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Transposon-host arms race: a saga of genome evolution. 转座子宿主军备竞赛：基因组进化的传奇。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-01 Epub Date: 2025-02-20 DOI: 10.1016/j.tig.2025.01.009
Yuka W Iwasaki, Keisuke Shoji, Shinichi Nakagwa, Tomoichiro Miyoshi, Yukihide Tomari
{"title":"Transposon-host arms race: a saga of genome evolution.","authors":"Yuka W Iwasaki, Keisuke Shoji, Shinichi Nakagwa, Tomoichiro Miyoshi, Yukihide Tomari","doi":"10.1016/j.tig.2025.01.009","DOIUrl":"10.1016/j.tig.2025.01.009","url":null,"abstract":"<p><p>Once considered 'junk DNA,' transposons or transposable elements (TEs) are now recognized as key drivers of genome evolution, contributing to genetic diversity, gene regulation, and species diversification. However, their ability to move within the genome poses a potential threat to genome integrity, promoting the evolution of robust host defense systems such as Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KRAB-ZFPs), the human silencing hub (HUSH) complex, 4.5SH RNAs, and PIWI-interacting RNAs (piRNAs). This ongoing evolutionary arms race between TEs and host defenses continuously reshapes genome architecture and function. This review outlines various host defense mechanisms and explores the dynamic coevolution of TEs and host defenses in animals, highlighting how the defense mechanisms not only safeguard the host genomes but also drive genetic innovation through the arms race.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"369-389"},"PeriodicalIF":13.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143470015","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
DEAD/DEAH-box RNA helicases shape the risk of neurodevelopmental disorders. 死亡/死亡盒RNA解旋酶影响神经发育障碍的风险。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-01 Epub Date: 2025-01-18 DOI: 10.1016/j.tig.2024.12.006
Chiara Fiorenzani, Adele Mossa, Silvia De Rubeis
{"title":"DEAD/DEAH-box RNA helicases shape the risk of neurodevelopmental disorders.","authors":"Chiara Fiorenzani, Adele Mossa, Silvia De Rubeis","doi":"10.1016/j.tig.2024.12.006","DOIUrl":"10.1016/j.tig.2024.12.006","url":null,"abstract":"<p><p>The DEAD/DEAH-box family of RNA helicases (RHs) is among the most abundant and conserved in eukaryotes. These proteins catalyze the remodeling of RNAs to regulate their splicing, stability, localization, and translation. Rare genetic variants in DEAD/DEAH-box proteins have recently emerged as being associated with neurodevelopmental disorders (NDDs). Analyses in cellular and animal models have uncovered fundamental roles for these proteins during brain development. We discuss the genetic and functional evidence that implicates DEAD/DEAH-box proteins in brain development and NDDs, with a focus on how structural insights from paralogous genes can be leveraged to advance our understanding of the pathogenic mechanisms at play.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"437-449"},"PeriodicalIF":13.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016594","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
Empowering continuous evolution of proteins by in vivo mutagenesis. 通过体内诱变使蛋白质不断进化。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-01 Epub Date: 2025-02-11 DOI: 10.1016/j.tig.2025.01.007
Zhanzhi Liu, Jing Wu
{"title":"Empowering continuous evolution of proteins by in vivo mutagenesis.","authors":"Zhanzhi Liu, Jing Wu","doi":"10.1016/j.tig.2025.01.007","DOIUrl":"10.1016/j.tig.2025.01.007","url":null,"abstract":"<p><p>In vivo mutagenesis enriches genetic polymorphism within cells, which is pivotal for triggering continuous evolution. Remarkable strides have been made in this field. Here, we summarize the current in vivo mutagenesis methods focusing on the theme of mutation range and provide an outlook on their future directions, offering inspiration to relevant researchers.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"364-368"},"PeriodicalIF":13.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411462","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
Evolution of piRNA-guided defense against transposable elements. pirna引导的转座因子防御的进化。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-01 Epub Date: 2024-12-12 DOI: 10.1016/j.tig.2024.11.011
Shashank Pritam, Sarah Signor
{"title":"Evolution of piRNA-guided defense against transposable elements.","authors":"Shashank Pritam, Sarah Signor","doi":"10.1016/j.tig.2024.11.011","DOIUrl":"10.1016/j.tig.2024.11.011","url":null,"abstract":"<p><p>Transposable elements (TEs) shape every aspect of genome biology, influencing genome stability, size, and organismal fitness. Following the 2007 discovery of the piRNA defense system, researchers have made numerous findings about organisms' defenses against these genomic invaders. TEs are suppressed by a 'genomic immune system', where TE insertions within specialized regions called PIWI-interacting RNA (piRNA) clusters produce small RNAs responsible for their suppression. The evolution of piRNA clusters and the piRNA system is only now being understood, largely because most research has been conducted in developmental biology labs using only one to two genotypes of Drosophila melanogaster. While piRNAs themselves were identified simultaneously in various organisms (flies, mice, rats, and zebrafish) in 2006-2007, detailed work on piRNA clusters has only recently expanded beyond D. melanogaster. By studying piRNA cluster evolution in various organisms from an evolutionary perspective, we are beginning to understand more about TE suppression mechanisms and organism-TE coevolution.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"390-401"},"PeriodicalIF":13.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822812","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
Conserved dynamics of natal down-to-juvenile feather transition. 幼崽羽毛过渡的保守动力学。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-01 Epub Date: 2025-01-09 DOI: 10.1016/j.tig.2024.12.007
Marie Manceau
{"title":"Conserved dynamics of natal down-to-juvenile feather transition.","authors":"Marie Manceau","doi":"10.1016/j.tig.2024.12.007","DOIUrl":"10.1016/j.tig.2024.12.007","url":null,"abstract":"<p><p>Despite the ecological importance of the feather cover during early avian life, the events controlling the transition from natal down to juvenile feathers are poorly understood. Chen et al. demonstrate that this transition is characterized by a series of morphological and molecular changes strikingly conserved between precocial and altricial species.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"362-363"},"PeriodicalIF":13.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967103","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. 宿主对不断升级的基因组冲突反应的创新。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-01 Epub 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":"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":"359-361"},"PeriodicalIF":13.6,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055473/pdf/","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":"OA","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981862/pdf/","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":"OA","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. snf2家族易位的遗传缓冲机制。
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
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
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