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Cell-free DNA from clinical testing as a resource of population genetic analysis. 将临床检测中的无细胞 DNA 作为群体遗传分析的资源。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-11-22 DOI: 10.1016/j.tig.2024.10.007
Huanhuan Zhu, Yu Wang, Linxuan Li, Lin Wang, Haiqiang Zhang, Xin Jin
{"title":"Cell-free DNA from clinical testing as a resource of population genetic analysis.","authors":"Huanhuan Zhu, Yu Wang, Linxuan Li, Lin Wang, Haiqiang Zhang, Xin Jin","doi":"10.1016/j.tig.2024.10.007","DOIUrl":"10.1016/j.tig.2024.10.007","url":null,"abstract":"<p><p>As a noninvasive biomarker, cell-free DNA (cfDNA) has achieved remarkable success in clinical applications. Notably, cfDNA is essentially DNA, and conducting whole-genome sequencing (WGS) can yield a wealth of genetic information. These invaluable data should not be confined to one-time use; instead, they should be leveraged for more comprehensive population genetic analysis, including genetic variation spectrum, population structure and genetic selection, and genome-wide association studies (GWASs), among others. Such research findings can, in turn, facilitate clinical practice, enabling more advanced and accurate disease predictions. This review explores the advantages, challenges, and current research areas of cfDNA in population genetics. We hope that this review can serve as a new chapter in the repurposing of cfDNA sequence data generated from clinical testing in population genetics.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"330-344"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142694015","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
We must not ignore eugenics in our genetics curriculum.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2025-03-27 DOI: 10.1016/j.tig.2025.02.002
Mark Peifer
{"title":"We must not ignore eugenics in our genetics curriculum.","authors":"Mark Peifer","doi":"10.1016/j.tig.2025.02.002","DOIUrl":"10.1016/j.tig.2025.02.002","url":null,"abstract":"<p><p>Eugenics, that promoted planned breeding to ensure 'racial improvement', was central to the development of genetics and led to horrifying policies. However, eugenics is not dead and continues to influence science and policy today. Thus, we should include eugenics in our undergraduate classes to remind students that scientists must speak out when others lie about science and use it to further their political views.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"261-265"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744447","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
Leveraging spatial multiomics to unravel tissue architecture in embryo development. 利用空间多组学揭示胚胎发育中的组织结构。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-12-07 DOI: 10.1016/j.tig.2024.11.007
Fuqing Jiang, Haoxian Wang, Zhuxia Li, Guizhong Cui, Guangdun Peng
{"title":"Leveraging spatial multiomics to unravel tissue architecture in embryo development.","authors":"Fuqing Jiang, Haoxian Wang, Zhuxia Li, Guizhong Cui, Guangdun Peng","doi":"10.1016/j.tig.2024.11.007","DOIUrl":"10.1016/j.tig.2024.11.007","url":null,"abstract":"<p><p>Spatial multiomics technologies have revolutionized biomedical research by enabling the simultaneous measurement of multiple omics modalities within intact tissue sections. This approach facilitates the reconstruction of 3D molecular architectures, providing unprecedented insights into complex cellular interactions and the intricate organization of biological systems, such as those underlying embryonic development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"271-274"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796415","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 long and short of hyperdivergent regions. 超发散区域的长和短
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-12-19 DOI: 10.1016/j.tig.2024.11.005
Nicolas D Moya, Stephanie M Yan, Rajiv C McCoy, Erik C Andersen
{"title":"The long and short of hyperdivergent regions.","authors":"Nicolas D Moya, Stephanie M Yan, Rajiv C McCoy, Erik C Andersen","doi":"10.1016/j.tig.2024.11.005","DOIUrl":"10.1016/j.tig.2024.11.005","url":null,"abstract":"<p><p>The increasing prevalence of genome sequencing and assembly has uncovered evidence of hyperdivergent genomic regions - loci with excess genetic diversity - in species across the tree of life. Hyperdivergent regions are often enriched for genes that mediate environmental responses, such as immunity, parasitism, and sensory perception. Especially in self-fertilizing species where the majority of the genome is homozygous, the existence of hyperdivergent regions might imply the historical action of evolutionary forces such as introgression and/or balancing selection. We anticipate that the application of new sequencing technologies, broader taxonomic sampling, and evolutionary modeling of hyperdivergent regions will provide insights into the mechanisms that generate and maintain genetic diversity within and between species.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"303-314"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873501","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
