Nature Reviews Genetics最新文献_第9页

Effects of regulatory variants across pig tissues 猪组织中调控变体的影响

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-02-01 DOI: 10.1038/s41576-024-00698-x

Henry Ertl

引用次数: 0

Selection on synonymous sites: the unwanted transcript hypothesis 同义位点上的选择：不需要的转录本假说。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-31 DOI: 10.1038/s41576-023-00686-7

Sofia Radrizzani, Grzegorz Kudla, Zsuzsanna Izsvák, Laurence D. Hurst

{"title":"Selection on synonymous sites: the unwanted transcript hypothesis","authors":"Sofia Radrizzani, Grzegorz Kudla, Zsuzsanna Izsvák, Laurence D. Hurst","doi":"10.1038/s41576-023-00686-7","DOIUrl":"10.1038/s41576-023-00686-7","url":null,"abstract":"Although translational selection to favour codons that match the most abundant tRNAs is not readily observed in humans, there is nonetheless selection in humans on synonymous mutations. We hypothesize that much of this synonymous site selection can be explained in terms of protection against unwanted RNAs — spurious transcripts, mis-spliced forms or RNAs derived from transposable elements or viruses. We propose not only that selection on synonymous sites functions to reduce the rate of creation of unwanted transcripts (for example, through selection on exonic splice enhancers and cryptic splice sites) but also that high-GC content (but low-CpG content), together with intron presence and position, is both particular to functional native mRNAs and used to recognize transcripts as native. In support of this hypothesis, transcription, nuclear export, liquid phase condensation and RNA degradation have all recently been shown to promote GC-rich transcripts and suppress AU/CpG-rich ones. With such ‘traps’ being set against AU/CpG-rich transcripts, the codon usage of native genes has, in turn, evolved to avoid such suppression. That parallel filters against AU/CpG-rich transcripts also affect the endosomal import of RNAs further supports the unwanted transcript hypothesis of synonymous site selection and explains the similar design rules that have enabled the successful use of transgenes and RNA vaccines. Multiple mechanisms have evolved to prevent or trap deleterious unwanted transcripts. The unwanted transcript hypothesis proposes that selection at synonymous sites favours mutations that prevent the generation of unwanted transcripts or that make native transcripts appear ‘wanted’ by being GC-rich.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 6","pages":"431-448"},"PeriodicalIF":42.7,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139651272","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

Inhibitors of bacterial immune systems: discovery, mechanisms and applications 细菌免疫系统抑制剂：发现、机制和应用。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-30 DOI: 10.1038/s41576-023-00676-9

David Mayo-Muñoz, Rafael Pinilla-Redondo, Sarah Camara-Wilpert, Nils Birkholz, Peter C. Fineran

{"title":"Inhibitors of bacterial immune systems: discovery, mechanisms and applications","authors":"David Mayo-Muñoz, Rafael Pinilla-Redondo, Sarah Camara-Wilpert, Nils Birkholz, Peter C. Fineran","doi":"10.1038/s41576-023-00676-9","DOIUrl":"10.1038/s41576-023-00676-9","url":null,"abstract":"To contend with the diversity and ubiquity of bacteriophages and other mobile genetic elements, bacteria have developed an arsenal of immune defence mechanisms. Bacterial defences include CRISPR–Cas, restriction–modification and a growing list of mechanistically diverse systems, which constitute the bacterial ‘immune system’. As a response, bacteriophages and mobile genetic elements have evolved direct and indirect mechanisms to circumvent or block bacterial defence pathways and ensure successful infection. Recent advances in methodological and computational approaches, as well as the increasing availability of genome sequences, have boosted the discovery of direct inhibitors of bacterial defence systems. In this Review, we discuss methods for the discovery of direct inhibitors, their diverse mechanisms of action and perspectives on their emerging applications in biotechnology and beyond. To successfully invade bacteria, bacteriophages and other mobile genetic elements must overcome numerous types of bacterial defence systems. Here, the authors review the discovery and mechanisms of direct inhibitors of bacterial defence systems, as well as their applications in biotechnology.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 4","pages":"237-254"},"PeriodicalIF":42.7,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642582","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

