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Annual review of genetics最新文献

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The tracrRNA in CRISPR Biology and Technologies. CRISPR 生物学和技术中的 tracrRNA。
IF 11.1 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":11.1,"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: 20
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
RAD51 Gene Family Structure and Function. RAD51基因家族结构与功能。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-07-14 DOI: 10.1146/annurev-genet-021920-092410
Braulio Bonilla, Sarah R Hengel, McKenzie K Grundy, Kara A Bernstein
{"title":"<i>RAD51</i> Gene Family Structure and Function.","authors":"Braulio Bonilla,&nbsp;Sarah R Hengel,&nbsp;McKenzie K Grundy,&nbsp;Kara A Bernstein","doi":"10.1146/annurev-genet-021920-092410","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-092410","url":null,"abstract":"<p><p>Accurate DNA repair and replication are critical for genomic stability and cancer prevention. <i>RAD51</i> and its gene family are key regulators of DNA fidelity through diverse roles in double-strand break repair, replication stress, and meiosis. RAD51 is an ATPase that forms a nucleoprotein filament on single-stranded DNA. RAD51 has the function of finding and invading homologous DNA sequences to enable accurate and timely DNA repair. Its paralogs, which arose from ancient gene duplications of <i>RAD51</i>, have evolved to regulate and promote RAD51 function. Underscoring its importance, misregulation of RAD51, and its paralogs, is associated with diseases such as cancer and Fanconi anemia. In this review, we focus on the mammalian RAD51 structure and function and highlight the use of model systems to enable mechanistic understanding of RAD51 cellular roles. We also discuss how misregulation of the <i>RAD51</i> gene family members contributes to disease and consider new approaches to pharmacologically inhibit RAD51.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"25-46"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-092410","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38157713","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: 92
Linking Genes to Shape in Plants Using Morphometrics. 利用形态计量学将植物的基因与形状联系起来。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-04 DOI: 10.1146/annurev-genet-022620-094553
Hao Xu, George W Bassel
{"title":"Linking Genes to Shape in Plants Using Morphometrics.","authors":"Hao Xu,&nbsp;George W Bassel","doi":"10.1146/annurev-genet-022620-094553","DOIUrl":"https://doi.org/10.1146/annurev-genet-022620-094553","url":null,"abstract":"<p><p>A transition from qualitative to quantitative descriptors of morphology has been facilitated through the growing field of morphometrics, representing the conversion of shapes and patterns into numbers. The analysis of plant form at the macromorphological scale using morphometric approaches quantifies what is commonly referred to as a phenotype. Quantitative phenotypic analysis of individuals with contrasting genotypes in turn provides a means to establish links between genes and shapes. The path from a gene to a morphological phenotype is, however, not direct, with instructive information progressing both across multiple scales of biological complexity and through nonintuitive feedback, such as mechanical signals. In this review, we explore morphometric approaches used to perform whole-plant phenotyping and quantitative approaches in capture processes in the mesoscales, which bridge the gaps between genes and shapes in plants. Quantitative frameworks involving both the computational simulation and the discretization of data into networks provide a putative path to predicting emergent shape from underlying genetic programs.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"417-437"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-022620-094553","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344805","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: 8
Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms. 线粒体是后生动物出现的基础:新陈代谢、基因组调控和复杂生物的诞生。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-08-28 DOI: 10.1146/annurev-genet-021920-105545
Hadar Medini, Tal Cohen, Dan Mishmar
{"title":"Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms.","authors":"Hadar Medini,&nbsp;Tal Cohen,&nbsp;Dan Mishmar","doi":"10.1146/annurev-genet-021920-105545","DOIUrl":"https://doi.org/10.1146/annurev-genet-021920-105545","url":null,"abstract":"<p><p>Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: (<i>a</i>) Differentiation and embryogenesis rely on mitochondrial function; (<i>b</i>) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and (<i>c</i>) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"151-166"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-021920-105545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38319653","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
New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation. 剖析作物数量性状变异上位性的新视野。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-01 DOI: 10.1146/annurev-genet-050720-122916
Sebastian Soyk, Matthias Benoit, Zachary B Lippman
{"title":"New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation.","authors":"Sebastian Soyk,&nbsp;Matthias Benoit,&nbsp;Zachary B Lippman","doi":"10.1146/annurev-genet-050720-122916","DOIUrl":"https://doi.org/10.1146/annurev-genet-050720-122916","url":null,"abstract":"<p><p>Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the cumulative effect of individual gene mutations. This deviation is due to epistasis, in which interactions between alleles are often unpredictable and quantitative in effect. Recent advances in genomics and genome-editing technologies are elevating the study of epistasis in crops. Using the traits and developmental pathways that were major targets in domestication and breeding, we highlight how epistasis is central in guiding the behavior of the genetic variation that shapes quantitative trait variation. We outline new strategies that illuminate how quantitative epistasis from modified gene dosage defines background dependencies. Advancing our understanding of epistasis in crops can reveal new principles and approaches to engineering targeted improvements in agriculture.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"287-307"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-050720-122916","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38331787","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
