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The impact of human accelerated regions on neuronal development.
IF 13.6 2区 生物学
Trends in Genetics Pub 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":"https://doi.org/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":""},"PeriodicalIF":13.6,"publicationDate":"2025-04-05","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
An innovation in host responses to escalating genomic conflicts.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-04 DOI: 10.1016/j.tig.2025.03.001
Emiliano Martí, Amanda M Larracuente
{"title":"An innovation in host responses to escalating genomic conflicts.","authors":"Emiliano Martí, Amanda M Larracuente","doi":"10.1016/j.tig.2025.03.001","DOIUrl":"https://doi.org/10.1016/j.tig.2025.03.001","url":null,"abstract":"<p><p>Conflicts between selfish elements and their hosts can trigger rapid structural and regulatory changes in genomes. Chen et al. discovered a novel species-specific innovation in response to a meiotic driver in Drosophila melanogaster. Their discovery highlights a new dimension in adaptive responses to selfish elements, with broad evolutionary consequences.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789184","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
DNA lesions piece together impossible trees.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-02 DOI: 10.1016/j.tig.2025.03.002
Claudia Arnedo-Pac, Sarah J Aitken
{"title":"DNA lesions piece together impossible trees.","authors":"Claudia Arnedo-Pac, Sarah J Aitken","doi":"10.1016/j.tig.2025.03.002","DOIUrl":"https://doi.org/10.1016/j.tig.2025.03.002","url":null,"abstract":"<p><p>DNA lesions can persist through multiple cell cycles, resulting in mutational strand asymmetry, multiallelic variation, and somatic mosaicism. But for how long do these lesions persist? Recent work from Spencer Chapman et al. shows that they can last for months to years, even arising from endogenous exposures in utero.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782008","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
Developmental evolution in fast-forward: insect male genital diversification. 快进的发育进化：昆虫雄性生殖器的多样化。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-11-21 DOI: 10.1016/j.tig.2024.10.005
Maria D S Nunes, Alistair P McGregor
{"title":"Developmental evolution in fast-forward: insect male genital diversification.","authors":"Maria D S Nunes, Alistair P McGregor","doi":"10.1016/j.tig.2024.10.005","DOIUrl":"10.1016/j.tig.2024.10.005","url":null,"abstract":"<p><p>Insect male genitalia are among the fastest evolving structures of animals. Studying these changes among closely related species represents a powerful approach to dissect developmental processes and genetic mechanisms underlying phenotypic diversification and the underlying evolutionary drivers. Here, we review recent breakthroughs in understanding the developmental and genetic bases of the evolution of genital organs among Drosophila species and other insects. This work has helped reveal how tissue and organ size evolve and understand the appearance of morphological novelties, and how these phenotypic changes are generated through altering gene expression and redeployment of gene regulatory networks. Future studies of genital evolution in Drosophila and a wider range of insects hold great promise to help understand the specification, differentiation, and diversification of organs more generally.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"345-356"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142694016","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
Keeping it safe: control of meiotic chromosome breakage. 保证安全：控制减数分裂染色体断裂。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-12-12 DOI: 10.1016/j.tig.2024.11.006
Adhithi R Raghavan, Andreas Hochwagen
{"title":"Keeping it safe: control of meiotic chromosome breakage.","authors":"Adhithi R Raghavan, Andreas Hochwagen","doi":"10.1016/j.tig.2024.11.006","DOIUrl":"10.1016/j.tig.2024.11.006","url":null,"abstract":"<p><p>Meiotic cells introduce numerous programmed DNA double-strand breaks (DSBs) into their genome to stimulate crossover recombination. DSB numbers must be high enough to ensure each homologous chromosome pair receives the obligate crossover required for accurate meiotic chromosome segregation. However, every DSB also increases the risk of aberrant or incomplete DNA repair, and thus genome instability. To mitigate these risks, meiotic cells have evolved an intricate network of controls that modulates the timing, levels, and genomic location of meiotic DSBs. This Review summarizes our current understanding of these controls with a particular focus on the mechanisms that prevent meiotic DSB formation at the wrong time or place, thereby guarding the genome from potentially catastrophic meiotic errors.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"315-329"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822852","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 language models: opportunities and challenges. 基因组语言模型：机遇与挑战。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2025-01-02 DOI: 10.1016/j.tig.2024.11.013
Gonzalo Benegas, Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S Song
