Pub Date : 2026-01-07DOI: 10.1016/j.ygeno.2026.111197
Yihan Li , Jiangwei Liu , Qian Wang , Yin Li , Xianzhong Wang , Jiaojiao Zhang
Adenosine triphosphate (ATP) is essential for sperm motility. We previously found that optimized non-thermal dielectric barrier discharge (DBD) plasma treatment enhanced boar sperm quality by increasing ATP levels. However, the molecular mechanisms underlying this process, particularly the role of competing endogenous RNA (ceRNA) networks, remain unclear. In this study, a total of 266 mRNAs, 163 miRNAs, and 37 circRNAs were identified as differentially expressed in boar spermatozoa treated with optimized DBD plasma. Functional enrichment analysis revealed that ATP-related pathways, including AMPK, mTOR, and cAMP signaling, were significantly enriched. A circRNA–miRNA–mRNA regulatory network was constructed, and two key ceRNA axes, circRNA7761–miR-7-3p–TECRL/CYP24A1/LOC100515741 and circRNA7508–miR-202-5p–CYP2A19/HHIP/WNT2, were identified in the network. These axes are predicted to enhance ATP production by regulating mitochondrial function and energy homeostasis, thereby improving sperm quality. This study provides novel mechanistic insights into the modulation of sperm energy metabolism by DBD plasma through ceRNA networks, thereby offering new theoretical foundations and potential molecular targets for improving male fertility and treating male infertility.
三磷酸腺苷（ATP）对精子的活力至关重要。我们之前发现，优化的非热介质阻挡放电（DBD）等离子体处理通过提高ATP水平来提高猪精子质量。然而，这一过程的分子机制，特别是内源性RNA （ceRNA）网络的竞争作用仍不清楚。在本研究中，共鉴定出266个mrna、163个mirna和37个circrna在经过优化的DBD血浆处理的猪精子中差异表达。功能富集分析显示，包括AMPK、mTOR和cAMP信号在内的atp相关通路显著富集。构建了一个circRNA-miRNA-mRNA调控网络，并在该网络中鉴定出两个关键的ceRNA轴circrna7761 - mir -7- 3d - tecrl /CYP24A1/LOC100515741和circRNA7508-miR-202-5p-CYP2A19/ hip /WNT2。预计这些轴通过调节线粒体功能和能量稳态来提高ATP的产生，从而提高精子质量。本研究为DBD血浆通过ceRNA网络调控精子能量代谢提供了新的机制见解，从而为提高男性生育能力和治疗男性不育症提供了新的理论基础和潜在的分子靶点。
{"title":"Identification and functional prediction of ceRNA networks regulating ATP levels in boar spermatozoa treated with non-thermal plasma","authors":"Yihan Li , Jiangwei Liu , Qian Wang , Yin Li , Xianzhong Wang , Jiaojiao Zhang","doi":"10.1016/j.ygeno.2026.111197","DOIUrl":"10.1016/j.ygeno.2026.111197","url":null,"abstract":"<div><div>Adenosine triphosphate (ATP) is essential for sperm motility. We previously found that optimized non-thermal dielectric barrier discharge (DBD) plasma treatment enhanced boar sperm quality by increasing ATP levels. However, the molecular mechanisms underlying this process, particularly the role of competing endogenous RNA (ceRNA) networks, remain unclear. In this study, a total of 266 mRNAs, 163 miRNAs, and 37 circRNAs were identified as differentially expressed in boar spermatozoa treated with optimized DBD plasma. Functional enrichment analysis revealed that ATP-related pathways, including AMPK, mTOR, and cAMP signaling, were significantly enriched. A circRNA–miRNA–mRNA regulatory network was constructed, and two key ceRNA axes, circRNA7761–miR-7-3p–TECRL/CYP24A1/LOC100515741 and circRNA7508–miR-202-5p–CYP2A19/HHIP/WNT2, were identified in the network. These axes are predicted to enhance ATP production by regulating mitochondrial function and energy homeostasis, thereby improving sperm quality. This study provides novel mechanistic insights into the modulation of sperm energy metabolism by DBD plasma through ceRNA networks, thereby offering new theoretical foundations and potential molecular targets for improving male fertility and treating male infertility.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111197"},"PeriodicalIF":3.0,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145943202","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}
Pub Date : 2026-01-05DOI: 10.1016/j.ygeno.2026.111194
Qianqian Pan, Mengyu Lou, Jing Jing, Tianwei Liu, Yan Huang, Shuang Li, Lu Zhu, Yong Liu, Sihuan Zhang, Yinghui Ling
Skeletal muscle development is crucial for goat meat production. While most research focuses on transcriptional regulation, translational control is often overlooked. This study integrated transcriptomic data to analyze the translational landscape during myogenic differentiation of goat skeletal muscle satellite cells (SMSCs). We found that differentiation pathways were activated at both levels, with enhancement at translation. Furthermore, we identified 25 novel lncORFs and 36 circORFs with coding potential. Among these, LncORF32653 and LncORF98488 encoded micropeptides promoting SMSCs proliferation and differentiation. We also identified circUSP25, encoding circUSP25-177aa, which inhibited proliferation but promoted differentiation. Thus, lncORF32653-53aa, lncORF98488-98aa, and circUSP25-177aa are key regulators of myogenesis, revealing the potential of RNAs annotated as non-coding to encode functional micropeptides.
