Advanced genetics (Hoboken, N.J.)最新文献_第6页

From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes. 从基因组化石到功能元件：假基因的进化故事。

Advanced genetics (Hoboken, N.J.) Pub Date : 2025-11-24 eCollection Date: 2025-12-01 DOI: 10.1002/ggn2.202500040

Mengyao Sun, Yanni Ma, Jia Yu

{"title":"From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.","authors":"Mengyao Sun, Yanni Ma, Jia Yu","doi":"10.1002/ggn2.202500040","DOIUrl":"10.1002/ggn2.202500040","url":null,"abstract":"Pseudogenes, as important products of genomic evolution, play unique regulatory roles in species adaptation. This review systematically summarizes the major types, functions, and regulatory mechanisms of metazoans pseudogenes, with a particular focus on their formation during primate evolution and the mechanisms underlying their retention in the human genome. Previous studies suggest that the loss of function in pseudogenes releases selective pressure, allowing them to evolve neutrally; furthermore, their latent functional or adaptive potential, such as reactivation, neofunctionalization, or evolutionary advantages conferred by gene silencing, further promotes their persistence. For instance, the integration of certain pseudogenes can introduce novel regulatory functions, while pseudogenization-induced gene inactivation may also provide selective benefits. Recent technological advances, including long-read sequencing, single-cell omics, and CRISPR-based functional interrogation, have greatly expanded our understanding of pseudogenes. We propose that pseudogene-mediated regulation plays a critical role in evolutionary processes and highlight their dynamic roles in both physiological and pathological contexts. We further discuss current research progress, limitations, and future directions, offering new perspectives for understanding genomic evolution and biomedical significance of pseudogenes.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"6 4","pages":"e00040"},"PeriodicalIF":0.0,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12747553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145866533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Identification of Cathepsin H and Metabolic Traits as Potential Biomarkers for Lung Cancer by Mendelian Randomization and Single-Cell Transcriptomics. 通过孟德尔随机化和单细胞转录组学鉴定组织蛋白酶H和代谢特征作为肺癌的潜在生物标志物。

Advanced genetics (Hoboken, N.J.) Pub Date : 2025-11-14 eCollection Date: 2025-12-01 DOI: 10.1002/ggn2.202500012

Chenghu Song, Weici Liu, Zhao He, Jiwei Liu, Ruixin Wang, Lei Wu, Yize Wang, Mingfeng Zheng, Dong Tian, Wenjun Mao

{"title":"Identification of Cathepsin H and Metabolic Traits as Potential Biomarkers for Lung Cancer by Mendelian Randomization and Single-Cell Transcriptomics.","authors":"Chenghu Song, Weici Liu, Zhao He, Jiwei Liu, Ruixin Wang, Lei Wu, Yize Wang, Mingfeng Zheng, Dong Tian, Wenjun Mao","doi":"10.1002/ggn2.202500012","DOIUrl":"10.1002/ggn2.202500012","url":null,"abstract":"Lung cancer is a major global malignancy with debated roles for cathepsin H (CTSH), a lysosomal protease, and underexplored regulation by metabolites. We analyzed lung cancer incidence and hyperglycemia-related mortality trends (1990-2021) using Joinpoint regression. Mendelian randomization (MR), meta-analysis, and two-step mediation examined CTSH and 233 metabolic traits. Single-cell RNA sequencing (scRNA-seq) and TCGA/HPA datasets validated CTSH expression. Lung cancer incidence decreased overall but rose in women, while fasting hyperglycemia-related mortality increased. CTSH elevated lung cancer and adenocarcinoma risks, with docosahexaenoic acid (22:6) and omega-3 fatty acids driving adenocarcinoma progression. A higher linoleic acid (18:2)/total fatty acid ratio reduced risk. scRNA-seq identified CTSH in myeloid cells, especially \"mo-Mac,\" which promoted tumors. CTSH expression patterns were evaluated using TCGA and HPA data, revealing protein-level overexpression in tumors with some divergence from transcriptomic results. CTSH is linked to lung cancer, particularly adenocarcinoma, with modest effects mediated by metabolites like omega-3 fatty acids. Its prominent expression in macrophages suggests novel therapeutic targets. These findings, though consistent, require further validation due to modest effect sizes and dataset heterogeneity.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"6 4","pages":"e00012"},"PeriodicalIF":0.0,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12747557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145866493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing. 直接RNA纳米孔测序检测RNA修饰的研究进展。

Advanced genetics (Hoboken, N.J.) Pub Date : 2025-10-06 eCollection Date: 2025-12-01 DOI: 10.1002/ggn2.202500041

Yaran Liu, Yang Li, Qiang Sun

{"title":"Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing.","authors":"Yaran Liu, Yang Li, Qiang Sun","doi":"10.1002/ggn2.202500041","DOIUrl":"10.1002/ggn2.202500041","url":null,"abstract":"RNA modifications add a dynamic and versatile regulatory layer to gene expression, influencing RNA stability, splicing, translation, and cellular responses. Despite their importance, traditional detection methods-such as antibody-based enrichment, chemical labeling, or indirect sequencing approaches-often suffer from limited resolution, biases, and an inability to capture modifications in their native RNA context. Oxford Nanopore Technologies (ONT) direct RNA sequencing (DRS) overcomes many of these limitations by enabling amplification-free, single-molecule, and single-nucleotide detection of diverse RNA modifications directly from native RNA molecules. In this review, recent advances in applying ONT DRS to characterize modifications beyond the extensively studied N6-methyladenosine (m6A), including 2'-O-methylation (Nm), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytidine (ac4C), N7-methylguanosine (m7G), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I) editing are summarized. Computational frameworks and basecalling innovations are highlighted that improve modification calling, with particular emphasis on approaches that detect co-occurring modifications and reveal their potential regulatory cross-talk within individual transcripts. Finally, emerging applications across synthetic systems, non-model organisms, and disease contexts are discussed, and offer a forward-looking perspective on integrating nanopore-based epitranscriptomics with multi-omics platforms to achieve a deeper and more comprehensive understanding of RNA regulation.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"6 4","pages":"e00041"},"PeriodicalIF":0.0,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12747559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145866516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Advanced genetics (Hoboken, N.J.) Pub Date : 2025-09-30