Packaging and delivery of genome-editing tools 基因组编辑工具的包装和交付

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-30 DOI: 10.1038/s41576-024-00701-5

Linda Koch

引用次数: 0

Transcriptional diversity along the intestinal crypt–villi axis 肠隐窝-绒毛轴的转录多样性

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-30 DOI: 10.1038/s41576-024-00700-6

Kylie R. James

引用次数: 0

Top predator decline has evolutionary as well as ecological effects 顶级掠食者的减少不仅会对生态产生影响，还会对进化产生影响。

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-26 DOI: 10.1038/s41576-024-00697-y

Kirsty Minton

引用次数: 0

Chromatin loops facilitate co-regulation of paralogues 染色质环促进了旁系亲属的共同调控

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-25 DOI: 10.1038/s41576-024-00694-1

Henry Ertl

引用次数: 0

Horizontal gene transfer in eukaryotes: aligning theory with data 真核生物中的水平基因转移：理论与数据的统一

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-23 DOI: 10.1038/s41576-023-00688-5

Patrick J. Keeling

引用次数: 0

The diversification of methods for studying cell–cell interactions and communication 研究细胞-细胞相互作用和交流的方法多样化

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-18 DOI: 10.1038/s41576-023-00685-8

Erick Armingol, Hratch M. Baghdassarian, Nathan E. Lewis

{"title":"The diversification of methods for studying cell–cell interactions and communication","authors":"Erick Armingol, Hratch M. Baghdassarian, Nathan E. Lewis","doi":"10.1038/s41576-023-00685-8","DOIUrl":"10.1038/s41576-023-00685-8","url":null,"abstract":"No cell lives in a vacuum, and the molecular interactions between cells define most phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and communication, thus accelerating the discovery of the roles of cells within their communities. Such research relies heavily on algorithms that infer which cells are interacting and the ligands and receptors involved. Specific pressures on different research niches are driving the evolution of next-generation computational tools, enabling new conceptual opportunities and technological advances. More sophisticated algorithms now account for the heterogeneity and spatial organization of cells, multiple ligand types and intracellular signalling events, and enable the use of larger and more complex datasets, including single-cell and spatial transcriptomics. Similarly, new high-throughput experimental methods are increasing the number and resolution of interactions that can be analysed simultaneously. Here, we explore recent progress in cell–cell interaction research and highlight the diversification of the next generation of tools, which have yielded a rich ecosystem of tools for different applications and are enabling invaluable discoveries. In this Review, the authors summarize recent progress in cell–cell interaction (CCI) research. They describe the recent evolution in computational tools that underpin CCI studies, discuss improvements in experimental methods enabling more high-throughput analyses of CCIs, and highlight future directions for the field.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 6","pages":"381-400"},"PeriodicalIF":42.7,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139489734","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 expanding diagnostic toolbox for rare genetic diseases 罕见遗传病诊断工具箱不断扩大

IF 42.7 1区生物学

Nature Reviews Genetics Pub Date : 2024-01-18 DOI: 10.1038/s41576-023-00683-w

Kristin D. Kernohan, Kym M. Boycott

{"title":"The expanding diagnostic toolbox for rare genetic diseases","authors":"Kristin D. Kernohan, Kym M. Boycott","doi":"10.1038/s41576-023-00683-w","DOIUrl":"10.1038/s41576-023-00683-w","url":null,"abstract":"Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively — through truly integrative multi-omics approaches and data sharing — the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases. Genomic technologies have greatly improved the diagnosis of rare genetic diseases. Here, the authors review emerging approaches for the identification of disease-causal genetic variants as well as omic technologies that show great potential for variant interpretation.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"25 6","pages":"401-415"},"PeriodicalIF":42.7,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139489740","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