{"title":"The translation landscape revealed the novel micropeptides involved in myogenic differentiation of goat skeletal muscle satellite cells.","authors":"Qianqian Pan, Mengyu Lou, Jing Jing, Tianwei Liu, Yan Huang, Shuang Li, Lu Zhu, Yong Liu, Sihuan Zhang, Yinghui Ling","doi":"10.1016/j.ygeno.2026.111194","DOIUrl":"https://doi.org/10.1016/j.ygeno.2026.111194","url":null,"abstract":"<p><p>Skeletal muscle development is crucial for goat meat production. While most research focuses on transcriptional regulation, translational control is often overlooked. This study integrated transcriptomic data to analyze the translational landscape during myogenic differentiation of goat skeletal muscle satellite cells (SMSCs). We found that differentiation pathways were activated at both levels, with enhancement at translation. Furthermore, we identified 25 novel lncORFs and 36 circORFs with coding potential. Among these, LncORF32653 and LncORF98488 encoded micropeptides promoting SMSCs proliferation and differentiation. We also identified circUSP25, encoding circUSP25-177aa, which inhibited proliferation but promoted differentiation. Thus, lncORF32653-53aa, lncORF98488-98aa, and circUSP25-177aa are key regulators of myogenesis, revealing the potential of RNAs annotated as non-coding to encode functional micropeptides.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111194"},"PeriodicalIF":3.0,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916794","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}
Pub Date : 2026-01-05DOI: 10.1016/j.ygeno.2025.111191
Chengqi Gao , Wei Xiao , Chao Zhu , Mengwei Liu , Zhenguo Zeng , Kun Xiao , Kuai Yu
The inflammatory responses of severe patients before and after Convalescent COVID-19 plasma (CCP) transfusion are poorly understood. To clarify the immune response and potential pro-inflammatory factors in severe patients after CCP transfusion, we performed single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) from severe COVID-19 patients before and 24 h after CCP transfusion. At 24 h after CCP transfusion, T and B cell proportions increased modestly without significant changes in TCR/BCR diversity. Importantly, concurrent upregulation of S100A8 in both CD4 memory T cells and B cells suggests that CCP transfusion may promote an inflammatory response in these cell subsets. Cell communication analysis revealed that CCP transfusion induced selective disruption of NK cell communication with TCR-negative T cells and BCR-positive B cells. Our data suggest CCP transfusion promoted the inflammatory response and interrupt the communication between adaptive immune cells and innate immune cells in severe COVID-19.