Regulation and Function of RNA Pseudouridylation in Human Cells. RNA假尿嘧啶化在人细胞中的调控和功能。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-01 DOI: 10.1146/annurev-genet-112618-043830
Erin K Borchardt, Nicole M Martinez, Wendy V Gilbert
{"title":"Regulation and Function of RNA Pseudouridylation in Human Cells.","authors":"Erin K Borchardt,&nbsp;Nicole M Martinez,&nbsp;Wendy V Gilbert","doi":"10.1146/annurev-genet-112618-043830","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043830","url":null,"abstract":"<p><p>Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"309-336"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043830","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38331789","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: 61
Pioneer Transcription Factors Initiating Gene Network Changes. 启动基因网络变化的先锋转录因子。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-04 DOI: 10.1146/annurev-genet-030220-015007
Kenneth S Zaret
{"title":"Pioneer Transcription Factors Initiating Gene Network Changes.","authors":"Kenneth S Zaret","doi":"10.1146/annurev-genet-030220-015007","DOIUrl":"https://doi.org/10.1146/annurev-genet-030220-015007","url":null,"abstract":"<p><p>Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA sequence motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inaccessible to other transcription factors. Pioneer factors subsequently enable other transcription factors, nucleosome remodeling complexes, and histone modifiers to engage chromatin, thereby initiating the formation of an activating or repressive regulatory sequence. Thus, pioneer factors endow the competence for fate changes in embryonic development, are essential for cellular reprogramming, and rewire gene networks in cancer cells. Recent studies with reconstituted nucleosomes in vitro and chromatin binding in vivo reveal that pioneer factors can directly perturb nucleosome structure and chromatin accessibility in different ways. This review focuses on our current understanding of the mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to our ability to control cell fates at will.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"367-385"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-030220-015007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344810","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: 197
The Sins of Our Forefathers: Paternal Impacts on De Novo Mutation Rate and Development. 我们祖先的罪过:父系对新生突变率和发育的影响。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-07-14 DOI: 10.1146/annurev-genet-112618-043617
R John Aitken, Geoffry N De Iuliis, Brett Nixon
{"title":"The Sins of Our Forefathers: Paternal Impacts on De Novo Mutation Rate and Development.","authors":"R John Aitken,&nbsp;Geoffry N De Iuliis,&nbsp;Brett Nixon","doi":"10.1146/annurev-genet-112618-043617","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043617","url":null,"abstract":"Spermatogonial stem cells (SSCs) are generally characterized by excellent DNA surveillance and repair, resulting in one of the lowest spontaneous mutation rates in the body. However, the barriers to mutagenesis can be overwhelmed under two sets of circumstances. First, replication errors may generate age-dependent mutations that provide the mutant cells with a selective advantage, leading to the clonal expansions responsible for dominant genetic diseases such as Apert syndrome and achondroplasia. The second mechanism centers on the vulnerability of the male germline to oxidative stress and the induction of oxidative DNA damage in spermatozoa. Defective repair of such oxidative damage in the fertilized oocyte results in the creation of mutations in the zygote that can influence the health and well-being of the offspring. A particular hot spot for such oxidative attack on chromosome 15 has been found to align with several mutations responsible for paternally mediated disease, including cancer, psychiatric disorders, and infertility. Expected final online publication date for the Annual Review of Genetics, Volume 54 is November 23, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"1-24"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043617","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38157710","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
Toxin-Antidote Elements Across the Tree of Life. 生命之树上的毒素解毒剂元素。
IF 11.1 1区 生物学
Annual review of genetics Pub Date : 2020-11-23 Epub Date: 2020-09-04 DOI: 10.1146/annurev-genet-112618-043659
Alejandro Burga, Eyal Ben-David, Leonid Kruglyak
{"title":"Toxin-Antidote Elements Across the Tree of Life.","authors":"Alejandro Burga,&nbsp;Eyal Ben-David,&nbsp;Leonid Kruglyak","doi":"10.1146/annurev-genet-112618-043659","DOIUrl":"https://doi.org/10.1146/annurev-genet-112618-043659","url":null,"abstract":"<p><p>In life's constant battle for survival, it takes one to kill but two to conquer. Toxin-antitoxin or toxin-antidote (TA) elements are genetic dyads that cheat the laws of inheritance to guarantee their transmission to the next generation. This seemingly simple genetic arrangement-a toxin linked to its antidote-is capable of quickly spreading and persisting in natural populations. TA elements were first discovered in bacterial plasmids in the 1980s and have recently been characterized in fungi, plants, and animals, where they underlie genetic incompatibilities and sterility in crosses between wild isolates. In this review, we provide a unified view of TA elements in both prokaryotic and eukaryotic organisms and highlight their similarities and differences at the evolutionary, genetic, and molecular levels. Finally, we propose several scenarios that could explain the paradox of the evolutionary origin of TA elements and argue that these elements may be key evolutionary players and that the full scope of their roles is only beginning to be uncovered.</p>","PeriodicalId":8035,"journal":{"name":"Annual review of genetics","volume":"54 ","pages":"387-415"},"PeriodicalIF":11.1,"publicationDate":"2020-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-genet-112618-043659","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38344806","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: 22
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