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The ABCs of the H2Bs: The histone H2B sequences, variants, and modifications. H2B的abc：组蛋白H2B序列、变异和修饰。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-06-01 Epub 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":"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":"506-521"},"PeriodicalIF":13.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12167159/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Contributions of epigenomic and epitranscriptomic methylation to animal colouration. 表观基因组和表转录组甲基化对动物着色的贡献。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-27 DOI: 10.1016/j.tig.2025.04.010
Nicholas Strowbridge, David R Vieites, Michael G Ritchie, Kathryn R Elmer
{"title":"Contributions of epigenomic and epitranscriptomic methylation to animal colouration.","authors":"Nicholas Strowbridge, David R Vieites, Michael G Ritchie, Kathryn R Elmer","doi":"10.1016/j.tig.2025.04.010","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.010","url":null,"abstract":"<p><p>Due to its high variation and its diversity of functional roles, animal colouration has long been a fascinating phenotype for geneticists. While the loci underpinning colour are relatively well known, there remain components of unexplained variation. The contribution of DNA and RNA methylation to these molecular mechanisms of colouration is only now being explored. Recent research has shown that DNA (m<sup>5</sup>C) methylation plays a role in plastic colouration change, the development of colour, and adult intra- and interindividual colouration differences. Studies on RNA (m<sup>6</sup>A) methylation are few but suggest that it also contributes to colour differences. Emerging advances in native DNA and RNA sequencing will allow a novel understanding of methylation contributions to colour evolution and development.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175832","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
Optimizing homology-directed repair for gene editing: the potential of single-stranded DNA donors. 优化基因编辑的同源修复：单链DNA供体的潜力。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-27 DOI: 10.1016/j.tig.2025.04.014
Ying-Ying Jin, Peng Zhang, De-Pei Liu
{"title":"Optimizing homology-directed repair for gene editing: the potential of single-stranded DNA donors.","authors":"Ying-Ying Jin, Peng Zhang, De-Pei Liu","doi":"10.1016/j.tig.2025.04.014","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.014","url":null,"abstract":"<p><p>CRISPR (clustered regularly interspaced short palindromic repeat) system-based precise genome editing remarkably impacts both scientific investigation and therapeutic practices. Among various techniques, DNA donor-mediated homology-directed repair (HDR) represents a promising method for precise gene editing. Although efficiency constraints have previously limited HDR, recent advancements have significantly enhanced its effectiveness. Therefore, it is essential to highlight the progress made in this field and to reassess the potential of the HDR approach. In this review, we explore the fundamental principles of HDR-dependent gene editing and evaluate current strategies to enhance HDR efficiency, with particular emphasis on single-stranded DNA (ssDNA) donor-mediated HDR. Finally, we discuss the prospects of high-efficiency ssDNA donor-mediated precise gene editing in laboratory research and clinical therapies.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175833","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
Unlocking the potential of CRISPR-associated transposons: from structural to functional insights. 解锁crispr相关转座子的潜力：从结构到功能洞察。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-19 DOI: 10.1016/j.tig.2025.04.005
Francisco Tenjo-Castaño, Sweta Suman Rout, Sanjay Dey, Guillermo Montoya
{"title":"Unlocking the potential of CRISPR-associated transposons: from structural to functional insights.","authors":"Francisco Tenjo-Castaño, Sweta Suman Rout, Sanjay Dey, Guillermo Montoya","doi":"10.1016/j.tig.2025.04.005","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.005","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR)-associated transposons (CASTs) are emerging genome-editing tools that enable RNA-guided DNA integration without inducing double-strand breaks (DSBs). Unlike CRISPR-associated (Cas) nucleases, CASTs use transposon machinery to insert large DNA segments with high precision, potentially reducing off-target effects and bypassing DNA damage responses. CASTs are categorized into classes 1 and 2, each employing distinct mechanisms for DNA targeting and integration. Recent structural insights have elucidated how CASTs recognize target sites, recruit transposases, and mediate insertion. These advances position CASTs as promising tools for genome engineering in bacteria and possibly in mammalian cells. Key challenges remain in enhancing efficiency and specificity, particularly for therapeutic use. Ongoing research aims to evolve CAST systems for precise, large-scale genome editing in human cells.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112787","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
Selection on the epigenome: small RNA inheritance in animal evolution. 表观基因组的选择：动物进化中的小RNA遗传。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-15 DOI: 10.1016/j.tig.2025.04.007
Isaac Harris, Simone Immler, Tracey Chapman, Alexei A Maklakov
{"title":"Selection on the epigenome: small RNA inheritance in animal evolution.","authors":"Isaac Harris, Simone Immler, Tracey Chapman, Alexei A Maklakov","doi":"10.1016/j.tig.2025.04.007","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.007","url":null,"abstract":"<p><p>The inheritance of small RNAs (sRNAs) is taxonomically widespread. Changing environments alter the production and presence of sRNAs in the germline, and this can in theory either increase offspring phenotypic variance as an evolutionary bet-hedging strategy or elicit predictive and adaptive phenotypic responses that increase offspring fitness. Nevertheless, the putative role of sRNA inheritance systems in adaptive evolution is still debated and it is currently unclear how selection acts on sRNAs. We outline two adaptive sRNA inheritance strategies - specialist and generalist - and discuss non-adaptive alternatives and the evolutionary implications of different strategies. Our review suggests that the role of natural selection in sRNA inheritance has been significantly overlooked, potentially leading to misinterpretations of the causal agents and the evolutionary implications of sRNA inheritance.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086953","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
Epitranscriptome-epigenome interactions in development and disease mechanisms. 发育和疾病机制中的表观转录组-表观基因组相互作用。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-14 DOI: 10.1016/j.tig.2025.04.009
Chengyu Li, Kexuan Chen, Xiaoyu Li, Xushen Xiong