{"title":"Single cell transcriptomic atlas reveals distinct immune signatures following transfusion of COVID-19 convalescent plasma in severe COVID-19","authors":"Chengqi Gao , Wei Xiao , Chao Zhu , Mengwei Liu , Zhenguo Zeng , Kun Xiao , Kuai Yu","doi":"10.1016/j.ygeno.2025.111191","DOIUrl":"10.1016/j.ygeno.2025.111191","url":null,"abstract":"<div><div>The inflammatory responses of severe patients before and after Convalescent COVID-19 plasma (CCP) transfusion are poorly understood. To clarify the immune response and potential pro-inflammatory factors in severe patients after CCP transfusion, we performed single-cell RNA sequencing on peripheral blood mononuclear cells (PBMCs) from severe COVID-19 patients before and 24 h after CCP transfusion. At 24 h after CCP transfusion, T and B cell proportions increased modestly without significant changes in TCR/BCR diversity. Importantly, concurrent upregulation of S100A8 in both CD4 memory T cells and B cells suggests that CCP transfusion may promote an inflammatory response in these cell subsets. Cell communication analysis revealed that CCP transfusion induced selective disruption of NK cell communication with TCR-negative T cells and BCR-positive B cells. Our data suggest CCP transfusion promoted the inflammatory response and interrupt the communication between adaptive immune cells and innate immune cells in severe COVID-19.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111191"},"PeriodicalIF":3.0,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916817","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}
Pub Date : 2026-01-04DOI: 10.1016/j.ygeno.2026.111193
Ziqiang Yang , Suyun Chen , Siman Shen , Wanglong Liu , Kun Ding , Fangni Cao , Simeng Li , Minjuan Zeng , Jianning Chen , Li Xu , Liangqing Zhang
Background
Ischemia–reperfusion (I/R) injury in the heart triggers oxidative stress and alters post-transcriptional gene regulation. Reactive oxygen species (ROS) generated during oxidative stress induce RNA modifications such as 8-oxo-guanosine (o8G). Other modifications including 5-methylcytosine (m5C) and 7-methylguanosine (m7G) may also contribute to cardiac dysfunction. While the roles of individual RNA modifications in I/R injury are increasingly recognized, the global dynamics and crosstalk among these modifications under oxidative stress remain largely unexplored.
Methods
We performed high-throughput sequencing specific to each modification, integrated with mRNA transcriptome profiling of an IR injury mouse model. Differentially modified transcripts were subjected to GO and KEGG enrichment analyses to elucidate their functional relevance. Mechanistically, we demonstrated that RNA modification regulators with distinct functional roles can physically interact with each other, as shown by co-immunoprecipitation and immunofluorescence assays. Global changes in RNA modification levels under the model conditions were assessed using dot blot analysis. Furthermore, the regulatory effects of these enzymes on target mRNA stability were evaluated via Actinomycin D transcriptional inhibition assays.
Results
We found that the levels of all three modifications, m5C, m7G, and o8G were increased in IR by dot blot and observed a significant upregulation of three modification peaks under I/R by MeRIP-seq. Both m5C and o8G were predominantly enriched in CDS, while m7G displayed a dynamic redistribution. Our study focuses on the co-regulation crosstalk among three modifications. Functionally, singly or combinatorially modified transcripts were enriched in actin cytoskeleton regulation. Mechanistically, the transcripts of the regulators can be modified by each other and QKI can modulate the global modification level of o8G. QKI and YBX1 interact with each other to cooperatively stabilize ACTN4 mRNA, thereby maintaining cytoskeletal integrity.
Conclusion
Our results establish that QKI and YBX1 modulate the actin cytoskeleton via a coordinated network of m5C, m7G, and o8G in I/R injury.
{"title":"Co-regulatory crosstalk between m5C, m7G, and o8G RNA modifications via QKI/YBX1 axis in myocardial ischemia-reperfusion injury","authors":"Ziqiang Yang , Suyun Chen , Siman Shen , Wanglong Liu , Kun Ding , Fangni Cao , Simeng Li , Minjuan Zeng , Jianning Chen , Li Xu , Liangqing Zhang","doi":"10.1016/j.ygeno.2026.111193","DOIUrl":"10.1016/j.ygeno.2026.111193","url":null,"abstract":"<div><h3>Background</h3><div>Ischemia–reperfusion (I/R) injury in the heart triggers oxidative stress and alters post-transcriptional gene regulation. Reactive oxygen species (ROS) generated during oxidative stress induce RNA modifications such as 8-oxo-guanosine (o8G). Other modifications including 5-methylcytosine (m5C) and 7-methylguanosine (m7G) may also contribute to cardiac dysfunction. While the roles of individual RNA modifications in I/R injury are increasingly recognized, the global dynamics and crosstalk among these modifications under oxidative stress remain largely unexplored.</div></div><div><h3>Methods</h3><div>We performed high-throughput sequencing specific to each modification, integrated with mRNA transcriptome profiling of an IR injury mouse model. Differentially modified transcripts were subjected to GO and KEGG enrichment analyses to elucidate their functional relevance. Mechanistically, we demonstrated that RNA modification regulators with distinct functional roles can physically interact with each other, as shown by co-immunoprecipitation and immunofluorescence assays. Global changes in RNA modification levels under the model conditions were assessed using dot blot analysis. Furthermore, the regulatory effects of these enzymes on target mRNA stability were evaluated via Actinomycin D transcriptional inhibition assays.