Functional genomic perspectives on plant terrestrialization.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-27 DOI: 10.1016/j.tig.2025.02.006
Cäcilia F Kunz, Elisa S Goldbecker, Jan de Vries
{"title":"Functional genomic perspectives on plant terrestrialization.","authors":"Cäcilia F Kunz, Elisa S Goldbecker, Jan de Vries","doi":"10.1016/j.tig.2025.02.006","DOIUrl":"https://doi.org/10.1016/j.tig.2025.02.006","url":null,"abstract":"<p><p>Plant evolutionary research has made leaps in exploring the deep evolutionary roots of embryophytes. A solid phylogenomic framework was established, allowing evolutionary inferences. Comparative genomic approaches revealed that many genes coding for transcription factors, morphogenetic regulators, specialized metabolic enzymes, phytohormone signaling, and more are not innovations of land plants but have a deep streptophyte algal ancestry. Are these just spurious homologs, or do they actualize traits we deem important in embryophytes? Building on streptophyte algae genome data, current endeavors delve into the functional significance of whole cohorts of homologs by leveraging the power of comparative high-throughput approaches. This ushered in the identification of recurrent themes in function, ultimately providing a functional genomic definition for the toolkit of plant terrestrialization.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744533","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
Cis-regulatory dynamics in plant domestication.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-25 DOI: 10.1016/j.tig.2025.02.005
Xiang Li, Robert J Schmitz
{"title":"Cis-regulatory dynamics in plant domestication.","authors":"Xiang Li, Robert J Schmitz","doi":"10.1016/j.tig.2025.02.005","DOIUrl":"https://doi.org/10.1016/j.tig.2025.02.005","url":null,"abstract":"<p><p>Cis-regulatory elements (CREs) are critical sequence determinants for spatiotemporal control of gene expression. Genetic variants within CREs have driven phenotypic transitions from wild to cultivated plants during domestication. This review summarizes our current understanding of genetic variants within CREs involved in plant domestication. We also propose avenues for studies to expand our understanding of both CRE biology and domestication processes, such as examining primary mechanisms that generate CRE genetic variants during plant domestication and investigating the roles of CREs in domestication syndrome. Additionally, we discuss existing challenges and highlight future opportunities for exploring CREs in plant domestication, emphasizing the potential of modifying CREs to contribute to crop improvement.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143722614","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 origins and evolution of translation factors.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-24 DOI: 10.1016/j.tig.2025.02.004
Evrim Fer, Tony Yao, Kaitlyn M McGrath, Aaron D Goldman, Betül Kaçar
{"title":"The origins and evolution of translation factors.","authors":"Evrim Fer, Tony Yao, Kaitlyn M McGrath, Aaron D Goldman, Betül Kaçar","doi":"10.1016/j.tig.2025.02.004","DOIUrl":"https://doi.org/10.1016/j.tig.2025.02.004","url":null,"abstract":"<p><p>Translation is an ancient molecular information processing system found in all living organisms. Over the past decade, significant progress has been made in uncovering the origins of early translation. Yet, the evolution of translation factors - key regulators of protein synthesis - remains poorly understood. This review synthesizes recent findings on translation factors, highlighting their structural diversity, evolutionary history, and organism-specific adaptations across the tree of life. We examine conserved translation factors, their coevolution, and their roles in different steps in translation: initiation, elongation, and termination. The early evolution of translation factors serves as a natural link between modern genetics and the origins of life. Traditionally rooted in chemistry and geology, incorporating evolutionary molecular biology into the studies of life's emergence provides a complementary perspective on this complex question.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712127","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
