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Advances in understanding LINE-1 regulation and function in the human genome. 人类基因组中LINE-1调控和功能的研究进展。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub Date: 2025-05-16 DOI: 10.1016/j.tig.2025.04.011
Xiufeng Li, Nian Liu
{"title":"Advances in understanding LINE-1 regulation and function in the human genome.","authors":"Xiufeng Li, Nian Liu","doi":"10.1016/j.tig.2025.04.011","DOIUrl":"10.1016/j.tig.2025.04.011","url":null,"abstract":"<p><p>LINE-1 (long interspersed nuclear element 1, L1) retrotransposons constitute ~17% of human DNA (~0.5 million genomic L1 copies) and exhibit context-dependent expression in different cell lines. Recent studies reveal that L1 is under multilayered control by diverse factors that either collaborate or compete with each other to ensure precise L1 activity. Remarkably, L1s have been co-opted as various transcription-dependent regulatory elements, such as promoters, enhancers, and topologically associating domain (TAD) boundaries, that regulate gene expression in zygotic genome activation, aging, cancer, and other disorders. This review highlights the regulation of L1 and its regulatory functions that influence disease and development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"577-589"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095563","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
Toward equitable biomarkers of aging: rethinking methylation clocks. 迈向公平的衰老生物标志物：重新思考甲基化时钟。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub Date: 2025-06-18 DOI: 10.1016/j.tig.2025.06.001
Selina Wu, Gita A Pathak, Zhangying Chen
{"title":"Toward equitable biomarkers of aging: rethinking methylation clocks.","authors":"Selina Wu, Gita A Pathak, Zhangying Chen","doi":"10.1016/j.tig.2025.06.001","DOIUrl":"10.1016/j.tig.2025.06.001","url":null,"abstract":"<p><p>DNA methylation clocks, which measure biological age by analyzing age-related DNA methylation patterns, offer powerful biomarkers of aging. But as a recent preprint highlights, current models underperform in diverse populations. The next generation of clocks must prioritize equity to avoid reinforcing disparities in precision aging and disease risk prediction.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"552-553"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12221226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327756","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
Moving towards sequencing-based metabolomics. 迈向基于测序的代谢组学。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-07-01 Epub Date: 2025-05-06 DOI: 10.1016/j.tig.2025.04.006
Alia Clark-ElSayed, Andrew D Ellington, Edward M Marcotte
{"title":"Moving towards sequencing-based metabolomics.","authors":"Alia Clark-ElSayed, Andrew D Ellington, Edward M Marcotte","doi":"10.1016/j.tig.2025.04.006","DOIUrl":"10.1016/j.tig.2025.04.006","url":null,"abstract":"<p><p>Metabolites are chemically heterogeneous and difficult to quantify in easily read formats. Recently, Tan and Fraser demonstrated that metabolites can be readily quantified by pairing aptamer function with DNA sequencing. This reflects a larger trend of sequencing for assessing biomolecule abundances, further leading to sequencing being a universal analytical tool.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"554-555"},"PeriodicalIF":13.6,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237595/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026890","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
Nascent RNA at the crossroad of transcription and replication. 新生RNA在转录和复制的十字路口。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-06-25 DOI: 10.1016/j.tig.2025.05.010
Ming-Yu Zhu, Yi-Zheng Zhang, Ting Guo, Jie Ren
{"title":"Nascent RNA at the crossroad of transcription and replication.","authors":"Ming-Yu Zhu, Yi-Zheng Zhang, Ting Guo, Jie Ren","doi":"10.1016/j.tig.2025.05.010","DOIUrl":"https://doi.org/10.1016/j.tig.2025.05.010","url":null,"abstract":"<p><p>The concurrent processes of DNA replication and RNA transcription pose a significant challenge to genome integrity. Nascent RNA, the newly synthesized transcript, is emerging as a critical determinant of transcription-replication conflict (TRC) outcomes, exerting influence through its modifications, its ability to form RNA:DNA hybrids (R-loops), its regulation of chromatin structure, and its interaction with protein complexes at the transcription-replication interface. Here, we synthesize recent advances on how nascent RNA modulates transcription dynamics, replication fork progression, and genome stability. We explore its paradoxical roles - both inducing replication stress and orchestrating protective responses - highlighting how RNA processing factors mitigate TRCs. Finally, we emphasize the need for innovative technologies to dissect the dynamic and context-dependent roles of nascent RNA and therapeutic potential for genomic instability-linked diseases.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509378","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
Invigorating ELSI: reflexive approaches to enhance policy development. 振兴经济、社会、经济指标：加强政策制定的反思性方法。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-06-18 DOI: 10.1016/j.tig.2025.05.006
Tadafumi Kubota, Aviad Raz, Jusaku Minari
{"title":"Invigorating ELSI: reflexive approaches to enhance policy development.","authors":"Tadafumi Kubota, Aviad Raz, Jusaku Minari","doi":"10.1016/j.tig.2025.05.006","DOIUrl":"https://doi.org/10.1016/j.tig.2025.05.006","url":null,"abstract":"<p><p>For 35 years, the Ethical, Legal, and Social Implications (ELSI) Research Program has addressed the societal implications of genomic research. However, its policy impact remains controversial. Here, we propose practical approaches for enhancing its policy impact by leveraging sociological studies on technology and critical arguments raised by ELSI scholars themselves.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327755","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
Investigating RNA dynamics from single molecule transcriptomes. 从单分子转录组研究RNA动力学。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-06-04 DOI: 10.1016/j.tig.2025.05.001
Sahiti Somalraju, Doaa Hassan Salem, Sarath Chandra Janga