</div></div><div><h3>Results</h3><div>We found that the levels of all three modifications, m5C, m7G, and o8G were increased in IR by dot blot and observed a significant upregulation of three modification peaks under I/R by MeRIP-seq. Both m5C and o8G were predominantly enriched in CDS, while m7G displayed a dynamic redistribution. Our study focuses on the co-regulation crosstalk among three modifications. Functionally, singly or combinatorially modified transcripts were enriched in actin cytoskeleton regulation. Mechanistically, the transcripts of the regulators can be modified by each other and QKI can modulate the global modification level of o8G. QKI and YBX1 interact with each other to cooperatively stabilize ACTN4 mRNA, thereby maintaining cytoskeletal integrity.</div></div><div><h3>Conclusion</h3><div>Our results establish that QKI and YBX1 modulate the actin cytoskeleton via a coordinated network of m5C, m7G, and o8G in I/R injury.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111193"},"PeriodicalIF":3.0,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145911189","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}
Pub Date : 2026-01-03DOI: 10.1016/j.ygeno.2025.111192
Lijie Li, Ganqiqige Cha, Fengsheng Zhang
Lead contamination in air, water, and soil has infiltrated foods and feeds, posing severe health risks to humans and animals and remaining a tough challenge. Yeast is a safe and efficient biosorbent for lead removal. This study explored W. anomalus QF-11 lead resistance via whole-genome sequencing, finding it tolerates up to 7000 mg/L Pb2+. Under 4000 mg/L Pb2+ stress, it enhances resistance by scavenging ROS, increasing soluble protein, boosting SOD, POD and CAT activities, and elevating glutathione and trehalose levels. Its genome annotates 63 ABC transporters and antioxidant genes involved in lead adsorption, transportation and compartmentalization, with SODC, SODM, VAN1, TSL1 and others significantly upregulated. This study provides a theoretical basis for W. anomalus QF-11 application as a Pb2+ biosorbent and data support for novel heavy metal adsorbent development.
{"title":"Mechanism of lead resistance in Wickerhamomyces anomalus: Insights from whole genome sequencing","authors":"Lijie Li, Ganqiqige Cha, Fengsheng Zhang","doi":"10.1016/j.ygeno.2025.111192","DOIUrl":"10.1016/j.ygeno.2025.111192","url":null,"abstract":"<div><div>Lead contamination in air, water, and soil has infiltrated foods and feeds, posing severe health risks to humans and animals and remaining a tough challenge. Yeast is a safe and efficient biosorbent for lead removal. This study explored <em>W. anomalus QF-11</em> lead resistance via whole-genome sequencing, finding it tolerates up to 7000 mg/L Pb<sup>2+</sup>. Under 4000 mg/L Pb<sup>2+</sup> stress, it enhances resistance by scavenging ROS, increasing soluble protein, boosting SOD, POD and CAT activities, and elevating glutathione and trehalose levels. Its genome annotates 63 ABC transporters and antioxidant genes involved in lead adsorption, transportation and compartmentalization, with SODC, SODM, VAN1, TSL1 and others significantly upregulated. This study provides a theoretical basis for <em>W. anomalus QF-11</em> application as a Pb<sup>2+</sup> biosorbent and data support for novel heavy metal adsorbent development.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111192"},"PeriodicalIF":3.0,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905906","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}
Pub Date : 2026-01-01DOI: 10.1016/j.ygeno.2025.111179
Dachen Liu , Hua Shi , Yihang Lin , Zhen Chen , Quan Zou
Spatial transcriptomics maps gene expression across tissues, yet data sparsity and noise challenge long-range dependency modeling, limiting accurate spatial domain delineation. In this study, we present TOGAR, a token-gated generative refinement model that unifies denoising, spatial enhancement, and clustering for spatial transcriptomics. Firstly, the model combines a graph convolutional network loss with a loss based on the zero-inflated negative binomial distribution to reduce noise and enhance signal clarity in sparse count data. It then employs a UGate-based diffusion backbone, which integrates token gating, gated linear attention, and rotary positional embedding for generative spatial refinement. Finally, similarity-guided averaging along diffusion trajectories provides stable spot-level estimates, and clustering of the refined representations produces spatial domains with sharp boundaries suitable for downstream analyses. We evaluate TOGAR across three spatial transcriptomics platforms. In benchmarks on twelve slices against seven popular methods, TOGAR consistently achieves or exceeds clustering accuracy, demonstrating superior stability. TOGAR effectively recovers coherent cortical layer organization, delineates fine-grained tumor subdomains associated with immune activity and extracellular matrix remodeling, and generates clearer, biologically interpretable domain boundaries. Notably, TOGAR excels in detecting extremely small and rare spatial structures, successfully identifying biologically important regions that other methods completely miss, while maintaining boundary integrity in complex multi-cluster structures and avoiding issues of over-connectivity or incomplete detection.
