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Annual review of genetics最新文献

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Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics. 通过衔接遗传学和生物物理学解剖生物体形态发生。
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-071819-103748
Nikhil Mishra, Carl-Philipp Heisenberg
{"title":"Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.","authors":"Nikhil Mishra,&nbsp;Carl-Philipp Heisenberg","doi":"10.1146/annurev-genet-071819-103748","DOIUrl":"https://doi.org/10.1146/annurev-genet-071819-103748","url":null,"abstract":"<p><p>Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"209-233"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39367370","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: 4
Perfecting Targeting in CRISPR. 完善CRISPR靶向技术。
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-071719-030438
Hainan Zhang, Tong Li, Yidi Sun, Hui Yang
{"title":"Perfecting Targeting in CRISPR.","authors":"Hainan Zhang,&nbsp;Tong Li,&nbsp;Yidi Sun,&nbsp;Hui Yang","doi":"10.1146/annurev-genet-071719-030438","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-030438","url":null,"abstract":"<p><p>CRISPR-based genome editing holds promise for genome engineering and other applications in diverse organisms. Defining and improving the genome-wide and transcriptome-wide specificities of these editing tools are essential for realizing their full potential in basic research and biomedical therapeutics. This review provides an overview of CRISPR-based DNA- and RNA-editing technologies, methods to quantify their specificities, and key solutions to reduce off-target effects for research and improve therapeutic applications.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"453-477"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39422785","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
Seq Your Destiny: Neural Crest Fate Determination in the Genomic Era. 测序你的命运:基因组时代的神经嵴命运决定。
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-071719-020954
Shashank Gandhi, Marianne E Bronner
{"title":"Seq Your Destiny: Neural Crest Fate Determination in the Genomic Era.","authors":"Shashank Gandhi,&nbsp;Marianne E Bronner","doi":"10.1146/annurev-genet-071719-020954","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020954","url":null,"abstract":"<p><p>Neural crest stem/progenitor cells arise early during vertebrate embryogenesis at the border of the forming central nervous system. They subsequently migrate throughout the body, eventually differentiating into diverse cell types ranging from neurons and glia of the peripheral nervous system to bones of the face, portions of the heart, and pigmentation of the skin. Along the body axis, the neural crest is heterogeneous, with different subpopulations arising in the head, neck, trunk, and tail regions, each characterized by distinct migratory patterns and developmental potential. Modern genomic approaches like single-cell RNA- and ATAC-sequencing (seq) have greatly enhanced our understanding of cell lineage trajectories and gene regulatory circuitry underlying the developmental progression of neural crest cells. Here, we discuss how genomic approaches have provided new insights into old questions in neural crest biology by elucidating transcriptional and posttranscriptional mechanisms that govern neural crest formation and the establishment of axial level identity.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"349-376"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39435407","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: 4
Plant Cell Identity in the Era of Single-Cell Transcriptomics. 单细胞转录组学时代的植物细胞身份。
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-071719-020453
Kook Hui Ryu, Yan Zhu, John Schiefelbein
{"title":"Plant Cell Identity in the Era of Single-Cell Transcriptomics.","authors":"Kook Hui Ryu,&nbsp;Yan Zhu,&nbsp;John Schiefelbein","doi":"10.1146/annurev-genet-071719-020453","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020453","url":null,"abstract":"<p><p>High-throughput single-cell transcriptomic approaches have revolutionized our view of gene expression at the level of individual cells, providing new insights into their heterogeneity, identities, and functions. Recently, technical challenges to the application of single-cell transcriptomics to plants have been overcome, and many plant organs and tissues have now been subjected to analyses at single-cell resolution. In this review, we describe these studies and their impact on our understanding of the diversity, differentiation, and activities of plant cells. We particularly highlight their impact on plant cell identity, including unprecedented views of cell transitions and definitions of rare and novel cell types. We also point out current challenges and future opportunities for the application and analyses of single-cell transcriptomics in plants.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"479-496"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39422781","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
Cold Shock Response in Bacteria. 细菌的冷休克反应。
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-071819-031654
Yan Zhang, Carol A Gross
{"title":"Cold Shock Response in Bacteria.","authors":"Yan Zhang,&nbsp;Carol A Gross","doi":"10.1146/annurev-genet-071819-031654","DOIUrl":"https://doi.org/10.1146/annurev-genet-071819-031654","url":null,"abstract":"<p><p>Bacteria often encounter temperature fluctuations in their natural habitats and must adapt to survive. The molecular response of bacteria to sudden temperature upshift or downshift is termed the heat shock response (HSR) or the cold shock response (CSR), respectively. Unlike the HSR, which activates a dedicated transcription factor that predominantly copes with heat-induced protein folding stress, the CSR is mediated by a diverse set of inputs. This review provides a picture of our current understanding of the CSR across bacteria. The fundamental aspects of CSR involved in sensing and adapting to temperature drop, including regulation of membrane fluidity, protein folding, DNA topology, RNA metabolism, and protein translation, are discussed. Special emphasis is placed on recent findings of a CSR circuitry in <i>Escherichia coli</i> mediated by cold shock family proteins and RNase R that monitors and modulates messenger RNA structure to facilitate global translation recovery during acclimation.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"377-400"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39422783","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: 35
Architecture and Dynamics of Meiotic Chromosomes. 减数分裂染色体的结构与动力学。
