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Why are RNA processing factors recruited to DNA double-strand breaks? 为什么 DNA 双链断裂处会招募 RNA 处理因子？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-11-19 DOI: 10.1016/j.tig.2024.10.008
Feras E Machour, Alma Sophia Barisaac, Nabieh Ayoub
{"title":"Why are RNA processing factors recruited to DNA double-strand breaks?","authors":"Feras E Machour, Alma Sophia Barisaac, Nabieh Ayoub","doi":"10.1016/j.tig.2024.10.008","DOIUrl":"10.1016/j.tig.2024.10.008","url":null,"abstract":"<p><p>DNA double-strand break (DSB) induction leads to local transcriptional silencing at damage sites, raising the question: Why are RNA processing factors (RPFs), including splicing factors, rapidly recruited to these sites? Recent findings show that DSBs cluster in a chromatin compartment termed the 'D compartment', where DNA damage response (DDR) genes relocate and undergo transcriptional activation. Here, we propose two non-mutually exclusive models to elucidate the rationale behind the recruitment of RPFs to DSB sites. First, RPFs circulate through the D compartment to process transcripts of the relocated DDR genes. Second, the D compartment serves as a 'post-translational modifications (PTMs) hub', altering RPF activity and leading to the production of unique DNA damage-induced transcripts, which are essential for orchestrating the DDR.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"194-200"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142683574","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
Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies. 用完整的灵长类基因组和先进的生物技术推进进化医学。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-12-02 DOI: 10.1016/j.tig.2024.11.001
Kaiyue Ma, Xiangyu Yang, Yafei Mao
{"title":"Advancing evolutionary medicine with complete primate genomes and advanced biotechnologies.","authors":"Kaiyue Ma, Xiangyu Yang, Yafei Mao","doi":"10.1016/j.tig.2024.11.001","DOIUrl":"10.1016/j.tig.2024.11.001","url":null,"abstract":"<p><p>Evolutionary medicine, which integrates evolutionary biology and medicine, significantly enhances our understanding of human traits and disease susceptibility. However, previous studies in this field have often focused on single-nucleotide variants due to technological limitations in characterizing complex genomic regions, hindering the comprehensive analyses of their evolutionary origins and clinical significance. In this review, we summarize recent advancements in complete telomere-to-telomere (T2T), primate genomes and other primate resources, and illustrate how these resources facilitate the research of complex regions. We focus on several biomedically relevant regions to examine the relationship between primate genome evolution and human diseases. We also highlight the potentials of high-throughput functional genomic technologies for assessing candidate loci. Finally, we discuss future directions for primate research within the context of evolutionary medicine.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"201-217"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774833","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
To genetic rescue or not? 要不要拯救基因？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-11-27 DOI: 10.1016/j.tig.2024.11.004
Karin Norén, Malin Hasselgren
{"title":"To genetic rescue or not?","authors":"Karin Norén, Malin Hasselgren","doi":"10.1016/j.tig.2024.11.004","DOIUrl":"10.1016/j.tig.2024.11.004","url":null,"abstract":"<p><p>Inbreeding depression and genetic rescue are central themes in conservation biology. Translocation is a tool to assist genetic rescue but is connected to risks. A new study by Quinn et al. used genomic data to evaluate translocations as a potential action in montane red fox, bringing important implications also for other threatened species.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"185-186"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741125","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
Ambient storage of genomic time capsules. 基因组时间胶囊的环境储存。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-12-29 DOI: 10.1016/j.tig.2024.11.012
Euan A Ashley
{"title":"Ambient storage of genomic time capsules.","authors":"Euan A Ashley","doi":"10.1016/j.tig.2024.11.012","DOIUrl":"10.1016/j.tig.2024.11.012","url":null,"abstract":"<p><p>While the cost of genome sequencing has decreased, -80°C DNA preservation and raw sequence data archiving remain expensive. Transitioning to room-temperature DNA preservation could reduce costs, lessen researchers' reliance on the electrical grid, and encourage a future proofing strategy of periodical updating with higher quality sequencing instead of long-term storage of raw signal data. A new technology recently described by Prince et al. that could help realize these goals is Thermoset-REinforced Xeropreservation (T-REX).</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"181-182"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907920","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
Bacterial intragenic inversions: a new layer of diversity. 细菌基因内反转：一个新的多样性层。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-12-19 DOI: 10.1016/j.tig.2024.12.002
Brantley Hall, Xiaofang Jiang
{"title":"Bacterial intragenic inversions: a new layer of diversity.","authors":"Brantley Hall, Xiaofang Jiang","doi":"10.1016/j.tig.2024.12.002","DOIUrl":"10.1016/j.tig.2024.12.002","url":null,"abstract":"<p><p>DNA inversions in bacteria were known to create diversity through intergenic or partial intergenic changes. Now, Chanin, West, et al. reveal intragenic inversions, enabling single genes to encode multiple protein variants via sequence recoding or truncation - an unexpected mechanism for expanding protein diversity without increasing genome size.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"183-184"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873498","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
Unraveling aging from transcriptomics. 从转录组学揭示衰老。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-10-17 DOI: 10.1016/j.tig.2024.09.006
Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han
{"title":"Unraveling aging from transcriptomics.","authors":"Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han","doi":"10.1016/j.tig.2024.09.006","DOIUrl":"10.1016/j.tig.2024.09.006","url":null,"abstract":"<p><p>Research into aging constitutes a pivotal endeavor aimed at elucidating the underlying biological mechanisms governing aging and age-associated diseases, as well as promoting healthy longevity. Recent advances in transcriptomic technologies, such as bulk RNA sequencing (RNA-seq), single-cell transcriptomics, and spatial transcriptomics, have revolutionized our ability to study aging at unprecedented resolution and scale. These technologies present novel opportunities for the discovery of biomarkers, elucidation of molecular pathways, and development of targeted therapeutic strategies for age-related disorders. This review surveys recent breakthroughs in different types of transcripts on aging, such as mRNA, long noncoding (lnc)RNA, tRNA, and miRNA, highlighting key findings and discussing their potential implications for future studies in this field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"218-235"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480921","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 new hypothesis to explain disease dominance. 一个解释疾病优势的新假说。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2025-01-08 DOI: 10.1016/j.tig.2024.11.009
Brian Juvik, Lara Falcucci, Pia R Lundegaard, Didier Y R Stainier
{"title":"A new hypothesis to explain disease dominance.","authors":"Brian Juvik, Lara Falcucci, Pia R Lundegaard, Didier Y R Stainier","doi":"10.1016/j.tig.2024.11.009","DOIUrl":"10.1016/j.tig.2024.11.009","url":null,"abstract":"<p><p>The onset and progression of dominant diseases are thought to result from haploinsufficiency or dominant negative effects. Here, we propose transcriptional adaptation (TA), a newly identified response to mRNA decay, as an additional cause of some dominant diseases. TA modulates the expression of so-called adapting genes, likely via mRNA decay products, resulting in genetic compensation or a worsening of the phenotype. Recent studies have challenged the current concepts of haploinsufficiency or poison proteins as the mechanisms underlying certain dominant diseases, including Brugada syndrome, hypertrophic cardiomyopathy, and frontotemporal lobar degeneration. We hypothesize that for these and other dominant diseases, when the underlying mutation leads to mRNA decay, the phenotype is due at least partly to the dysregulation of gene expression via TA.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"187-193"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958929","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 euglenoid genomics: unravelling the fascinating biology of a complex clade. 曙光基因组学的进展：揭开一个复杂支系迷人的生物学面纱。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-08-14 DOI: 10.1016/j.tig.2024.07.007
Oskar Fields, Michael J Hammond, Xiao Xu, Ellis C O'Neill
{"title":"Advances in euglenoid genomics: unravelling the fascinating biology of a complex clade.","authors":"Oskar Fields, Michael J Hammond, Xiao Xu, Ellis C O'Neill","doi":"10.1016/j.tig.2024.07.007","DOIUrl":"10.1016/j.tig.2024.07.007","url":null,"abstract":"<p><p>Euglenids have long been studied due to their unique physiology and versatile metabolism, providing underpinnings for much of our understanding of photosynthesis and biochemistry, and a growing opportunity in biotechnology. Until recently there has been a lack of genetic studies due to their large and complex genomes, but recently new technologies have begun to unveil their genetic capabilities. Whilst much research has focused on the model organism Euglena gracilis, other members of the euglenids have now started to receive due attention. Currently only poor nuclear genome assemblies of E. gracilis and Rhabdomonas costata are available, but there are many more plastid genome sequences and an increasing number of transcriptomes. As more assemblies become available, there are great opportunities to understand the fundamental biology of these organisms and to exploit them for biotechnology.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"251-260"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989529","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 ABCs of the H2Bs: The histone H2B sequences, variants, and modifications.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-20 DOI: 10.1016/j.tig.2025.01.003
Anna J Voss, Erica Korb
{"title":"The ABCs of the H2Bs: The histone H2B sequences, variants, and modifications.","authors":"Anna J Voss, Erica Korb","doi":"10.1016/j.tig.2025.01.003","DOIUrl":"https://doi.org/10.1016/j.tig.2025.01.003","url":null,"abstract":"<p><p>Histone proteins are the building blocks of chromatin, and function by wrapping DNA into complex structures that control gene expression. Histone proteins are regulated by post-translational modifications (PTMs) and by histone variant exchange. In this review, we will provide an overview of one of these histones: H2B. We will first define the sequences of human and mouse H2B proteins and discuss potential designations for canonical H2B. We will also describe the differential functions of H2B variants compared with canonical H2B. Finally, we will summarize known H2B modifications and their functions in regulating transcription. Through review of H2B genes, proteins, variants, and modifications, we aim to highlight the importance of H2B for epigenetic and transcriptional regulation of the cell.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143473214","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
Transposon-host arms race: a saga of genome evolution.
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-19 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":"https://doi.org/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":""},"PeriodicalIF":13.6,"publicationDate":"2025-02-19","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
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