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Epitranscriptome-epigenome interactions in development and disease mechanisms. 发育和疾病机制中的表观转录组-表观基因组相互作用。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-05-15 DOI: 10.1016/j.tig.2025.04.009
Chengyu Li, Kexuan Chen, Xiaoyu Li, Xushen Xiong
{"title":"Epitranscriptome-epigenome interactions in development and disease mechanisms.","authors":"Chengyu Li, Kexuan Chen, Xiaoyu Li, Xushen Xiong","doi":"10.1016/j.tig.2025.04.009","DOIUrl":"10.1016/j.tig.2025.04.009","url":null,"abstract":"<p><p>Crosstalk between epitranscriptomic modifications to RNA and epigenomic modifications to DNA and histones plays fundamental roles in development and disease. Here, we summarize two major regulatory modes of the crosstalk between the epigenome and epitranscriptome. In the 'cis mode', the crosstalk occurs co-transcriptionally, with direct interactions observed between epigenetic modifications mediated by their regulators. In the 'trans mode', the modification of an epigenetic layer regulates the expression of another epigenetic layer's writers/erasers and subsequently induces downstream epigenetic alteration. Additionally, we focus on the functional roles of the crosstalk mechanism in physiological and pathological contexts, including development, differentiation, cancer, and complex genetic diseases. Lastly, we discuss the potential future directions for a systematic understanding of epigenetic crosstalk in development and disease.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"691-705"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081696","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
Mendel elucidated: Big Science comes to the humble garden pea. 孟德尔阐明：“大科学降临到不起眼的豌豆上。”
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-06-26 DOI: 10.1016/j.tig.2025.06.007
Norman F Weeden
{"title":"Mendel elucidated: Big Science comes to the humble garden pea.","authors":"Norman F Weeden","doi":"10.1016/j.tig.2025.06.007","DOIUrl":"10.1016/j.tig.2025.06.007","url":null,"abstract":"<p><p>News flash: in a recent article by Feng et al., one of Mendel 'factors' is shown not to result in the expected 3:1 segregation ratio, and about half of the traits he investigated are produced by large insertions or deletions. Do genetic textbooks need to be revised?</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"635-636"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512808","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
Genomic newborn screening: exploring opportunities and navigating pitfalls while ensuring inclusivity. 新生儿基因组筛查：在确保包容性的同时探索机会和克服缺陷。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-04-28 DOI: 10.1016/j.tig.2025.04.001
Alban Ziegler, Wendy K Chung
{"title":"Genomic newborn screening: exploring opportunities and navigating pitfalls while ensuring inclusivity.","authors":"Alban Ziegler, Wendy K Chung","doi":"10.1016/j.tig.2025.04.001","DOIUrl":"10.1016/j.tig.2025.04.001","url":null,"abstract":"<p><p>Advances in genome sequencing (GS) have led to consented research evaluating DNA sequencing as a first-tier screening tool to expand the conditions included in newborn screening (NBS). Those pilot studies are confirming its feasibility but also delineate challenges to be solved. Preliminary results are guiding the design of infrastructure to address these challenges.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"631-634"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058338","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
Psychiatric disorders: teasing apart genetic similarities and differences. 精神疾病：梳理基因的异同。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-07-04 DOI: 10.1016/j.tig.2025.06.012
Jiayi Xu, Laura M Huckins
{"title":"Psychiatric disorders: teasing apart genetic similarities and differences.","authors":"Jiayi Xu, Laura M Huckins","doi":"10.1016/j.tig.2025.06.012","DOIUrl":"10.1016/j.tig.2025.06.012","url":null,"abstract":"<p><p>Given the high comorbidity between psychiatric disorders, previous studies have focused on genetic factors shared across the disorders. In a recent preprint, Grotzinger et al. comprehensively investigated shared and disorder-specific genetic factors across 14 neuropsychiatric disorders. Here, we discuss how this investigation could improve psychiatric nosology and therapeutic development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"640-642"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568073","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
Advancing GWAS of human communication. 推进人类交流的GWAS。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-06-18 DOI: 10.1016/j.tig.2025.05.009
Rosa S Gisladottir
{"title":"Advancing GWAS of human communication.","authors":"Rosa S Gisladottir","doi":"10.1016/j.tig.2025.05.009","DOIUrl":"10.1016/j.tig.2025.05.009","url":null,"abstract":"<p><p>The last decade has seen an explosion in genome-wide association studies (GWAS) on almost any imaginable phenotype. Unfortunately, humanity's most distinctive trait - communication, broadly construed - has been underserved. In this forum article I review recent advances and promising avenues that may help us understand the genetics and evolution of human communication.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"643-646"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334455","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
Unlocking the potential of CRISPR-associated transposons: from structural to functional insights. 解锁crispr相关转座子的潜力：从结构到功能洞察。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-08-01 Epub Date: 2025-05-19 DOI: 10.1016/j.tig.2025.04.005
Francisco Tenjo-Castaño, Sweta Suman Rout, Sanjay Dey, Guillermo Montoya