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-071719-020235
Sarah N Ur, Kevin D Corbett
{"title":"Architecture and Dynamics of Meiotic Chromosomes.","authors":"Sarah N Ur,&nbsp;Kevin D Corbett","doi":"10.1146/annurev-genet-071719-020235","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020235","url":null,"abstract":"<p><p>The specialized two-stage meiotic cell division program halves a cell's chromosome complement in preparation for sexual reproduction. This reduction in ploidy requires that in meiotic prophase, each pair of homologous chromosomes (homologs) identify one another and form physical links through DNA recombination. Here, we review recent advances in understanding the complex morphological changes that chromosomes undergo during meiotic prophase to promote homolog identification and crossing over. We focus on the structural maintenance of chromosomes (SMC) family cohesin complexes and the meiotic chromosome axis, which together organize chromosomes and promote recombination. We then discuss the architecture and dynamics of the conserved synaptonemal complex (SC), which assembles between homologs and mediates local and global feedback to ensure high fidelity in meiotic recombination. Finally, we discuss exciting new advances, including mechanisms for boosting recombination on particular chromosomes or chromosomal domains and the implications of a new liquid crystal model for SC assembly and structure.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"497-526"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39422869","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: 23
Prevalence and Adaptive Impact of Introgression. 渗透的普遍性及其适应性影响。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-27 DOI: 10.1146/annurev-genet-021821-020805
Nathaniel B Edelman, James Mallet
{"title":"Prevalence and Adaptive Impact of Introgression.","authors":"Nathaniel B Edelman,&nbsp;James Mallet","doi":"10.1146/annurev-genet-021821-020805","DOIUrl":"https://doi.org/10.1146/annurev-genet-021821-020805","url":null,"abstract":"<p><p>Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"265-283"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39464831","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: 63
Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria. 细菌中应激信号核苷酸警报素(p)ppGpp的调控主题和变化。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 DOI: 10.1146/annurev-genet-021821-025827
Brent W Anderson, Danny K Fung, Jue D Wang
{"title":"Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria.","authors":"Brent W Anderson,&nbsp;Danny K Fung,&nbsp;Jue D Wang","doi":"10.1146/annurev-genet-021821-025827","DOIUrl":"https://doi.org/10.1146/annurev-genet-021821-025827","url":null,"abstract":"<p><p>Bacterial stress-signaling alarmones are important components of a protective network against diverse stresses such as nutrient starvation and antibiotic assault. pppGpp and ppGpp, collectively (p)ppGpp, have well-documented regulatory roles in gene expression and protein translation. Recent work has highlighted another key function of (p)ppGpp: inducing rapid and coordinated changes in cellular metabolism by regulating enzymatic activities, especially those involved in purine nucleotide synthesis. Failure of metabolic regulation by (p)ppGpp results in the loss of coordination between metabolic and macromolecular processes, leading to cellular toxicity. In this review, we document how (p)ppGpp and newly characterized nucleotides pGpp and (p)ppApp directly regulate these enzymatic targets for metabolic remodeling. We examine targets' common determinants for alarmone interaction as well as their evolutionary diversification. We highlight classical and emerging themes in nucleotide signaling, including oligomerization and allostery along with metabolic interconversion and crosstalk, illustrating how they allow optimized bacterial adaptation to their environmental niches.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"55 ","pages":"115-133"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10209448","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: 39
Museum Genomics. 博物馆基因组学。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-23 DOI: 10.1146/annurev-genet-071719-020506
Daren C Card, Beth Shapiro, Gonzalo Giribet, Craig Moritz, Scott V Edwards
{"title":"Museum Genomics.","authors":"Daren C Card,&nbsp;Beth Shapiro,&nbsp;Gonzalo Giribet,&nbsp;Craig Moritz,&nbsp;Scott V Edwards","doi":"10.1146/annurev-genet-071719-020506","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020506","url":null,"abstract":"<p><p>Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"633-659"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39464476","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: 35
Genomic and Epigenetic Foundations of Neocentromere Formation. 新着丝粒形成的基因组和表观遗传学基础。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2021-11-23 Epub Date: 2021-09-08 DOI: 10.1146/annurev-genet-071719-020924
Evon M DeBose-Scarlett, Beth A Sullivan
{"title":"Genomic and Epigenetic Foundations of Neocentromere Formation.","authors":"Evon M DeBose-Scarlett,&nbsp;Beth A Sullivan","doi":"10.1146/annurev-genet-071719-020924","DOIUrl":"https://doi.org/10.1146/annurev-genet-071719-020924","url":null,"abstract":"<p><p>Centromeres are essential to genome inheritance, serving as the site of kinetochore assembly and coordinating chromosome segregation during cell division. Abnormal centromere function is associated with birth defects, infertility, and cancer. Normally, centromeres are assembled and maintained at the same chromosomal location. However, ectopic centromeres form spontaneously at new genomic locations and contribute to genome instability and developmental defects as well as to acquired and congenital human disease. Studies in model organisms have suggested that certain regions of the genome, including pericentromeres, heterochromatin, and regions of open chromatin or active transcription, support neocentromere activation. However, there is no universal mechanism that explains neocentromere formation. This review focuses on recent technological and intellectual advances in neocentromere research and proposes future areas of study. Understanding neocentromere biology will provide a better perspective on chromosome and genome organization and functional context for information generated from the Human Genome Project, ENCODE, and other large genomics consortia.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":" ","pages":"331-348"},"PeriodicalIF":11.1,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39395731","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
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