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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
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
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 13.6 2区 生物学
Trends in Genetics Pub 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":"https://doi.org/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":""},"PeriodicalIF":13.6,"publicationDate":"2025-06-26","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
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