{"title":"Investigating RNA dynamics from single molecule transcriptomes.","authors":"Sahiti Somalraju, Doaa Hassan Salem, Sarath Chandra Janga","doi":"10.1016/j.tig.2025.05.001","DOIUrl":"10.1016/j.tig.2025.05.001","url":null,"abstract":"<p><p>Investigating RNA dynamics is crucial for uncovering fundamental mechanisms, such as alternative splicing, RNA stability, and post-transcriptional modifications, all processes with implications for identifying therapeutic targets and advancing knowledge of cellular function and regulation. Advances in long-read sequencing technologies, particularly from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), offer unprecedented insights into RNA dynamics at single molecule and single nucleotide resolutions. In this review, we examine protocols and methods for analyzing RNA dynamics, focusing on isoform detection, poly(A) tail length quantification, and mapping of RNA modifications. We envision that these high-throughput, transcriptome-wide data sets, combined with integrated software systems, will transform workflows for studying single molecule RNA dynamics. Such advances will help unravel the complexities of gene regulation and deepen our understanding of cellular processes.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":16.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12353502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235963","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
What does evolution make? Learning in living lineages and machines. 进化创造了什么？学习活的血统和机器。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-06-01 Epub Date: 2025-06-10 DOI: 10.1016/j.tig.2025.04.002
Benedikt Hartl, Michael Levin
{"title":"What does evolution make? Learning in living lineages and machines.","authors":"Benedikt Hartl, Michael Levin","doi":"10.1016/j.tig.2025.04.002","DOIUrl":"10.1016/j.tig.2025.04.002","url":null,"abstract":"<p><p>How does genomic information unfold, to give rise to self-constructing living organisms with problem-solving capacities at all levels of organization? We review recent progress that unifies work in developmental genetics and machine learning (ML) to understand mapping of genes to traits. We emphasize the deep symmetries between evolution and learning, which cast the genome as instantiating a generative model. The layer of physiological computations between genotype and phenotype provides a powerful degree of plasticity and robustness, not merely complexity and indirect mapping, which strongly impacts individual and evolutionary-scale dynamics. Ideas from ML and neuroscience now provide a versatile, quantitative formalism for understanding what evolution learns and how developmental and regenerative morphogenesis interpret the deep lessons of the past to solve new problems. This emerging understanding of the informational architecture of living material is poised to impact not only genetics and evolutionary developmental biology but also regenerative medicine and synthetic morphoengineering.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"480-496"},"PeriodicalIF":13.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276720","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
Revealing microRNA regulation in single cells. 揭示单细胞中的microRNA调控。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-06-01 Epub Date: 2025-01-24 DOI: 10.1016/j.tig.2024.12.009
Ranjan K Maji, Matthias S Leisegang, Reinier A Boon, Marcel H Schulz
{"title":"Revealing microRNA regulation in single cells.","authors":"Ranjan K Maji, Matthias S Leisegang, Reinier A Boon, Marcel H Schulz","doi":"10.1016/j.tig.2024.12.009","DOIUrl":"10.1016/j.tig.2024.12.009","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are key regulators of gene expression and control cellular functions in physiological and pathophysiological states. miRNAs play important roles in disease, stress, and development, and are now being investigated for therapeutic approaches. Alternative processing of miRNAs during biogenesis results in the generation of miRNA isoforms (isomiRs) which further diversify miRNA gene regulation. Single-cell RNA-sequencing (scsRNA-seq) technologies, together with computational strategies, enable exploration of miRNAs, isomiRs, and interacting RNAs at the cellular level. By integration with other miRNA-associated single-cell modalities, miRNA roles can be resolved at different stages of processing and regulation. In this review we discuss (i) single-cell experimental assays that measure miRNA and isomiR abundances, and (ii) computational methods for their analysis to investigate the mechanisms of miRNA biogenesis and post-transcriptional regulation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"522-536"},"PeriodicalIF":13.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043201","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
Genetic databases in the era of 'DSI' benefit-sharing. “DSI”惠益分享时代的基因数据库。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-06-01 Epub Date: 2025-04-17 DOI: 10.1016/j.tig.2025.03.004
Mathieu Rouard, Amber Hartman Scholz, Michael Halewood
{"title":"Genetic databases in the era of 'DSI' benefit-sharing.","authors":"Mathieu Rouard, Amber Hartman Scholz, Michael Halewood","doi":"10.1016/j.tig.2025.03.004","DOIUrl":"10.1016/j.tig.2025.03.004","url":null,"abstract":"<p><p>Genetic databases drive research by enabling open access. Recently, parties to the Convention on Biological Diversity agreed on new rules for sharing benefits from the use of digital sequence information (DSI) which upholds open access, and also imposed new requirements for data depositors, database managers, and users.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"451-455"},"PeriodicalIF":13.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034558","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 impact of human accelerated regions on neuronal development. 人类加速区对神经元发育的影响。
IF 16.3 2区 生物学
Trends in Genetics Pub Date : 2025-06-01 Epub Date: 2025-04-05 DOI: 10.1016/j.tig.2025.03.005
Jose Manuel Ruiz-Jiménez, Gabriel Santpere
{"title":"The impact of human accelerated regions on neuronal development.","authors":"Jose Manuel Ruiz-Jiménez, Gabriel Santpere","doi":"10.1016/j.tig.2025.03.005","DOIUrl":"10.1016/j.tig.2025.03.005","url":null,"abstract":"<p><p>Human accelerated regions (HARs) are the fastest-evolving sequences in the human genome since the divergence from chimpanzees. Some of these regions are suspected to have contributed to the evolution of unique human brain features. Recently, Cui et al. conducted a large-scale study identifying which HARs may have influenced neuronal function.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"459-461"},"PeriodicalIF":16.3,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796362","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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