Pub Date : 2026-01-01Epub Date: 2025-11-26DOI: 10.1016/j.ygeno.2025.111162
Fulei Wei , Xianzhi Zuo , Qiangdong Yang , Qianwen Li , Faxin Jin , Rui Ma , Guoliang Sun , Mingming Cui , Yuqiong Meng
Rainbow trout (Oncorhynchus mykiss) is one of the most widely farmed salmonid species globally. To investigate the mechanisms regulating muscle fat content and enhancing tolerance to high-lipid diets, transcriptomic changes in muscle tissues (myotomes and myosepta) were analyzed after treatment with an elevated dietary lipid level (30 %). The results revealed that myotomes and myosepta employed distinct strategies to maintain lipid homeostasis under elevated dietary lipids. Myotomes suppressed lipid deposition by upregulating lipoic acid synthesis to enhance lipolysis and reducing lipoprotein sialylation, while myosepta inhibited lipid storage through AMP metabolism modulation in adipocytes and the decreased function of phosphatidylinositol-4-phosphate (PI4P) binding. Beyond these tissue-specific strategies, both myotomes and myosepta also adopted some common approaches against lipid surplus. The downregulation of GFRAL4 balanced energy acquisition, and MBLH2-mediated lipolysis prevented ectopic deposition. Crucially, miRNAs coordinated tissue-specific and systemic adaptations to dietary lipid fluctuations mainly by targeting key genes involved in lipid metabolism pathways. Overall, these findings identified potential protein targets and regulatory pathways for regulating myoseptal fat content to improve meat flavor attributes, and elucidated the metabolic adaptation mechanisms of triploid rainbow trout to high-lipid diets.
{"title":"Divergent miRNA-mRNA networks contribute to tissue-specific lipid homeostasis in triploid rainbow trout skeletal muscle during high-lipid diet challenge","authors":"Fulei Wei , Xianzhi Zuo , Qiangdong Yang , Qianwen Li , Faxin Jin , Rui Ma , Guoliang Sun , Mingming Cui , Yuqiong Meng","doi":"10.1016/j.ygeno.2025.111162","DOIUrl":"10.1016/j.ygeno.2025.111162","url":null,"abstract":"<div><div>Rainbow trout (<em>Oncorhynchus mykiss</em>) is one of the most widely farmed salmonid species globally. To investigate the mechanisms regulating muscle fat content and enhancing tolerance to high-lipid diets, transcriptomic changes in muscle tissues (<em>myotomes</em> and <em>myosepta</em>) were analyzed after treatment with an elevated dietary lipid level (30 %). The results revealed that <em>myotomes</em> and <em>myosepta</em> employed distinct strategies to maintain lipid homeostasis under elevated dietary lipids. <em>Myotomes</em> suppressed lipid deposition by upregulating lipoic acid synthesis to enhance lipolysis and reducing lipoprotein sialylation, while <em>myosepta</em> inhibited lipid storage through AMP metabolism modulation in adipocytes and the decreased function of phosphatidylinositol-4-phosphate (PI4P) binding. Beyond these tissue-specific strategies, both <em>myotomes</em> and <em>myosepta</em> also adopted some common approaches against lipid surplus. The downregulation of <em>GFRAL4</em> balanced energy acquisition, and <em>MBLH2-</em>mediated lipolysis prevented ectopic deposition. Crucially, miRNAs coordinated tissue-specific and systemic adaptations to dietary lipid fluctuations mainly by targeting key genes involved in lipid metabolism pathways. Overall, these findings identified potential protein targets and regulatory pathways for regulating myoseptal fat content to improve meat flavor attributes, and elucidated the metabolic adaptation mechanisms of triploid rainbow trout to high-lipid diets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111162"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145632239","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 : 2026-01-01Epub Date: 2025-12-16DOI: 10.1016/j.ygeno.2025.111175
Xinbo Ji , Rui Zhang , Didi Shan , Tongwei Shi , Yingxin Wang , Yao Tang , Zexin Zhan , Yichang Jiao , Hongxu Wang , Jianing Li , Dongdong Wang , Jingwen Xu , Chuanzhu Yan , Fuchen Liu