{"title":"TOGAR: Token-gated generative refinement for high-fidelity spatial transcriptomics and robust spatial domain clustering","authors":"Dachen Liu , Hua Shi , Yihang Lin , Zhen Chen , Quan Zou","doi":"10.1016/j.ygeno.2025.111179","DOIUrl":"10.1016/j.ygeno.2025.111179","url":null,"abstract":"<div><div>Spatial transcriptomics maps gene expression across tissues, yet data sparsity and noise challenge long-range dependency modeling, limiting accurate spatial domain delineation. In this study, we present TOGAR, a token-gated generative refinement model that unifies denoising, spatial enhancement, and clustering for spatial transcriptomics. Firstly, the model combines a graph convolutional network loss with a loss based on the zero-inflated negative binomial distribution to reduce noise and enhance signal clarity in sparse count data. It then employs a UGate-based diffusion backbone, which integrates token gating, gated linear attention, and rotary positional embedding for generative spatial refinement. Finally, similarity-guided averaging along diffusion trajectories provides stable spot-level estimates, and clustering of the refined representations produces spatial domains with sharp boundaries suitable for downstream analyses. We evaluate TOGAR across three spatial transcriptomics platforms. In benchmarks on twelve slices against seven popular methods, TOGAR consistently achieves or exceeds clustering accuracy, demonstrating superior stability. TOGAR effectively recovers coherent cortical layer organization, delineates fine-grained tumor subdomains associated with immune activity and extracellular matrix remodeling, and generates clearer, biologically interpretable domain boundaries. Notably, TOGAR excels in detecting extremely small and rare spatial structures, successfully identifying biologically important regions that other methods completely miss, while maintaining boundary integrity in complex multi-cluster structures and avoiding issues of over-connectivity or incomplete detection.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111179"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145803967","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}
Pub Date : 2026-01-01DOI: 10.1016/j.ygeno.2025.111187
Juntao Zhang , Hengqian He , Fang Wang , Huilei Yu , Bowen Liu , Jingwen Yang , Qinkang Lu
Primary open-angle glaucoma (POAG) is the most prevalent type of glaucoma, and early-stage optic neuropathy may cause visual field defects. As these early defects have minimal effects on vision, they are often overlooked, resulting in the loss of optimal treatment timing. Urgent identification of novel early diagnostic biomarkers is needed. In this study, blood samples from 30 POAG patients and 30 healthy controls were analyzed for Small Non-Coding RNAs (sncRNAs) transcriptomics and validated. We performed PANDORA-seq to profile quantitative sncRNAs signature, and a total of 169 differentially expressed sncRNAs were identified, including 147 PIWI-interacting RNAs, 10 microRNAs, and 12 transfer RNA-derived small RNAs. Functional enrichment analysis of sncRNAs target genes revealed significant involvement in key pathological processes, including apoptosis, inflammation, and intraocular pressure homeostasis. Regulatory network analysis demonstrated substantial functional overlap among different sncRNAs groups, suggesting potential cooperative roles in POAG pathogenesis. The expressions of 6 candidate sncRNAs were validated by quantitative real-time polymerase chain reaction, confirming the downregulation of tsRNA-5009b-ValCAC (p < 0.05), piR-hsa-767,596 (p < 0.05), piR-hsa-731,834 (p < 0.01) and hsa-miR-451a (p < 0.05) in POAG patients. Besides, receiver operating characteristic (ROC) curve analysis demonstrated that individual sncRNAs exhibited moderate diagnostic performance, with hsa-miR-451a showing good performance (AUC = 0.83).Our study provides novel insights into the role of sncRNAs in POAG and highlights their potential as diagnostic biomarkers for early disease detection and monitoring.