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Editorial Board: (Advanced Genetics 3/06) 编委会：（Advanced Genetics 3/06）

Advanced genetics (Hoboken, N.J.) Pub Date : 2025-09-30 DOI: 10.1002/ggn2.70012

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Advanced genetics (Hoboken, N.J.) Pub Date : 2025-09-30

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Two Decades of Optogenetic Tools: A Retrospective and a Look Ahead (Advanced Genetics 3/06) 光遗传学工具的二十年：回顾与展望（高级遗传学3/06）

Advanced genetics (Hoboken, N.J.) Pub Date : 2025-09-30 DOI: 10.1002/ggn2.70013

Xiao Duan, Mo Zhu, Shiqiang Gao

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Advanced genetics (Hoboken, N.J.) Pub Date : 2025-09-16

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3D Genome Architecture in Stem Cell Lineage Commitment: from Structural Organization to Precision Regulation 干细胞谱系承诺中的三维基因组结构：从结构组织到精确调节

Advanced genetics (Hoboken, N.J.) Pub Date : 2025-09-16 DOI: 10.1002/ggn2.202500035

Yanchi He, Wenrui Li, Lin Li, Ying Yang, Yutong Lu, Yufei Pan, Qing Wang, Yuqiang Sun, Yuxuan Xie, Mingyue Wu, Peng Luo, Wansu Sun, Hengguo Zhang

{"title":"3D Genome Architecture in Stem Cell Lineage Commitment: from Structural Organization to Precision Regulation","authors":"Yanchi He, Wenrui Li, Lin Li, Ying Yang, Yutong Lu, Yufei Pan, Qing Wang, Yuqiang Sun, Yuxuan Xie, Mingyue Wu, Peng Luo, Wansu Sun, Hengguo Zhang","doi":"10.1002/ggn2.202500035","DOIUrl":"https://doi.org/10.1002/ggn2.202500035","url":null,"abstract":"Stem cell lineage commitment is governed by intricate interactions between epigenetic mechanisms and 3D genome organization. Traditional linear epigenetics, including DNA methylation and histone modifications, cannot fully elucidate the complex spatiotemporal regulation of gene expression. Recent advances in spatial genomics technologies, such as high-throughput chromosome conformation capture (Hi-C), single-cell Hi-C, and Chromatin immunoprecipitation combined with Hi-C (Hi-ChIP), have provided unprecedented insights into genome architecture, revealing key structural units like chromatin compartments, topologically associating domains (TADs), and chromatin loops. These structures dynamically reorganize during differentiation, influencing transcriptional accessibility and lineage-specific gene activation. Additionally, liquid-liquid phase separation (LLPS)-mediated transcriptional condensates, such as transcription factories and super-enhancers, have emerged as essential regulators of gene expression patterns during cell fate transitions. The integration of multiomics data and artificial intelligence-driven predictive modeling further enhances the understanding of these regulatory networks. Despite ongoing technical challenges, including limitations in resolution, data complexity, and causal inference, recent advances continue to push the field forward. Engineered interventions such as CRISPR-based spatial genome editing and AI-powered computational platforms hold great promise for translating structural insights into targeted therapeutic strategies in regenerative medicine.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://advanced.onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202500035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145196855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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How Everything Is Connected to Everything Else – Population-Specific Connections between Adaptive Evolution, Disease Susceptibility, and Drug Responsiveness 万物是如何相互联系的——适应性进化、疾病易感性和药物反应之间的群体特异性联系

Advanced genetics (Hoboken, N.J.) Pub Date : 2025-09-10 DOI: 10.1002/ggn2.202500018

Ji Tang, Hao Zhu

{"title":"How Everything Is Connected to Everything Else – Population-Specific Connections between Adaptive Evolution, Disease Susceptibility, and Drug Responsiveness","authors":"Ji Tang, Hao Zhu","doi":"10.1002/ggn2.202500018","DOIUrl":"https://doi.org/10.1002/ggn2.202500018","url":null,"abstract":"The genome is like a kaleidoscope through which researchers have obtained varied findings, including favored mutations, disease susceptibility sites, and drug-responsive sites. Whether these findings have inherent connections is a question deserving investigation. Favored mutations enable humans to adapt to changing environments and lifestyles; however, the adaptation may come with some costs. This is because a favored mutation can change the frequency of varied neutral nucleotides across a large genomic region, and a favored mutation may become disfavored as environments and lifestyles change further. These are the best-known classes of connections whose causes and consequences have been understood. However, many favored mutations remain unidentified. Using a deep learning network (DeepFavored) that integrates statistical tests and is trained on large datasets, favored mutations are recently identified in 17 human populations. The analyses of the results, in conjunction with genome-wide association study (GWAS) data, suggest that the connection between adaptive evolution, disease susceptibility, and drug responsiveness (referred to as a trade-off) is extensive and highly population-specific. The analyses, along with other emerging evidence, suggest that there are other types of connections. In this commentary, these issues are discussed from both retrospective and prospective views, including current challenges and future directions.","PeriodicalId":72071,"journal":{"name":"Advanced genetics (Hoboken, N.J.)","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://advanced.onlinelibrary.wiley.com/doi/epdf/10.1002/ggn2.202500018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145196688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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