Myotonic dystrophy type 1 (DM1) is characterized by sequestration of RNA-binding proteins and widespread transcriptomic dysregulation, yet isoform-level transcriptomic landscapes remain incompletely defined. Here, we performed integrated long-read (PacBio Iso-Seq) and short-read (Illumina RNA-seq) profiling of primary fibroblasts from DM1 patients and healthy controls. Long-read sequencing identified >15,000 transcript isoforms in DM1 fibroblasts, revealing extensive alternative splicing and novel transcript discovery beyond short-read resolution. Isoform-switching analysis uncovered 104 significant events, particularly affecting signaling and cytoskeletal pathways, independent of gene-level expression changes. Differential promoter usage further highlighted transcriptional rewiring, with 106 dysregulated promoters, over two-thirds of which were previously unannotated. Moreover, systematic splicing analysis detected >1200 significantly altered events, predominantly alternative first exons, converging on extracellular matrix remodeling and muscle contractility pathways. Together, these data provide an isoform-resolved landscape of DM1 fibroblasts, demonstrating that transcript-level remodeling-including alternative splicing, isoform switching, and promoter dysregulation-constitutes a critical regulatory layer underlying DM1 pathogenesis.
{"title":"Transcriptome-wide isoform and promoter remodeling in DM1 fibroblasts uncovered by long-read RNA sequencing","authors":"Xinbo Ji , Rui Zhang , Didi Shan , Tongwei Shi , Yingxin Wang , Yao Tang , Zexin Zhan , Yichang Jiao , Hongxu Wang , Jianing Li , Dongdong Wang , Jingwen Xu , Chuanzhu Yan , Fuchen Liu","doi":"10.1016/j.ygeno.2025.111175","DOIUrl":"10.1016/j.ygeno.2025.111175","url":null,"abstract":"<div><div>Myotonic dystrophy type 1 (DM1) is characterized by sequestration of RNA-binding proteins and widespread transcriptomic dysregulation, yet isoform-level transcriptomic landscapes remain incompletely defined. Here, we performed integrated long-read (PacBio Iso-Seq) and short-read (Illumina RNA-seq) profiling of primary fibroblasts from DM1 patients and healthy controls. Long-read sequencing identified >15,000 transcript isoforms in DM1 fibroblasts, revealing extensive alternative splicing and novel transcript discovery beyond short-read resolution. Isoform-switching analysis uncovered 104 significant events, particularly affecting signaling and cytoskeletal pathways, independent of gene-level expression changes. Differential promoter usage further highlighted transcriptional rewiring, with 106 dysregulated promoters, over two-thirds of which were previously unannotated. Moreover, systematic splicing analysis detected >1200 significantly altered events, predominantly alternative first exons, converging on extracellular matrix remodeling and muscle contractility pathways. Together, these data provide an isoform-resolved landscape of DM1 fibroblasts, demonstrating that transcript-level remodeling-including alternative splicing, isoform switching, and promoter dysregulation-constitutes a critical regulatory layer underlying DM1 pathogenesis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111175"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145780790","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 : 2026-01-01Epub Date: 2025-12-19DOI: 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 : 2026-01-01Epub Date: 2025-12-25DOI: 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 : 2026-01-01Epub Date: 2025-12-09DOI: 10.1016/j.ygeno.2025.111172
Xueyan Ma , Lujie Wen , Dongpo Xu , Wu Jin , Haibo Wen , Huaishun Shen
Corbicula fluminea exhibits two distinct shell color morphs: yellow and black. This study reveals molecular mechanisms behind shell color variation in the Asian clam C. fluminea (yellow vs. black morphs) through comparative transcriptomics of edge/central mantle tissues. Transcriptome assembly identified 24, 174 annotated genes and 2, 234 novel genes. Comparative analyses revealed 238 common differentially expressed genes (DEGs) shared between the YC vs YE and BC vs BE comparisons, along with 575 DEGs in BC vs YC and 460 DEGs in BE vs YE. Transcriptomic profiling demonstrated that Biomineralization genes (calcium/organic matrix-related) showed region-specific expression, driving shell formation. Melanogenesis pathway enrichment and pigmentation genes (tyrosinase, calmodulin, sulfotransferase) may play an important role in pigmentation in C. fluminea. This study expands our understanding of shell biomineralization and pigment deposition in C. fluminea, providing important insights into the genetic and biochemical regulation of shell diversity in bivalves.
