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Annual review of genetics最新文献

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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
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
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
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
The Drama of Wallerian Degeneration: The Cast, Crew, and Script. 沃勒堕落的戏剧:演员、工作人员和剧本。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-08-05 DOI: 10.1146/annurev-genet-071819-103917
Kai Zhang, Mingsheng Jiang, Yanshan Fang
{"title":"The Drama of Wallerian Degeneration: The Cast, Crew, and Script.","authors":"Kai Zhang,&nbsp;Mingsheng Jiang,&nbsp;Yanshan Fang","doi":"10.1146/annurev-genet-071819-103917","DOIUrl":"https://doi.org/10.1146/annurev-genet-071819-103917","url":null,"abstract":"<p><p>Significant advances have been made in recent years in identifying the genetic components of Wallerian degeneration, the process that brings the progressive destruction and removal of injured axons. It has now been accepted that Wallerian degeneration is an active and dynamic cellular process that is well regulated at molecular and cellular levels. In this review, we describe our current understanding of Wallerian degeneration, focusing on the molecular players and mechanisms that mediate the injury response, activate the degenerative program, transduce the death signal, execute the destruction order, and finally, clear away the debris. By highlighting the starring roles and sketching out the molecular script of Wallerian degeneration, we hope to provide a useful framework to understand Wallerian and Wallerian-like degeneration and to lay a foundation for developing new therapeutic strategies to treat axon degeneration in neural injury as well as in neurodegenerative disease.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"93-113"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39286848","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
The tracrRNA in CRISPR Biology and Technologies. CRISPR 生物学和技术中的 tracrRNA。
IF 8.7 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-08-20 DOI: 10.1146/annurev-genet-071719-022559
Chunyu Liao, Chase L Beisel
{"title":"The tracrRNA in CRISPR Biology and Technologies.","authors":"Chunyu Liao, Chase L Beisel","doi":"10.1146/annurev-genet-071719-022559","DOIUrl":"10.1146/annurev-genet-071719-022559","url":null,"abstract":"<p><p>CRISPR-Cas adaptive immune systems in bacteria and archaea utilize short CRISPR RNAs (crRNAs) to guide sequence-specific recognition and clearance of foreign genetic material. Multiple crRNAs are stored together in a compact format called a CRISPR array that is transcribed and processed into the individual crRNAs. While the exact processing mechanisms vary widely, some CRISPR-Cas systems, including those encoding the Cas9 nuclease, rely on a <i>trans</i>-activating crRNA (tracrRNA). The tracrRNA was discovered in 2011 and was quickly co-opted to create single-guide RNAs as core components of CRISPR-Cas9 technologies. Since then, further studies have uncovered processes extending beyond the traditional role of tracrRNA in crRNA biogenesis, revealed Cas nucleases besides Cas9 that are dependent on tracrRNAs, and established new applications based on tracrRNA engineering. In this review, we describe the biology of the tracrRNA and how its ongoing characterization has garnered new insights into prokaryotic immune defense and enabled key technological advances.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"55 ","pages":"161-181"},"PeriodicalIF":8.7,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614092/pdf/EMS160043.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9177046","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
Functional Diversification of Chromatin on Rapid Evolutionary Timescales. 染色质在快速进化时间尺度上的功能多样化。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 DOI: 10.1146/annurev-genet-071719-020301
Cara L Brand, Mia T Levine
{"title":"Functional Diversification of Chromatin on Rapid Evolutionary Timescales.","authors":"Cara L Brand,&nbsp;Mia T Levine","doi":"10.1146/annurev-genet-071719-020301","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020301","url":null,"abstract":"<p><p>Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat-packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"401-425"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9235829/pdf/nihms-1815448.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39904020","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: 7
Evolution and Plasticity of Genome-Wide Meiotic Recombination Rates. 全基因组减数分裂重组率的进化和可塑性。
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-021721-033821
Ian R Henderson, Kirsten Bomblies
{"title":"Evolution and Plasticity of Genome-Wide Meiotic Recombination Rates.","authors":"Ian R Henderson,&nbsp;Kirsten Bomblies","doi":"10.1146/annurev-genet-021721-033821","DOIUrl":"https://doi.org/10.1146/annurev-genet-021721-033821","url":null,"abstract":"<p><p>Sex, as well as meiotic recombination between homologous chromosomes, is nearly ubiquitous among eukaryotes. In those species that use it, recombination is important for chromosome segregation during gamete production, and thus for fertility. Strikingly, although in most species only one crossover event per chromosome is required to ensure proper segregation, recombination rates vary considerably above this minimum and show variation within and among species. However, whether this variation in recombination is adaptive or neutral and what might shape it remain unclear. Empirical studies and theory support the idea that recombination is generally beneficial but can also have costs. Here, we review variation in genome-wide recombination rates, explore what might cause this, and discuss what is known about its mechanistic basis. We end by discussing the environmental sensitivity of meiosis and recombination rates, how these features may relate to adaptation, and their implications for a broader understanding of recombination rate evolution.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"23-43"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39224640","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: 21
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