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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
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
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
The origins and evolution of translation factors. 翻译因子的起源与演变。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub 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":"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":"590-600"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237606/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Genomics Preprint Club: rethinking peer review through community and dialogue. 基因组学预印本俱乐部：通过社区和对话重新思考同行评审。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub Date: 2025-05-26 DOI: 10.1016/j.tig.2025.04.012
Judit García-González, Lathan Liou
{"title":"The Genomics Preprint Club: rethinking peer review through community and dialogue.","authors":"Judit García-González, Lathan Liou","doi":"10.1016/j.tig.2025.04.012","DOIUrl":"10.1016/j.tig.2025.04.012","url":null,"abstract":"","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"547-551"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162976","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
Chromatin accessibility provides a window into the genetic etiology of human brain disease. 染色质可及性为人类大脑疾病的遗传病因提供了一个窗口。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub Date: 2025-01-23 DOI: 10.1016/j.tig.2025.01.001
Jaroslav Bendl, John F Fullard, Kiran Girdhar, Pengfei Dong, Roman Kosoy, Biao Zeng, Gabriel E Hoffman, Panos Roussos
{"title":"Chromatin accessibility provides a window into the genetic etiology of human brain disease.","authors":"Jaroslav Bendl, John F Fullard, Kiran Girdhar, Pengfei Dong, Roman Kosoy, Biao Zeng, Gabriel E Hoffman, Panos Roussos","doi":"10.1016/j.tig.2025.01.001","DOIUrl":"10.1016/j.tig.2025.01.001","url":null,"abstract":"<p><p>Neuropsychiatric and neurodegenerative diseases have a significant genetic component. Risk variants often affect the noncoding genome, altering cis-regulatory elements (CREs) and chromatin structure, ultimately impacting gene expression. Chromatin accessibility profiling methods, especially assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), have been used to pinpoint disease-associated SNPs and link them to affected genes and cell types in the brain. The integration of single-cell technologies with genome-wide association studies (GWAS) and transcriptomic data has further advanced our understanding of cell-specific chromatin dynamics. This review discusses recent findings regarding the role played by chromatin accessibility in brain disease, highlighting the need for high-quality data and rigorous computational tools. Future directions include spatial chromatin studies and CRISPR-based functional validation to bridge genetic discovery and clinical applications, paving the way for targeted gene-regulatory therapies.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"601-616"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043200","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
Functional genomic perspectives on plant terrestrialization. 植物陆地化的功能基因组观点。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub 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":"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":"617-629"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","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
Can genomic analysis actually estimate past population size? 基因组分析真的能估计过去的人口规模吗？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub Date: 2025-04-25 DOI: 10.1016/j.tig.2025.03.003
Janeesh K Bansal, Richard A Nichols
{"title":"Can genomic analysis actually estimate past population size?","authors":"Janeesh K Bansal, Richard A Nichols","doi":"10.1016/j.tig.2025.03.003","DOIUrl":"10.1016/j.tig.2025.03.003","url":null,"abstract":"<p><p>Genomic data can be used to reconstruct population size over thousands of generations, using a new class of algorithms [sequentially Markovian coalescent (SMC) methods]. These analyses often show a recent decline in N<sub>e</sub> (effective size), which at face value implies a conservation or demographic crisis: a population crash and loss of genetic diversity. This interpretation is frequently mistaken. Here we outline how SMC methods work, why they generate this misleading signal, and suggest simple approaches for exploiting the rich information produced by these algorithms. In most species, genomic patterns reflect major changes in the species' range and subdivision over tens or hundreds of thousands of years. Consequently, collaboration between geneticists, palaeoecologists, palaeoclimatologists, and geologists is crucial for evaluating the outputs of SMC algorithms.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"559-567"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042514","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
RNA methylation in retrotransposon control. 逆转录转座子控制中的RNA甲基化。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub Date: 2025-05-21 DOI: 10.1016/j.tig.2025.04.013
Basil Barter, Jungnam Cho
{"title":"RNA methylation in retrotransposon control.","authors":"Basil Barter, Jungnam Cho","doi":"10.1016/j.tig.2025.04.013","DOIUrl":"10.1016/j.tig.2025.04.013","url":null,"abstract":"<p><p>N6-methyladenosine (m6A) regulates retrotransposon activity, shifting between repression and activation across different species and developmental stages. It promotes RNA decay, sequestration, or stability, influencing genome integrity, adaptation, and disease. This article explores the dual role of m6A in retrotransposon control, highlighting its evolutionary significance in genome regulation and cellular differentiation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"556-558"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129519","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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