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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
Mechanisms of snoRNAs in cancer treatment resistance: from molecular insights to clinical applications. snoRNAs在癌症治疗耐药中的作用机制：从分子认识到临床应用。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-11 DOI: 10.1016/j.tig.2025.06.004
Xiwen Yan, Bo Chen, Xinyue Song, Ying Zhou, Feng Jin, Ang Zheng
{"title":"Mechanisms of snoRNAs in cancer treatment resistance: from molecular insights to clinical applications.","authors":"Xiwen Yan, Bo Chen, Xinyue Song, Ying Zhou, Feng Jin, Ang Zheng","doi":"10.1016/j.tig.2025.06.004","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.004","url":null,"abstract":"<p><p>Small nucleolar RNAs (snoRNAs), traditionally regarded as guides for RNA modification, have emerged as critical regulators of tumor progression and treatment resistance. This review comprehensively outlines the roles of snoRNAs and their host genes in mediating cancer treatment resistance, with an emphasis on mechanisms involving epigenetic regulation, metabolic reprogramming, and tumor microenvironment (TME) remodeling. It further explores their potential as predictive biomarkers for cancer diagnosis, prognosis, and treatment response. In addition, the review addresses current technical challenges related to detection standardization and clinical translation. Future research is expected to establish a solid theoretical foundation and practical strategies to overcome drug resistance and promote the development of personalized cancer therapy.</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":"144621204","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
Animal origins: looping back in time. 动物起源：回到过去。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-10 DOI: 10.1016/j.tig.2025.06.013
Omar Matar, Ferdinand Marlétaz
{"title":"Animal origins: looping back in time.","authors":"Omar Matar, Ferdinand Marlétaz","doi":"10.1016/j.tig.2025.06.013","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.013","url":null,"abstract":"<p><p>How did the chromatin folding mechanisms controlling gene regulation emerge during animal evolution? Kim et al. surveyed chromatin folding at high-resolution in unicellular relatives of animals as well as non-bilaterian animal lineages. They found that chromatin loops appeared concomitantly with complex gene regulation and uncovered an unexpected diversity of chromatin looping mechanisms.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621202","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
Expanding horizons of CRISPR applications beyond genome editing. 拓展CRISPR在基因组编辑之外的应用领域。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-10 DOI: 10.1016/j.tig.2025.06.003
Yu Liang, Shengkun Tong, Jingyu Zhang, Gao-Yi Tan, Lixin Zhang, Sang Yup Lee, Yaojun Tong
{"title":"Expanding horizons of CRISPR applications beyond genome editing.","authors":"Yu Liang, Shengkun Tong, Jingyu Zhang, Gao-Yi Tan, Lixin Zhang, Sang Yup Lee, Yaojun Tong","doi":"10.1016/j.tig.2025.06.003","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.003","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR) technologies have rapidly evolved beyond genome editing, transforming fields such as molecular diagnostics, biosensing, transcriptional regulation, molecular imaging, protein interaction mapping, and single-cell analysis. Emerging CRISPR-based diagnostics harness the collateral cleavage activity of CRISPR-associated (Cas) enzymes for rapid nucleic acid detection. Advanced biosensors extend CRISPR's capabilities to detect ions, metabolites, and proteins by integrating synthetic biology components. Catalytically inactive Cas proteins enable precise gene regulation and live-cell imaging of nucleic acids, whereas CRISPR-guided proximity labeling has revolutionized the mapping of biomolecular interactions. Recent single-cell CRISPR screens provide unprecedented resolution of cellular heterogeneity. Future research will focus on overcoming current limitations. The integration of CRISPR technologies with artificial intelligence (AI), spatial omics, and microfluidics is expected to further amplify their impact.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144621203","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
m6A in the coding sequence: linking deposition, translation, and decay. 编码序列中的m6A：连接沉积、翻译和衰变。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-07 DOI: 10.1016/j.tig.2025.06.002
Miona Ćorović, Peter Hoch-Kraft, You Zhou, Sarah Hallstein, Julian König, Kathi Zarnack
{"title":"m<sup>6</sup>A in the coding sequence: linking deposition, translation, and decay.","authors":"Miona Ćorović, Peter Hoch-Kraft, You Zhou, Sarah Hallstein, Julian König, Kathi Zarnack","doi":"10.1016/j.tig.2025.06.002","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.002","url":null,"abstract":"<p><p>N6-methyladenosine (m<sup>6</sup>A) is the most abundant internal modification in mRNA and plays a crucial role in regulating mRNA turnover. This review explores the characteristics of m<sup>6</sup>A sites in the coding sequence (CDS) and their influence on mRNA decay, with a focus on the newly discovered CDS-m<sup>6</sup>A decay (CMD) pathway - a translation-dependent mechanism that promotes rapid and efficient degradation. Further, we examine how splicing-associated factors influence m<sup>6</sup>A deposition and discuss the enrichment of CMD targets in processing bodies (P-bodies). We emphasize the interplay between m<sup>6</sup>A modification and decay, and propose that targeting the CMD pathway could offer novel therapeutic strategies for diseases such as cancer and metabolic disorders.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592934","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
Breaking bad: when clitellate genomes go rogue. 绝命毒师：当纤毛虫基因组失控时。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-05 DOI: 10.1016/j.tig.2025.06.006
Carlos Vargas-Chávez, Aoife McLysaght, Rosa Fernández
{"title":"Breaking bad: when clitellate genomes go rogue.","authors":"Carlos Vargas-Chávez, Aoife McLysaght, Rosa Fernández","doi":"10.1016/j.tig.2025.06.006","DOIUrl":"https://doi.org/10.1016/j.tig.2025.06.006","url":null,"abstract":"<p><p>Clitellate genomes are the result of a profound genome reshaping compared to marine annelids, as if their genomes had exploded into thousands of atomic pieces and were reassembled in a different order by evolution. Recent studies not only revealed widespread gene order shuffling and massive rearrangements but also point to a potential adaptive rationale for this architectural chaos. What triggered such extreme rearrangements, and what molecular logic (if any) underlies their persistence? What is the role of spatial organization and regulatory rewiring in the maintenance of functional integrity in how the genome adjusts to this newly disordered architecture? By synthesizing current discoveries, this review outlines the mechanisms, consequences, and evolutionary paradoxes of genome rearrangement in clitellates, highlighting them as models of extreme yet functional genome plasticity.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144576974","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 13.6 2区 生物学
Trends in Genetics Pub 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":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 13.6 2区 生物学
Trends in Genetics Pub 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":"https://doi.org/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":""},"PeriodicalIF":13.6,"publicationDate":"2025-07-02","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
Dynamics of replication timing during mammalian development. 哺乳动物发育过程中复制时间的动力学。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub 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":"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":"568-576"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","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
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