Dynamics of replication timing during mammalian development.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-12 DOI: 10.1016/j.tig.2025.01.010
Tsunetoshi Nakatani
{"title":"Dynamics of replication timing during mammalian development.","authors":"Tsunetoshi Nakatani","doi":"10.1016/j.tig.2025.01.010","DOIUrl":"https://doi.org/10.1016/j.tig.2025.01.010","url":null,"abstract":"<p><p>Recent developments in low-input genomics techniques have greatly advanced the analysis of the order in which DNA is replicated in the genome - that is, replication timing (RT) - and its interrelationships with other processes. RT correlates or anticorrelates with genomic-specific parameters such as gene expression, chromatin accessibility, histone modifications, and the 3D structure of the genome, but the significance of how they influence each other and how they relate to biological processes remains unclear. In this review I discuss the results of recent analyses of RT, the time at which it is remodeled and consolidated during embryogenesis, how it influences development and differentiation, and the regulatory mechanisms and factors involved.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626813","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
Strategies for studying sex differences in brain aging.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-04 DOI: 10.1016/j.tig.2025.02.001
Victor A Ansere, Seung-Soo Kim, Francesca Marino, Katherine Morillo, Dena B Dubal, Coleen T Murphy, Yousin Suh, Bérénice A Benayoun
{"title":"Strategies for studying sex differences in brain aging.","authors":"Victor A Ansere, Seung-Soo Kim, Francesca Marino, Katherine Morillo, Dena B Dubal, Coleen T Murphy, Yousin Suh, Bérénice A Benayoun","doi":"10.1016/j.tig.2025.02.001","DOIUrl":"https://doi.org/10.1016/j.tig.2025.02.001","url":null,"abstract":"<p><p>Studying sex effects and their underlying mechanisms is of major relevance to understanding brain health. Despite growing interests, experimentally studying sex differences, particularly in the context of aging, remains challenging. Since sex chromosomal content influences gonadal development, separating the effects of gonadal hormones and chromosomal factors requires specific model systems. Here, we highlight rodent and tractable models for examining sex dimorphism in brain and cognitive aging. In addition, we discuss multi-omic and bioinformatic approaches that yield biological insights from animal and human studies. This review provides a comprehensive overview of the diverse toolkit now available to advance our understanding of sex differences in brain aging.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143558825","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
Role of ATP-dependent chromatin remodelers in meiosis. 依赖 ATP 的染色质重塑器在减数分裂中的作用
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-11-16 DOI: 10.1016/j.tig.2024.10.004
Sheetal Paliwal, Partha Dey, Swarangi Tambat, Akira Shinohara, Gunjan Mehta
{"title":"Role of ATP-dependent chromatin remodelers in meiosis.","authors":"Sheetal Paliwal, Partha Dey, Swarangi Tambat, Akira Shinohara, Gunjan Mehta","doi":"10.1016/j.tig.2024.10.004","DOIUrl":"10.1016/j.tig.2024.10.004","url":null,"abstract":"<p><p>In eukaryotic cells, DNA is wrapped around histone octamers to compact the genome. Although such compaction is required for the precise segregation of the genome during cell division, it restricts the DNA-protein interactions essential for several cellular processes. During meiosis, a specialized cell division process that produces gametes, several DNA-protein interactions are crucial for assembling meiosis-specific chromosome structures, meiotic recombination, chromosome segregation, and transcriptional regulation. The role of chromatin remodelers (CRs) in facilitating DNA-protein transactions during mitosis is well appreciated, whereas how they facilitate meiosis-specific processes is poorly understood. In this review, we summarize experimental evidence supporting the role of CRs in meiosis in various model systems and suggest future perspectives to advance the field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"236-250"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645208","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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