.1146/annurev-genet-072920-022154
John C Schimenti, Rui Huang, Liangdao Li, Ryan James
{"title":"Genome Maintenance in Mammalian Stem Cells.","authors":"John C Schimenti,&nbsp;Rui Huang,&nbsp;Liangdao Li,&nbsp;Ryan James","doi":"10.1146/annurev-genet-072920-022154","DOIUrl":"https://doi.org/10.1146/annurev-genet-072920-022154","url":null,"abstract":"<p><p>Various stem cells in the body are tasked with maintaining tissue homeostasis throughout the life of an organism and thus must be resilient to intrinsic and extrinsic challenges such as infection and injury. Crucial to these challenges is genome maintenance because a high mutational load and persistent DNA lesions impact the production of essential gene products at proper levels and compromise optimal stem cell renewal and differentiation. Genome maintenance requires a robust and well-regulated DNA damage response suited to maintaining specific niches and tissues. In this review, we explore the similarities and differences between diverse stem cell types derived from (or preceding) all germ layers, including extraembryonic tissues. These cells utilize different strategies, including implementation of robust repair mechanisms, modulation of cell cycle checkpoints best suited to eliminating compromised cells, minimization of cell divisions, and differentiation in response to excessive damage.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"145-164"},"PeriodicalIF":11.1,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10750333","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
Asymmetric Histone Inheritance: Establishment, Recognition, and Execution. 不对称组蛋白遗传:建立、识别和执行。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 DOI: 10.1146/annurev-genet-072920-125226
Jennifer A Urban, Rajesh Ranjan, Xin Chen
{"title":"Asymmetric Histone Inheritance: Establishment, Recognition, and Execution.","authors":"Jennifer A Urban,&nbsp;Rajesh Ranjan,&nbsp;Xin Chen","doi":"10.1146/annurev-genet-072920-125226","DOIUrl":"https://doi.org/10.1146/annurev-genet-072920-125226","url":null,"abstract":"<p><p>The discovery of biased histone inheritance in asymmetrically dividing <i>Drosophila melanogaster</i> male germline stem cells demonstrates one means to produce two distinct daughter cells with identical genetic material. This inspired further studies in different systems, which revealed that this phenomenon may be a widespread mechanism to introduce cellular diversity. While the extent of asymmetric histone inheritance could vary among systems, this phenomenon is proposed to occur in three steps: first, establishment of histone asymmetry between sister chromatids during DNA replication; second, recognition of sister chromatids carrying asymmetric histone information during mitosis; and third, execution of this asymmetry in the resulting daughter cells. By compiling the current knowledge from diverse eukaryotic systems, this review comprehensively details and compares known chromatin factors, mitotic machinery components, and cell cycle regulators that may contribute to each of these three steps. Also discussed are potential mechanisms that introduce and regulate variable histone inheritance modes and how these different modes may contribute to cell fate decisions in multicellular organisms.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"113-143"},"PeriodicalIF":11.1,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10054593/pdf/nihms-1881686.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9262808","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: 1
APOBEC-Induced Mutagenesis in Cancer. apobecc诱导的癌症突变。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 DOI: 10.1146/annurev-genet-072920-035840
Tony M Mertz, Christopher D Collins, Madeline Dennis, Margo Coxon, Steven A Roberts
{"title":"APOBEC-Induced Mutagenesis in Cancer.","authors":"Tony M Mertz,&nbsp;Christopher D Collins,&nbsp;Madeline Dennis,&nbsp;Margo Coxon,&nbsp;Steven A Roberts","doi":"10.1146/annurev-genet-072920-035840","DOIUrl":"https://doi.org/10.1146/annurev-genet-072920-035840","url":null,"abstract":"<p><p>The initiation, progression, and relapse of cancers often result from mutations occurring within somatic cells. Consequently, processes that elevate mutation rates accelerate carcinogenesis and hinder the development of long-lasting therapeutics. Recent sequencing of human cancer genomes has identified patterns of mutations, termed mutation signatures, many of which correspond to specific environmentally induced and endogenous mutation processes. Some of the most frequently observed mutation signatures are caused by dysregulated activity of APOBECs, which deaminate cytidines in single-stranded DNA at specific sequence motifs causing C-to-T and C-to-G substitutions. In humans, APOBEC-generated genetic heterogeneity in tumor cells contributes to carcinogenesis, metastasis, and resistance to therapeutics. Here, we review the current understanding of APOBECs' role in cancer mutagenesis and impact on disease and the biological processes that influence APOBEC mutagenic capacity.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"229-252"},"PeriodicalIF":11.1,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10381887","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: 11
The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. 植物基因组及其他转座因子生命周期的表观遗传控制。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 DOI: 10.1146/annurev-genet-072920-015534
Peng Liu, Diego Cuerda-Gil, Saima Shahid, R Keith Slotkin
{"title":"The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond.","authors":"Peng Liu,&nbsp;Diego Cuerda-Gil,&nbsp;Saima Shahid,&nbsp;R Keith Slotkin","doi":"10.1146/annurev-genet-072920-015534","DOIUrl":"https://doi.org/10.1146/annurev-genet-072920-015534","url":null,"abstract":"<p><p>Within the life cycle of a living organism, another life cycle exists for the selfish genome inhabitants, which are called transposable elements (TEs). These mobile sequences invade, duplicate, amplify, and diversify within a genome, increasing the genome's size and generating new mutations. Cells act to defend their genome, but rather than permanently destroying TEs, they use chromatin-level repression and epigenetic inheritance to silence TE activity. This level of silencing is ephemeral and reversible, leading to a dynamic equilibrium between TE suppression and reactivation within a host genome. The coexistence of the TE and host genome can also lead to the domestication of the TE to serve in host genome evolution and function. In this review, we describe the life cycle of a TE, with emphasis on how epigenetic regulation is harnessed to control TEs for host genome stability and innovation.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"63-87"},"PeriodicalIF":11.1,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10385650","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
Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. 生殖发生：探索内源性年轻化程序，了解细胞老化和质量控制。
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 Epub Date: 2022-07-25 DOI: 10.1146/annurev-genet-080320-025104
Tina L Sing, Gloria A Brar, Elçin Ünal
{"title":"Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control.","authors":"Tina L Sing, Gloria A Brar, Elçin Ünal","doi":"10.1146/annurev-genet-080320-025104","DOIUrl":"10.1146/annurev-genet-080320-025104","url":null,"abstract":"<p><p>Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"89-112"},"PeriodicalIF":8.7,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9712276/pdf/nihms-1845767.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10835946","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
Scalable Functional Assays for the Interpretation of Human Genetic Variation. 用于解释人类遗传变异的可扩展功能测试。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 Epub Date: 2022-09-02 DOI: 10.1146/annurev-genet-072920-032107
Daniel Tabet, Victoria Parikh, Prashant Mali, Frederick P Roth, Melina Claussnitzer
{"title":"Scalable Functional Assays for the Interpretation of Human Genetic Variation.","authors":"Daniel Tabet, Victoria Parikh, Prashant Mali, Frederick P Roth, Melina Claussnitzer","doi":"10.1146/annurev-genet-072920-032107","DOIUrl":"10.1146/annurev-genet-072920-032107","url":null,"abstract":"<p><p>Scalable sequence-function studies have enabled the systematic analysis and cataloging of hundreds of thousands of coding and noncoding genetic variants in the human genome. This has improved clinical variant interpretation and provided insights into the molecular, biophysical, and cellular effects of genetic variants at an astonishing scale and resolution across the spectrum of allele frequencies. In this review, we explore current applications and prospects for the field and outline the principles underlying scalable functional assay design, with a focus on the study of single-nucleotide coding and noncoding variants.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"441-465"},"PeriodicalIF":11.1,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10765852","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
Quiescence in Saccharomyces cerevisiae. 酿酒酵母的静止状态。
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 DOI: 10.1146/annurev-genet-080320-023632
Linda L Breeden, Toshio Tsukiyama
{"title":"Quiescence in <i>Saccharomyces cerevisiae</i>.","authors":"Linda L Breeden, Toshio Tsukiyama","doi":"10.1146/annurev-genet-080320-023632","DOIUrl":"10.1146/annurev-genet-080320-023632","url":null,"abstract":"<p><p>Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in <i>Saccharomyces cerevisiae</i>, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"253-278"},"PeriodicalIF":8.7,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10065535","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
The Awesome Power of Human Genetics of Infectious Disease. 人类传染病遗传学的惊人力量。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 DOI: 10.1146/annurev-genet-080320-010449
Kyle D Gibbs, Benjamin H Schott, Dennis C Ko
{"title":"The Awesome Power of Human Genetics of Infectious Disease.","authors":"Kyle D Gibbs,&nbsp;Benjamin H Schott,&nbsp;Dennis C Ko","doi":"10.1146/annurev-genet-080320-010449","DOIUrl":"https://doi.org/10.1146/annurev-genet-080320-010449","url":null,"abstract":"<p><p>Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility to infectious diseases. This is exemplified by multiple loci associated with leprosy, malaria, HIV, tuberculosis, and coronavirus disease 2019 (COVID-19), which illuminate genetic architecture and implicate pathways underlying pathophysiology. Despite these successes, most of the heritability of infectious diseases remains to be explained. As the field advances, current limitations may be overcome by applying methodological innovations such as cellular GWA studies and phenome-wide association (PheWA) studies as well as by improving methodological rigor with more precise case definitions, deeper phenotyping, increased cohort diversity, and functional validation of candidate loci in the laboratory or human challenge studies.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"41-62"},"PeriodicalIF":11.1,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9674325","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: 3
Enhancer Function and Evolutionary Roles of Human Accelerated Regions. 人类加速区的增强子功能和进化作用
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2022-11-30 Epub Date: 2022-09-07 DOI: 10.1146/annurev-genet-071819-103933
Sean Whalen, Katherine S Pollard
{"title":"Enhancer Function and Evolutionary Roles of Human Accelerated Regions.","authors":"Sean Whalen, Katherine S Pollard","doi":"10.1146/annurev-genet-071819-103933","DOIUrl":"10.1146/annurev-genet-071819-103933","url":null,"abstract":"<p><p>Human accelerated regions (HARs) are the fastest-evolving sequences in the human genome. When HARs were discovered in 2006, their function was mysterious due to scant annotation of the noncoding genome. Diverse technologies, from transgenic animals to machine learning, have consistently shown that HARs function as gene regulatory enhancers with significant enrichment in neurodevelopment. It is now possible to quantitatively measure the enhancer activity of thousands of HARs in parallel and model how each nucleotide contributes to gene expression. These strategies have revealed that many human HAR sequences function differently than their chimpanzee orthologs, though individual nucleotide changes in the same HAR may have opposite effects, consistent with compensatory substitutions. To fully evaluate the role of HARs in human evolution, it will be necessary to experimentally and computationally dissect them across more cell types and developmental stages.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"56 ","pages":"423-439"},"PeriodicalIF":8.7,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9712246/pdf/nihms-1843916.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9208524","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
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