{"title":"Unlocking the potential of CRISPR-associated transposons: from structural to functional insights.","authors":"Francisco Tenjo-Castaño, Sweta Suman Rout, Sanjay Dey, Guillermo Montoya","doi":"10.1016/j.tig.2025.04.005","DOIUrl":"10.1016/j.tig.2025.04.005","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR)-associated transposons (CASTs) are emerging genome-editing tools that enable RNA-guided DNA integration without inducing double-strand breaks (DSBs). Unlike CRISPR-associated (Cas) nucleases, CASTs use transposon machinery to insert large DNA segments with high precision, potentially reducing off-target effects and bypassing DNA damage responses. CASTs are categorized into classes 1 and 2, each employing distinct mechanisms for DNA targeting and integration. Recent structural insights have elucidated how CASTs recognize target sites, recruit transposases, and mediate insertion. These advances position CASTs as promising tools for genome engineering in bacteria and possibly in mammalian cells. Key challenges remain in enhancing efficiency and specificity, particularly for therapeutic use. Ongoing research aims to evolve CAST systems for precise, large-scale genome editing in human cells.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"660-677"},"PeriodicalIF":16.3,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112787","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
Cross-kingdom RNA communication in plant-bacterial interaction. 植物-细菌相互作用中的跨界RNA通讯。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-07-30 DOI: 10.1016/j.tig.2025.07.004
Ronald Palermo, Arne Weiberg
{"title":"Cross-kingdom RNA communication in plant-bacterial interaction.","authors":"Ronald Palermo, Arne Weiberg","doi":"10.1016/j.tig.2025.07.004","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.004","url":null,"abstract":"<p><p>Boundaries of cross-kingdom RNA communication are now being expanded, with recent work showing that plants deliver gene-silencing RNA into bacteria. Ravet et al. report that both extracellular vesicular and nonvesicular RNAs are biologically active, challenging the current models of RNA secretion and delivery during plant-bacterial communication.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762345","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
Decoding genomic landscapes of introgression. 解码基因渗入的基因组景观。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-23 DOI: 10.1016/j.tig.2025.07.001
Xin Huang, Josef Hackl, Martin Kuhlwilm
{"title":"Decoding genomic landscapes of introgression.","authors":"Xin Huang, Josef Hackl, Martin Kuhlwilm","doi":"10.1016/j.tig.2025.07.001","DOIUrl":"https://doi.org/10.1016/j.tig.2025.07.001","url":null,"abstract":"<p><p>Genomic landscapes of introgression provide valuable information on how different evolutionary processes interact and leave signatures in genomes. The recent expansion of genomic datasets across diverse taxa, together with advances in methodological development, have created new opportunities to investigate the impact of introgression along individual genomes in various clades, making the precise identification of introgressed loci a rapidly evolving area of research. In this review we summarize recent methodological progress within three major categories: summary statistics, probabilistic modeling, and supervised learning. We examine how these approaches have been applied to data beyond humans and discuss the challenges associated with their application. Finally, we outline future directions for each category, including accessible implementation, transparent analysis, and systematic benchmarking.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709868","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
Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities. 组织中空间分辨的microRNA表达：技术、挑战和机遇。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-11 DOI: 10.1016/j.tig.2025.06.005
Agustín Robles-Remacho, Yimin Zou, Marco Grillo, Mats Nilsson
{"title":"Spatially resolved microRNA expression in tissues: technologies, challenges, and opportunities.","authors":"Agustín Robles-Remacho, Yimin Zou, Marco Grillo, Mats Nilsson","doi":"10.1016/j.tig.2025.06.005","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.005","url":null,"abstract":"<p><p>As the field of spatial omics continues to expand, the spatially resolved profiling of microRNA (miRNA) expression in tissues, or 'spatial miRNomics,' remains in its infancy, with only a few initial pioneering studies to date. MiRNA expression exhibits distinct spatial, temporal, and cell type-specific patterns, and the dysregulation of these patterns is associated with numerous pathological conditions. This highlights the potential of miRNAs as targets for spatial transcriptomic studies in translational and clinical research. In this review, we examine the current landscape of spatial technologies for miRNA detection from foundational methods to cutting-edge innovations, and we discuss conceptual and technical challenges. We also outline the biomedical implications of spatial miRNA profiling and set out future directions for exploring the spatial dimension of gene regulation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621221","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
Splicing inhibits premature cleavage and polyadenylation. 剪接抑制过早裂解和聚腺苷酸化。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-11 DOI: 10.1016/j.tig.2025.06.011
Sheng Yang, Mengzhao Li, Chengguo Yao
{"title":"Splicing inhibits premature cleavage and polyadenylation.","authors":"Sheng Yang, Mengzhao Li, Chengguo Yao","doi":"10.1016/j.tig.2025.06.011","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.011","url":null,"abstract":"<p><p>Small nuclear ribonucleoproteins (snRNPs) U1/U2/U4/U6 are critical constituents of the spliceosome. Recent studies showed that each of them exhibits a role in the inhibition of global PCPA (premature cleavage and polyadenylation), thereby supporting the hypothesis that the splicing process inhibits PCPA. In this forum article we summarize evidence to reinforce this hypothesis and envision potential mechanisms.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621222","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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