{"title":"Comprehensive small non-coding RNA profiling reveals novel diagnostic biomarkers for primary open-angle glaucoma","authors":"Juntao Zhang , Hengqian He , Fang Wang , Huilei Yu , Bowen Liu , Jingwen Yang , Qinkang Lu","doi":"10.1016/j.ygeno.2025.111187","DOIUrl":"10.1016/j.ygeno.2025.111187","url":null,"abstract":"<div><div>Primary open-angle glaucoma (POAG) is the most prevalent type of glaucoma, and early-stage optic neuropathy may cause visual field defects. As these early defects have minimal effects on vision, they are often overlooked, resulting in the loss of optimal treatment timing. Urgent identification of novel early diagnostic biomarkers is needed. In this study, blood samples from 30 POAG patients and 30 healthy controls were analyzed for Small Non-Coding RNAs (sncRNAs) transcriptomics and validated. We performed PANDORA-seq to profile quantitative sncRNAs signature, and a total of 169 differentially expressed sncRNAs were identified, including 147 PIWI-interacting RNAs, 10 microRNAs, and 12 transfer RNA-derived small RNAs. Functional enrichment analysis of sncRNAs target genes revealed significant involvement in key pathological processes, including apoptosis, inflammation, and intraocular pressure homeostasis. Regulatory network analysis demonstrated substantial functional overlap among different sncRNAs groups, suggesting potential cooperative roles in POAG pathogenesis. The expressions of 6 candidate sncRNAs were validated by quantitative real-time polymerase chain reaction, confirming the downregulation of tsRNA-5009b-ValCAC (<em>p</em> < 0.05), piR-hsa-767,596 (<em>p</em> < 0.05), piR-hsa-731,834 (<em>p</em> < 0.01) and hsa-miR-451a (p < 0.05) in POAG patients. Besides, receiver operating characteristic (ROC) curve analysis demonstrated that individual sncRNAs exhibited moderate diagnostic performance, with hsa-miR-451a showing good performance (AUC = 0.83).Our study provides novel insights into the role of sncRNAs in POAG and highlights their potential as diagnostic biomarkers for early disease detection and monitoring.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111187"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846464","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}
Pub Date : 2026-01-01DOI: 10.1016/j.ygeno.2025.111180
Meijun Song , Wenjie Duan , Duomin Liang , Dinghui Dai , Li Li , Hongping Zhang
Transposable elements (TEs), once considered “junk” DNA, constitute nearly half of the mammalian genome and can replicate and reposition within the host genome. Advances in omics technologies have improved the capture and annotation of TEs, enabling functional studies. Here, we review TEs classification, structure, regulation, and annotation methods. TEs act as regulatory elements or non-coding RNAs, influencing gene networks and cell fate. While once thought inactive in somatic cells, recent evidence suggests that TEs remain transcriptionally active in various tissues, contributing to function. Focusing on skeletal muscle development, pathological regeneration, and aging, we discuss TEs expression patterns and their potential functional. TEs exhibit stage-specific expression during muscle development and are implicated in muscle-related diseases. Building on the transposon theory of aging, we summarize the increased TEs transcription and chromatin accessibility in aging muscle. Understanding TEs in skeletal muscle biology provides insights into muscle development and age-related functional decline.
{"title":"Transposable elements as dynamic regulators of skeletal muscle development, regeneration and aging","authors":"Meijun Song , Wenjie Duan , Duomin Liang , Dinghui Dai , Li Li , Hongping Zhang","doi":"10.1016/j.ygeno.2025.111180","DOIUrl":"10.1016/j.ygeno.2025.111180","url":null,"abstract":"<div><div>Transposable elements (TEs), once considered “junk” DNA, constitute nearly half of the mammalian genome and can replicate and reposition within the host genome. Advances in omics technologies have improved the capture and annotation of TEs, enabling functional studies. Here, we review TEs classification, structure, regulation, and annotation methods. TEs act as regulatory elements or non-coding RNAs, influencing gene networks and cell fate. While once thought inactive in somatic cells, recent evidence suggests that TEs remain transcriptionally active in various tissues, contributing to function. Focusing on skeletal muscle development, pathological regeneration, and aging, we discuss TEs expression patterns and their potential functional. TEs exhibit stage-specific expression during muscle development and are implicated in muscle-related diseases. Building on the transposon theory of aging, we summarize the increased TEs transcription and chromatin accessibility in aging muscle. Understanding TEs in skeletal muscle biology provides insights into muscle development and age-related functional decline.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111180"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892264","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}
Pub Date : 2026-01-01DOI: 10.1016/j.ygeno.2025.111181
Jiacheng Gan, Qiurong Ji, Wei Gao, Yu Zhang, Xianhua Zhang, Rengeerli Sa, Shengzhen Hou, Linsheng Gui
Background
The black Tibetan sheep is an important local livestock breed. Deciphering the genetic and molecular mechanisms governing their growth and development is crucial for breeding programs. However, research on their serum metabolome and population genetic structure remains limited.
