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Unraveling immunity: insights from biobank-scale data. 解开免疫力：来自生物银行规模数据的见解。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-09-01 Epub Date: 2025-08-07 DOI: 10.1016/j.tig.2025.07.008
Ashley Richardson, Kailash Bp, Chad H Hogan
{"title":"Unraveling immunity: insights from biobank-scale data.","authors":"Ashley Richardson, Kailash Bp, Chad H Hogan","doi":"10.1016/j.tig.2025.07.008","DOIUrl":"10.1016/j.tig.2025.07.008","url":null,"abstract":"<p><p>The scale and granularity of biobanks are reshaping the future of immunogenetics, enabling breakthroughs at a pace never before possible. Here, we highlight two recent preprints that apply novel statistical methods to biobank data to understand how inherited variants shape immune traits and disease risk.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"730-732"},"PeriodicalIF":16.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12478156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144805322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Epigenetic perspectives on wheat speciation, adaptation, and development. 小麦物种形成、适应和发育的表观遗传学观点。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-09-01 Epub Date: 2025-05-09 DOI: 10.1016/j.tig.2025.04.008
Xuemei Liu, Dongzhi Wang, Zhaoheng Zhang, Xuelei Lin, Jun Xiao
{"title":"Epigenetic perspectives on wheat speciation, adaptation, and development.","authors":"Xuemei Liu, Dongzhi Wang, Zhaoheng Zhang, Xuelei Lin, Jun Xiao","doi":"10.1016/j.tig.2025.04.008","DOIUrl":"10.1016/j.tig.2025.04.008","url":null,"abstract":"<p><p>Bread wheat (Triticum aestivum) has undergone a complex evolutionary history shaped by polyploidization, domestication, and adaptation. Recent advances in multiomics approaches have shed light on the role of epigenetic mechanisms, including DNA methylation, histone modification, chromatin accessibility, and noncoding RNAs, in regulating gene expression throughout these processes. Epigenomic reprogramming contributes to genome stability and subgenome differentiation and modulates key agronomic traits by influencing flowering time, environmental responses, and developmental programs. This review synthesizes current insights into epigenetic regulation of wheat speciation, adaptation, and development, highlighting their potential applications in crop improvement. A deeper understanding of these mechanisms will facilitate targeted breeding strategies leveraging epigenetic variations to enhance wheat resilience and productivity in the face of changing environments.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"817-829"},"PeriodicalIF":16.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Sleeping less with a SIK3 mutation. SIK3基因突变导致睡眠不足。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-09-01 Epub Date: 2025-07-02 DOI: 10.1016/j.tig.2025.06.008
Xin Yin, Qinghua Liu
{"title":"Sleeping less with a SIK3 mutation.","authors":"Xin Yin, Qinghua Liu","doi":"10.1016/j.tig.2025.06.008","DOIUrl":"10.1016/j.tig.2025.06.008","url":null,"abstract":"<p><p>Natural short sleepers (NSS) need only 4-6 h of sleep per night to function efficiently without negative health effects. Chen et al. recently found an NSS mutation in the salt-induced kinase 3 (SIK3) gene, shedding new light on the genetic basis of human sleep regulation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"733-734"},"PeriodicalIF":16.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Selection on the epigenome: small RNA inheritance in animal evolution. 表观基因组的选择：动物进化中的小RNA遗传。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-09-01 Epub Date: 2025-05-15 DOI: 10.1016/j.tig.2025.04.007
Isaac Harris, Simone Immler, Tracey Chapman, Alexei A Maklakov
{"title":"Selection on the epigenome: small RNA inheritance in animal evolution.","authors":"Isaac Harris, Simone Immler, Tracey Chapman, Alexei A Maklakov","doi":"10.1016/j.tig.2025.04.007","DOIUrl":"10.1016/j.tig.2025.04.007","url":null,"abstract":"<p><p>The inheritance of small RNAs (sRNAs) is taxonomically widespread. Changing environments alter the production and presence of sRNAs in the germline, and this can in theory either increase offspring phenotypic variance as an evolutionary bet-hedging strategy or elicit predictive and adaptive phenotypic responses that increase offspring fitness. Nevertheless, the putative role of sRNA inheritance systems in adaptive evolution is still debated and it is currently unclear how selection acts on sRNAs. We outline two adaptive sRNA inheritance strategies - specialist and generalist - and discuss non-adaptive alternatives and the evolutionary implications of different strategies. Our review suggests that the role of natural selection in sRNA inheritance has been significantly overlooked, potentially leading to misinterpretations of the causal agents and the evolutionary implications of sRNA inheritance.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"804-816"},"PeriodicalIF":16.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Optimizing homology-directed repair for gene editing: the potential of single-stranded DNA donors. 优化基因编辑的同源修复：单链DNA供体的潜力。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-09-01 Epub Date: 2025-05-27 DOI: 10.1016/j.tig.2025.04.014
Ying-Ying Jin, Peng Zhang, De-Pei Liu
{"title":"Optimizing homology-directed repair for gene editing: the potential of single-stranded DNA donors.","authors":"Ying-Ying Jin, Peng Zhang, De-Pei Liu","doi":"10.1016/j.tig.2025.04.014","DOIUrl":"10.1016/j.tig.2025.04.014","url":null,"abstract":"<p><p>CRISPR (clustered regularly interspaced short palindromic repeat) system-based precise genome editing remarkably impacts both scientific investigation and therapeutic practices. Among various techniques, DNA donor-mediated homology-directed repair (HDR) represents a promising method for precise gene editing. Although efficiency constraints have previously limited HDR, recent advancements have significantly enhanced its effectiveness. Therefore, it is essential to highlight the progress made in this field and to reassess the potential of the HDR approach. In this review, we explore the fundamental principles of HDR-dependent gene editing and evaluate current strategies to enhance HDR efficiency, with particular emphasis on single-stranded DNA (ssDNA) donor-mediated HDR. Finally, we discuss the prospects of high-efficiency ssDNA donor-mediated precise gene editing in laboratory research and clinical therapies.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"788-803"},"PeriodicalIF":16.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 rare-to-common disease journey: a winding road to new therapies. 罕见病到常见病的历程：通往新疗法的曲折之路。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-09-01 Epub Date: 2025-06-02 DOI: 10.1016/j.tig.2025.05.003
