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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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981857/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cis-regulatory dynamics in plant domestication. 植物驯化中的顺式调控动力学。
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
Strategies for studying sex differences in brain aging. 研究脑老化性别差异的策略。
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
Why are RNA processing factors recruited to DNA double-strand breaks? 为什么 DNA 双链断裂处会招募 RNA 处理因子？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-11-19 DOI: 10.1016/j.tig.2024.10.008
Feras E Machour, Alma Sophia Barisaac, Nabieh Ayoub
{"title":"Why are RNA processing factors recruited to DNA double-strand breaks?","authors":"Feras E Machour, Alma Sophia Barisaac, Nabieh Ayoub","doi":"10.1016/j.tig.2024.10.008","DOIUrl":"10.1016/j.tig.2024.10.008","url":null,"abstract":"<p><p>DNA double-strand break (DSB) induction leads to local transcriptional silencing at damage sites, raising the question: Why are RNA processing factors (RPFs), including splicing factors, rapidly recruited to these sites? Recent findings show that DSBs cluster in a chromatin compartment termed the 'D compartment', where DNA damage response (DDR) genes relocate and undergo transcriptional activation. Here, we propose two non-mutually exclusive models to elucidate the rationale behind the recruitment of RPFs to DSB sites. First, RPFs circulate through the D compartment to process transcripts of the relocated DDR genes. Second, the D compartment serves as a 'post-translational modifications (PTMs) hub', altering RPF activity and leading to the production of unique DNA damage-induced transcripts, which are essential for orchestrating the DDR.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"194-200"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142683574","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
Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies. 用完整的灵长类基因组和先进的生物技术推进进化医学。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-12-02 DOI: 10.1016/j.tig.2024.11.001
Kaiyue Ma, Xiangyu Yang, Yafei Mao
{"title":"Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies.","authors":"Kaiyue Ma, Xiangyu Yang, Yafei Mao","doi":"10.1016/j.tig.2024.11.001","DOIUrl":"10.1016/j.tig.2024.11.001","url":null,"abstract":"<p><p>Evolutionary medicine, which integrates evolutionary biology and medicine, significantly enhances our understanding of human traits and disease susceptibility. However, previous studies in this field have often focused on single-nucleotide variants due to technological limitations in characterizing complex genomic regions, hindering the comprehensive analyses of their evolutionary origins and clinical significance. In this review, we summarize recent advancements in complete telomere-to-telomere (T2T), primate genomes and other primate resources, and illustrate how these resources facilitate the research of complex regions. We focus on several biomedically relevant regions to examine the relationship between primate genome evolution and human diseases. We also highlight the potentials of high-throughput functional genomic technologies for assessing candidate loci. Finally, we discuss future directions for primate research within the context of evolutionary medicine.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"201-217"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774833","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
To genetic rescue or not? 要不要拯救基因？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-11-27 DOI: 10.1016/j.tig.2024.11.004
Karin Norén, Malin Hasselgren
{"title":"To genetic rescue or not?","authors":"Karin Norén, Malin Hasselgren","doi":"10.1016/j.tig.2024.11.004","DOIUrl":"10.1016/j.tig.2024.11.004","url":null,"abstract":"<p><p>Inbreeding depression and genetic rescue are central themes in conservation biology. Translocation is a tool to assist genetic rescue but is connected to risks. A new study by Quinn et al. used genomic data to evaluate translocations as a potential action in montane red fox, bringing important implications also for other threatened species.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"185-186"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741125","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
Ambient storage of genomic time capsules. 基因组时间胶囊的环境储存。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-12-29 DOI: 10.1016/j.tig.2024.11.012
Euan A Ashley
{"title":"Ambient storage of genomic time capsules.","authors":"Euan A Ashley","doi":"10.1016/j.tig.2024.11.012","DOIUrl":"10.1016/j.tig.2024.11.012","url":null,"abstract":"<p><p>While the cost of genome sequencing has decreased, -80°C DNA preservation and raw sequence data archiving remain expensive. Transitioning to room-temperature DNA preservation could reduce costs, lessen researchers' reliance on the electrical grid, and encourage a future proofing strategy of periodical updating with higher quality sequencing instead of long-term storage of raw signal data. A new technology recently described by Prince et al. that could help realize these goals is Thermoset-REinforced Xeropreservation (T-REX).</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"181-182"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907920","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
Bacterial intragenic inversions: a new layer of diversity. 细菌基因内反转：一个新的多样性层。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-12-19 DOI: 10.1016/j.tig.2024.12.002
Brantley Hall, Xiaofang Jiang
{"title":"Bacterial intragenic inversions: a new layer of diversity.","authors":"Brantley Hall, Xiaofang Jiang","doi":"10.1016/j.tig.2024.12.002","DOIUrl":"10.1016/j.tig.2024.12.002","url":null,"abstract":"<p><p>DNA inversions in bacteria were known to create diversity through intergenic or partial intergenic changes. Now, Chanin, West, et al. reveal intragenic inversions, enabling single genes to encode multiple protein variants via sequence recoding or truncation - an unexpected mechanism for expanding protein diversity without increasing genome size.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"183-184"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873498","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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