{"title":"Transcriptomic analysis of distinct mantle regions in yellow- and black-shelled Asian clam (Corbicula fluminea): Identification of genes associated with Shell biomineralization and pigment deposition","authors":"Xueyan Ma , Lujie Wen , Dongpo Xu , Wu Jin , Haibo Wen , Huaishun Shen","doi":"10.1016/j.ygeno.2025.111172","DOIUrl":"10.1016/j.ygeno.2025.111172","url":null,"abstract":"<div><div><em>Corbicula fluminea</em> exhibits two distinct shell color morphs: yellow and black. This study reveals molecular mechanisms behind shell color variation in the Asian clam <em>C. fluminea</em> (yellow vs. black morphs) through comparative transcriptomics of edge/central mantle tissues. Transcriptome assembly identified 24, 174 annotated genes and 2, 234 novel genes. Comparative analyses revealed 238 common differentially expressed genes (DEGs) shared between the YC vs YE and BC vs BE comparisons, along with 575 DEGs in BC vs YC and 460 DEGs in BE vs YE. Transcriptomic profiling demonstrated that Biomineralization genes (calcium/organic matrix-related) showed region-specific expression, driving shell formation. Melanogenesis pathway enrichment and pigmentation genes (tyrosinase, calmodulin, sulfotransferase) may play an important role in pigmentation in <em>C. fluminea</em>. This study expands our understanding of shell biomineralization and pigment deposition in <em>C. fluminea</em>, providing important insights into the genetic and biochemical regulation of shell diversity in bivalves.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111172"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145742021","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 : 2026-01-01Epub Date: 2025-12-11DOI: 10.1016/j.ygeno.2025.111173
Fei Li , Jinbang Qin , Zhaomin Yao , Yiping Xu , Yabing Zhu , Yan Wang , Lan Huang , Wenxuan Luo , Zhiguo Wang , Fengfeng Zhou
N7-methylguanosine (m7G) is a common RNA modification linked to multiple diseases. Accurate detection of m7G sites is vital for elucidating its biological roles, but conventional methods are often laborious and costly. AI-based approaches offer alternatives, yet most rely on balanced datasets, ignoring real-world imbalances where negative samples vastly outnumber positives. This discrepancy may lead to overestimated model performance. To address this, we reconstructed independent test sets with low positive-to-negative ratios and benchmarked various models. We propose OCm7G, an ensemble of one-class classifiers with hierarchical thresholding. OCm7G achieves performance comparable to state-of-the-art methods on balanced sets and surpasses them in highly imbalanced scenarios, despite using only 52.5 % of the training data. Moreover, OCm7G offers interpretable predictions, aiding researchers in understanding model decisions. The source code and datasets are publicly available at: https://github.com/lidaosheng/OCm7G.