Methods
We performed a genome-wide association study (GWAS) integrating phenotypic growth traits and the serum metabolome in a cohort of 210 black Tibetan sheep, using genomic data from single nucleotide polymorphism (SNP) chip genotyping. Additionally, population genetic structure was analyzed via whole-genome resequencing (WGR).
Results
In this study, metabolome genome-wide association study (mGWAS) at the genome-wide level yielded 3,886,784 SNPs and quantified 3267 metabolites. Among them, 56,366 SNPs and 1008 metabolites were identified as significant, and five candidate genes (ZBTB38, CDK6, ZFP36L1, PRSS53, and FHIT) related to the growth and development traits of black Tibetan sheep were screened out. Notably, two of these genes, ZFP36L1 and PRSS53, were simultaneously detected in both the GWAS of phenotypic traits and mGWAS. These genes are strongly linked to certain organic compounds, including L-leucine, L-tryptophan, and pantothenic acid. Furthermore, these genes are primarily enriched in pathways including the mTOR signaling pathway, protein digestion and absorption, regulation of fat cell differentiation, glucose metabolic process, and pantothenate and coenzyme A (CoA) biosynthesis. Concurrently, WGR-based analysis of population genetic structure revealed a close genetic relationship and low differentiation among black Tibetan sheep, white Tibetan sheep, and Euler sheep.
Conclusions
In conclusion, based on the above analysis, the genetic regions, candidate genes, and enriched pathways that may significantly affect the metabolites of black Tibetan sheep were identified. These findings bridge the gap between the genome and the phenotypic traits, as many of these metabolites are key intermediates or regulators involved in growth and development processes. Combined with the elucidated population genetic structure, this study provides a solid foundation for future research into the mechanisms driving growth and development traits in this breed.
{"title":"Genetic mechanisms and population structure of growth and development in black Tibetan sheep revealed by genome-wide association study and whole-genome resequencing","authors":"Jiacheng Gan, Qiurong Ji, Wei Gao, Yu Zhang, Xianhua Zhang, Rengeerli Sa, Shengzhen Hou, Linsheng Gui","doi":"10.1016/j.ygeno.2025.111181","DOIUrl":"10.1016/j.ygeno.2025.111181","url":null,"abstract":"<div><h3>Background</h3><div>The black Tibetan sheep is an important local livestock breed. Deciphering the genetic and molecular mechanisms governing their growth and development is crucial for breeding programs. However, research on their serum metabolome and population genetic structure remains limited.</div></div><div><h3>Methods</h3><div>We performed a genome-wide association study (GWAS) integrating phenotypic growth traits and the serum metabolome in a cohort of 210 black Tibetan sheep, using genomic data from single nucleotide polymorphism (SNP) chip genotyping. Additionally, population genetic structure was analyzed via whole-genome resequencing (WGR).</div></div><div><h3>Results</h3><div>In this study, metabolome genome-wide association study (mGWAS) at the genome-wide level yielded 3,886,784 SNPs and quantified 3267 metabolites. Among them, 56,366 SNPs and 1008 metabolites were identified as significant, and five candidate genes (<em>ZBTB38, CDK6, ZFP36L1, PRSS53,</em> and <em>FHIT</em>) related to the growth and development traits of black Tibetan sheep were screened out. Notably, two of these genes, <em>ZFP36L1</em> and <em>PRSS53</em>, were simultaneously detected in both the GWAS of phenotypic traits and mGWAS. These genes are strongly linked to certain organic compounds, including L-leucine, L-tryptophan, and pantothenic acid. Furthermore, these genes are primarily enriched in pathways including the mTOR signaling pathway, protein digestion and absorption, regulation of fat cell differentiation, glucose metabolic process, and pantothenate and coenzyme A (CoA) biosynthesis. Concurrently, WGR-based analysis of population genetic structure revealed a close genetic relationship and low differentiation among black Tibetan sheep, white Tibetan sheep, and Euler sheep.