{"title":"Genomic language models: opportunities and challenges.","authors":"Gonzalo Benegas, Chengzhong Ye, Carlos Albors, Jianan Canal Li, Yun S Song","doi":"10.1016/j.tig.2024.11.013","DOIUrl":"10.1016/j.tig.2024.11.013","url":null,"abstract":"<p><p>Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of natural language processing is to understand sequences of words, a major objective in biology is to understand biological sequences. Genomic language models (gLMs), which are LLMs trained on DNA sequences, have the potential to significantly advance our understanding of genomes and how DNA elements at various scales interact to give rise to complex functions. To showcase this potential, we highlight key applications of gLMs, including functional constraint prediction, sequence design, and transfer learning. Despite notable recent progress, however, developing effective and efficient gLMs presents numerous challenges, especially for species with large, complex genomes. Here, we discuss major considerations for developing and evaluating gLMs.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"286-302"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928772","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 buffering mechanisms in SNF2-family translocases.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2025-01-30 DOI: 10.1016/j.tig.2025.01.005
Sumedha Agashe, Alessandro Vindigni
{"title":"Genetic buffering mechanisms in SNF2-family translocases.","authors":"Sumedha Agashe, Alessandro Vindigni","doi":"10.1016/j.tig.2025.01.005","DOIUrl":"10.1016/j.tig.2025.01.005","url":null,"abstract":"<p><p>SNF2-family DNA translocases, a large family of ATPases, have poorly defined roles in genomic stability. In a recent study, Feng et al. identified a synthetic lethal interaction between the SNF2 translocase SMARCAL1 and Fanconi anemia (FA) group M (FANCM), revealing a new genetic buffering mechanism that maintains genome stability by aiding DNA replication at loci enriched in simple repeats.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"266-267"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076334","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
A more elaborate genetic clock for clonal species. 克隆物种的遗传时钟更加精细。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-11-26 DOI: 10.1016/j.tig.2024.11.002
Jinhee Ryu, Yeonjin Kim, Young Seok Ju
{"title":"A more elaborate genetic clock for clonal species.","authors":"Jinhee Ryu, Yeonjin Kim, Young Seok Ju","doi":"10.1016/j.tig.2024.11.002","DOIUrl":"10.1016/j.tig.2024.11.002","url":null,"abstract":"<p><p>The genetic clock is a well-established tool used in evolutionary biology for estimating divergence times between species, individuals, or cells based on DNA sequence changes. Yu et al. have revisited the clock to make it applicable to clonal multicellular organisms that expand through asexual reproduction mechanisms, enabling more comprehensive evolutionary tracking.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"268-270"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740780","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
Q-rich activation domains: flexible 'rulers' for transcription start site selection? 富q激活域：转录起始位点选择的灵活“尺子”？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2024-12-07 DOI: 10.1016/j.tig.2024.11.008
Andrea Bernardini, Roberto Mantovani
{"title":"Q-rich activation domains: flexible 'rulers' for transcription start site selection?","authors":"Andrea Bernardini, Roberto Mantovani","doi":"10.1016/j.tig.2024.11.008","DOIUrl":"10.1016/j.tig.2024.11.008","url":null,"abstract":"<p><p>Recent findings broadened the function of RNA polymerase II (Pol II) proximal promoter motifs from quantitative regulators of transcription to important determinants of transcription start site (TSS) position. These motifs are recognized by transcription factors (TFs) that we propose to term 'ruler' TFs (rTFs), such as NRF1, NF-Y, YY1, ZNF143, BANP, and members of the SP, ETS, and CRE families, sharing as a common feature a glutamine-rich (Q-rich) effector domain also enriched in valine, isoleucine, and threonine (QVIT-rich). We propose that rTFs guide TSS location by constraining the position of the pre-initiation complex (PIC) during its promoter recognition phase through a specialized, and still enigmatic, class of activation domains.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"275-285"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796418","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
Mitochondrial-derived microproteins: from discovery to function: (Trends in Genetics, 41:2 pp:132-145, 2025).
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-04-01 Epub Date: 2025-03-05 DOI: 10.1016/j.tig.2025.02.003
Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen
{"title":"Mitochondrial-derived microproteins: from discovery to function: (Trends in Genetics, 41:2 pp:132-145, 2025).","authors":"Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen","doi":"10.1016/j.tig.2025.02.003","DOIUrl":"10.1016/j.tig.2025.02.003","url":null,"abstract":"","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"357"},"PeriodicalIF":13.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574725","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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