Laura Reinholdt, Elissa Chesler, Martin Pera, Nadia Rosenthal
{"title":"The rare-to-common disease journey: a winding road to new therapies.","authors":"Laura Reinholdt, Elissa Chesler, Martin Pera, Nadia Rosenthal","doi":"10.1016/j.tig.2025.05.003","DOIUrl":"10.1016/j.tig.2025.05.003","url":null,"abstract":"<p><p>The study of genetic variants that cause rare diseases has been a central strategy of genetic research for the last century, but the contribution of rare variants to the multifactorial inheritance of common diseases has only recently emerged as an avenue to accelerate functional mapping of the human genome. This perspective defines rare and common diseases, surveys prospects for integrating their study to decipher pathogenic mechanisms, and cites current clinical hurdles of disease translation. We discuss the premise that research into rare disease etiology can inform our understanding of common illnesses and vice versa, identify impediments to progress in translating rare disease findings into common disease treatments, and offer suggestions for realizing the benefits of global health research in the discovery of rare disease variants.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"762-773"},"PeriodicalIF":16.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Interruptions impact clinical features of repeat expansion diseases, but how are they gained and lost? 中断影响重复扩张疾病的临床特征，但它们是如何获得和失去的？
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-29 DOI: 10.1016/j.tig.2025.07.005
Alys N Aston, Vincent Dion
{"title":"Interruptions impact clinical features of repeat expansion diseases, but how are they gained and lost?","authors":"Alys N Aston, Vincent Dion","doi":"10.1016/j.tig.2025.07.005","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.005","url":null,"abstract":"<p><p>Interruptions within expanded tandem repeats reduce somatic expansion and alter the severity of the resulting diseases. Consequently, much has been done to identify interruptions in the human population and assess their clinical impact. However, how interruptions are gained and lost is unknown. Here, we propose that synthesis-dependent microhomology-mediated end joining (SD-MMEJ) can account for most, if not all, the dynamic changes in interruptions within expanded repeats. SD-MMEJ explains the locus specificity of interruptions, why they appear near the 5' and 3' ends of expanded tracts, and how complex alleles arise within a single generation. Understanding interruption dynamics is fundamental to repeat expansion disease aetiology and therapeutic development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144978974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Complex diseases meet deep phenotyping and generative AI. 复杂疾病满足深度表型和生成人工智能。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-29 DOI: 10.1016/j.tig.2025.08.005
Jordi Merino
{"title":"Complex diseases meet deep phenotyping and generative AI.","authors":"Jordi Merino","doi":"10.1016/j.tig.2025.08.005","DOIUrl":"https://doi.org/10.1016/j.tig.2025.08.005","url":null,"abstract":"<p><p>Complex diseases are heterogeneous and evolve along a continuum, limiting individual-level prediction with current approaches. The Human Phenotype Project (HPP) integrates deep phenotyping with generative artificial intelligence (AI) to identify early deviations in health parameters. While the project has already provided significant insights, the challenge is converting these findings into actionable, equitable, and scalable interventions, advancing precision healthcare across diverse populations.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145034712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Toward DNA-based taxonomy of prokaryotes and microeukaryotes. 原核生物和微真核生物基于dna的分类研究。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-29 DOI: 10.1016/j.tig.2025.07.009
Leho Tedersoo, Stefan Geisen, Ying Chang, R Henrik Nilsson
{"title":"Toward DNA-based taxonomy of prokaryotes and microeukaryotes.","authors":"Leho Tedersoo, Stefan Geisen, Ying Chang, R Henrik Nilsson","doi":"10.1016/j.tig.2025.07.009","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.009","url":null,"abstract":"<p><p>The current nomenclatural rules regulating the naming of microorganisms are too conservative from the perspective of recent developments in molecular genetics tools and organism discovery. The taxonomy of microorganisms would greatly benefit from a conceptual shift toward DNA-based approaches. Current informal practices of DNA-based taxonomy include the use of DNA sequences for species description and type material. Here, we analyze the pros and cons of DNA-based taxonomic approaches and propose guidelines and examples for their appropriate use in descriptions of species and higher-ranking taxa. To facilitate taxon description and communication, we call for a broader use of DNA samples, genome and genetic marker sequences in typifying and diagnosing species and higher-ranking taxa if physical voucher strains or specimens are unavailable.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Déjà vu in clubroot resistance: same genes, new names. 在棍棒抵抗中，d郁闷：同样的基因，新的名字。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-26 DOI: 10.1016/j.tig.2025.07.013
Jiaxu Wu, Soham Mukhopadhyay, Edel Pérez-López
{"title":"Déjà vu in clubroot resistance: same genes, new names.","authors":"Jiaxu Wu, Soham Mukhopadhyay, Edel Pérez-López","doi":"10.1016/j.tig.2025.07.013","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.013","url":null,"abstract":"<p><p>Despite decades of clubroot research, only three resistance (R) genes have been validated. However, many of the 'new' R genes are, in fact, identical to or allelic with these three. In this forum article we advocate for more concerted efforts to reduce redundancies in reporting 'novel' R genes and to focus on establishing a common nomenclature system.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144979030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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