{"title":"Epitranscriptome-epigenome interactions in development and disease mechanisms.","authors":"Chengyu Li, Kexuan Chen, Xiaoyu Li, Xushen Xiong","doi":"10.1016/j.tig.2025.04.009","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.009","url":null,"abstract":"<p><p>Crosstalk between epitranscriptomic modifications to RNA and epigenomic modifications to DNA and histones plays fundamental roles in development and disease. Here, we summarize two major regulatory modes of the crosstalk between the epigenome and epitranscriptome. In the 'cis mode', the crosstalk occurs co-transcriptionally, with direct interactions observed between epigenetic modifications mediated by their regulators. In the 'trans mode', the modification of an epigenetic layer regulates the expression of another epigenetic layer's writers/erasers and subsequently induces downstream epigenetic alteration. Additionally, we focus on the functional roles of the crosstalk mechanism in physiological and pathological contexts, including development, differentiation, cancer, and complex genetic diseases. Lastly, we discuss the potential future directions for a systematic understanding of epigenetic crosstalk in development and disease.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081696","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
Epigenetic perspectives on wheat speciation, adaptation, and development. 小麦物种形成、适应和发育的表观遗传学观点。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-09 DOI: 10.1016/j.tig.2025.04.008
Xuemei Liu, Dongzhi Wang, Zhaoheng Zhang, Xuelei Lin, Jun Xiao
{"title":"Epigenetic perspectives on wheat speciation, adaptation, and development.","authors":"Xuemei Liu, Dongzhi Wang, Zhaoheng Zhang, Xuelei Lin, Jun Xiao","doi":"10.1016/j.tig.2025.04.008","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.008","url":null,"abstract":"<p><p>Bread wheat (Triticum aestivum) has undergone a complex evolutionary history shaped by polyploidization, domestication, and adaptation. Recent advances in multiomics approaches have shed light on the role of epigenetic mechanisms, including DNA methylation, histone modification, chromatin accessibility, and noncoding RNAs, in regulating gene expression throughout these processes. Epigenomic reprogramming contributes to genome stability and subgenome differentiation and modulates key agronomic traits by influencing flowering time, environmental responses, and developmental programs. This review synthesizes current insights into epigenetic regulation of wheat speciation, adaptation, and development, highlighting their potential applications in crop improvement. A deeper understanding of these mechanisms will facilitate targeted breeding strategies leveraging epigenetic variations to enhance wheat resilience and productivity in the face of changing environments.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052874","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
New dimensions in the molecular genetics of insect chemoreception. 昆虫化学接受分子遗传学的新维度。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-07 DOI: 10.1016/j.tig.2025.04.003
Gaëlle J S Talross, John R Carlson
{"title":"New dimensions in the molecular genetics of insect chemoreception.","authors":"Gaëlle J S Talross, John R Carlson","doi":"10.1016/j.tig.2025.04.003","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.003","url":null,"abstract":"<p><p>Chemoreception is the foundation of olfaction and taste, which in insects underlie the detection of humans to whom they spread disease and crops that they ravage. Recent advances have provided clear and in some cases surprising new insights into the molecular genetics of chemoreception. We describe mechanisms that govern the choice of a single Odorant receptor gene by an olfactory receptor neuron in Drosophila. We highlight genetic and epigenetic mechanisms by which chemoreceptor expression can be modulated. Exitrons, RNA editing, and pseudo-pseudogenes in chemosensory systems are described. We summarize key insights from the recent structural determinations of odorant and taste receptors. Finally, new molecular components of chemosensory systems, including long noncoding RNAs, are described.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063273","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
Molecular circuits for genomic recording of cellular events. 细胞事件基因组记录的分子电路。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-06 DOI: 10.1016/j.tig.2025.04.004
Wei Chen, Junhong Choi
{"title":"Molecular circuits for genomic recording of cellular events.","authors":"Wei Chen, Junhong Choi","doi":"10.1016/j.tig.2025.04.004","DOIUrl":"https://doi.org/10.1016/j.tig.2025.04.004","url":null,"abstract":"<p><p>Advances in precise genome editing are enabling genomic recordings of cellular events. Since the initial demonstration of CRISPR-based genome editing, the field of genomic recording has witnessed key strides in lineage recording, where clonal lineage relationships among cells are indirectly recorded as synthetic mutations. However, methods for directly recording and reconstructing past cellular events are still limited, and their potential for revealing new insights into cell fate decisions has yet to be realized. The field needs new sensing modules and genetic circuit architectures that faithfully encode past cellular states into genomic DNA recordings to achieve such goals. Here we review recently developed strategies to construct diverse sensors and explore how emerging synthetic biology tools may help to build molecular circuits for genomic recording of diverse cellular events.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144044657","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
Intragenomic mutational heterogeneity: structural and functional insights from gene evolution. 基因组内突变异质性：基因进化的结构和功能见解。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-05-05 DOI: 10.1016/j.tig.2025.03.007
Yuichiro Hara, Shigehiro Kuraku
{"title":"Intragenomic mutational heterogeneity: structural and functional insights from gene evolution.","authors":"Yuichiro Hara, Shigehiro Kuraku","doi":"10.1016/j.tig.2025.03.007","DOIUrl":"https://doi.org/10.1016/j.tig.2025.03.007","url":null,"abstract":"<p><p>Variation of mutation rates between species has been documented over decades, but the variation between different regions of a genome has been less often discussed. Recent studies using high-quality sequence data have revealed previously unknown levels of intragenomic heterogeneity of mutation rates and their association with other structural and functional features of DNA sequences. This article reviews accumulating evidence of this intragenomic heterogeneity and speculates its cause and influence on organismal phenotypes.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050042","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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