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A more elaborate genetic clock for clonal species. 克隆物种的遗传时钟更加精细。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-11-26 DOI: 10.1016/j.tig.2024.11.002
Jinhee Ryu, Yeonjin Kim, Young Seok Ju
{"title":"A more elaborate genetic clock for clonal species.","authors":"Jinhee Ryu, Yeonjin Kim, Young Seok Ju","doi":"10.1016/j.tig.2024.11.002","DOIUrl":"10.1016/j.tig.2024.11.002","url":null,"abstract":"<p><p>The genetic clock is a well-established tool used in evolutionary biology for estimating divergence times between species, individuals, or cells based on DNA sequence changes. Yu et al. have revisited the clock to make it applicable to clonal multicellular organisms that expand through asexual reproduction mechanisms, enabling more comprehensive evolutionary tracking.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"268-270"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740780","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
Q-rich activation domains: flexible 'rulers' for transcription start site selection? 富q激活域：转录起始位点选择的灵活“尺子”？
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.2024.11.008
Andrea Bernardini, Roberto Mantovani
{"title":"Q-rich activation domains: flexible 'rulers' for transcription start site selection?","authors":"Andrea Bernardini, Roberto Mantovani","doi":"10.1016/j.tig.2024.11.008","DOIUrl":"10.1016/j.tig.2024.11.008","url":null,"abstract":"<p><p>Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term 'ruler' TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"275-285"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796418","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
Mitochondrial-derived microproteins: from discovery to function: (Trends in Genetics, 41:2 pp:132-145, 2025). 线粒体来源的微蛋白：从发现到功能：（遗传学趋势，41:2 pp:132- 145,2025）。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2025-03-05 DOI: 10.1016/j.tig.2025.02.003
Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen
{"title":"Mitochondrial-derived microproteins: from discovery to function: (Trends in Genetics, 41:2 pp:132-145, 2025).","authors":"Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen","doi":"10.1016/j.tig.2025.02.003","DOIUrl":"10.1016/j.tig.2025.02.003","url":null,"abstract":"","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"357"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574725","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
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. 优生学应该在我们的遗传学课程中占有一席之地。
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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12021430/pdf/","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":"OA","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":"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
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
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