</div></div><div><h3>Conclusions</h3><div>In conclusion, based on the above analysis, the genetic regions, candidate genes, and enriched pathways that may significantly affect the metabolites of black Tibetan sheep were identified. These findings bridge the gap between the genome and the phenotypic traits, as many of these metabolites are key intermediates or regulators involved in growth and development processes. Combined with the elucidated population genetic structure, this study provides a solid foundation for future research into the mechanisms driving growth and development traits in this breed.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111181"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843576","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}
Pub Date : 2026-01-01DOI: 10.1016/j.ygeno.2025.111186
Keyi Zhang , Lin Liu , Peiyao Wu , Lei Zhao , Jieyu Zhou , Yafei Wu
Fusobacterium nucleatum (F. nucleatum), a key periodontal pathogen, is increasingly detected in atherosclerotic plaques, yet its epigenetic regulatory mechanisms in atherosclerosis remain enigmatic. This study investigates how F. nucleatum reshapes the non-coding RNA landscape to drive atherosclerosis progression. Periodontal infection with F. nucleatum significantly increased atherosclerotic lesion area (p < 0.001) and necrotic core ratio, while reducing collagen content (p < 0.05) in ApoE−/− mice. Whole transcriptome sequencing of arterial tissues identified 847 differentially expressed mRNAs, 16 miRNAs, 19 circRNAs, and 76 lncRNAs linked to lipid metabolism and plaque instability. Focusing on atherosclerosis-associated signaling pathways, we constructed a competing endogenous RNA (ceRNA) network in F. nucleatum-infected ApoE−/− mice. Notably, we highlighted two key regulatory axes: (circRNA5047/lncRNA Ext1)-miR-18a-3p-Cflar-Autophagy and (circRNA5047/lncRNA Ext1)-miR-669f-3p-Itpr1-Autophagy. These findings provide novel insights into the role of F. nucleatum in atherosclerosis and establish a foundation for further investigation into its underlying mechanisms.
{"title":"Fusobacterium nucleatum exacerbates atherosclerosis progression via ceRNA network-mediated epigenetic reprogramming","authors":"Keyi Zhang , Lin Liu , Peiyao Wu , Lei Zhao , Jieyu Zhou , Yafei Wu","doi":"10.1016/j.ygeno.2025.111186","DOIUrl":"10.1016/j.ygeno.2025.111186","url":null,"abstract":"<div><div><em>Fusobacterium nucleatum (F. nucleatum),</em> a key periodontal pathogen, is increasingly detected in atherosclerotic plaques, yet its epigenetic regulatory mechanisms in atherosclerosis remain enigmatic. This study investigates how <em>F. nucleatum</em> reshapes the non-coding RNA landscape to drive atherosclerosis progression. Periodontal infection with <em>F. nucleatum</em> significantly increased atherosclerotic lesion area (<em>p</em> < 0.001) and necrotic core ratio, while reducing collagen content (<em>p</em> < 0.05) in <em>ApoE</em><sup><em>−/−</em></sup> mice. Whole transcriptome sequencing of arterial tissues identified 847 differentially expressed mRNAs, 16 miRNAs, 19 circRNAs, and 76 lncRNAs linked to lipid metabolism and plaque instability. Focusing on atherosclerosis-associated signaling pathways, we constructed a competing endogenous RNA (ceRNA) network in <em>F. nucleatum</em>-infected <em>ApoE</em><sup>−/−</sup> mice. Notably, we highlighted two key regulatory axes: <em>(circRNA5047/lncRNA Ext1)-miR-18a-3p-Cflar-Autophagy</em> and <em>(circRNA5047/lncRNA Ext1)-miR-669f-3p-Itpr1-Autophagy</em>. These findings provide novel insights into the role of <em>F. nucleatum</em> in atherosclerosis and establish a foundation for further investigation into its underlying mechanisms.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111186"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846479","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}
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