{"title":"OCm7G: An interpretable one-class predictor for m7G methylation sites trained with limit negative samples","authors":"Fei Li , Jinbang Qin , Zhaomin Yao , Yiping Xu , Yabing Zhu , Yan Wang , Lan Huang , Wenxuan Luo , Zhiguo Wang , Fengfeng Zhou","doi":"10.1016/j.ygeno.2025.111173","DOIUrl":"10.1016/j.ygeno.2025.111173","url":null,"abstract":"<div><div>N7-methylguanosine (m7G) is a common RNA modification linked to multiple diseases. Accurate detection of m7G sites is vital for elucidating its biological roles, but conventional methods are often laborious and costly. AI-based approaches offer alternatives, yet most rely on balanced datasets, ignoring real-world imbalances where negative samples vastly outnumber positives. This discrepancy may lead to overestimated model performance. To address this, we reconstructed independent test sets with low positive-to-negative ratios and benchmarked various models. We propose OCm7G, an ensemble of one-class classifiers with hierarchical thresholding. OCm7G achieves performance comparable to state-of-the-art methods on balanced sets and surpasses them in highly imbalanced scenarios, despite using only 52.5 % of the training data. Moreover, OCm7G offers interpretable predictions, aiding researchers in understanding model decisions. The source code and datasets are publicly available at: <span><span>https://github.com/lidaosheng/OCm7G</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111173"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145752036","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 : 2026-01-01Epub Date: 2025-12-31DOI: 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 : 2026-01-01Epub Date: 2025-12-24DOI: 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 : 2026-01-01Epub Date: 2025-12-25DOI: 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}
Pub Date : 2026-01-01Epub Date: 2025-12-29DOI: 10.1016/j.ygeno.2025.111188
Monika Stefaniuk-Szmukier , Tomasz Szmatoła , Anna Steg , Grzegorz Smołucha , Katarzyna Ropka-Molik
The avian cerebellum is pivotal for multisensory integration and motor control during flight, yet its molecular adaptation to prolonged exertion remains incompletely defined. We profiled cerebellar transcriptomes of ten racing pigeons before and after a 300-km homing flight using whole-transcriptome RNA sequencing. Differential expression analysis revealed robust remodeling of metabolic and proteostatic pathways, including upregulation of SLC35D2, consistent with enhanced UDP-GlcNAc flux through the hexosamine biosynthetic pathway aligned with birds' naturally high glycaemia. Increased VLDLR expression links lipid handling to the reelin signalling cascade, suggesting contributions to navigation and synaptic plasticity, whereas downregulation of HTR1F indicates region-specific serotonergic modulation with exercise. Co-expression network analysis (WGCNA) identified modules enriched for endoplasmic reticulum protein processing and stress responses (PLAA, RAD23, ERN1), alongside intensified ribosome and RNA biogenesis, reflecting an elevated demand for protein synthesis and quality control. Functional enrichment (WebGestalt,) highlighted among others ribosome biogenesis, core metabolic pathways, RNA transport. These insights contribute to understanding the genetic and molecular mechanisms underpinning avian navigation and performance, providing a foundation for further research into flight-related neurophysiology.
{"title":"RNA-Seq reveals flight-induced changes in cerebellar transcriptomic profiles of racing pigeons","authors":"Monika Stefaniuk-Szmukier , Tomasz Szmatoła , Anna Steg , Grzegorz Smołucha , Katarzyna Ropka-Molik","doi":"10.1016/j.ygeno.2025.111188","DOIUrl":"10.1016/j.ygeno.2025.111188","url":null,"abstract":"<div><div>The avian cerebellum is pivotal for multisensory integration and motor control during flight, yet its molecular adaptation to prolonged exertion remains incompletely defined. We profiled cerebellar transcriptomes of ten racing pigeons before and after a 300-km homing flight using whole-transcriptome RNA sequencing. Differential expression analysis revealed robust remodeling of metabolic and proteostatic pathways, including upregulation of <em>SLC35D2</em>, consistent with enhanced UDP-GlcNAc flux through the hexosamine biosynthetic pathway aligned with birds' naturally high glycaemia. Increased <em>VLDLR</em> expression links lipid handling to the reelin signalling cascade, suggesting contributions to navigation and synaptic plasticity, whereas downregulation of <em>HTR1F</em> indicates region-specific serotonergic modulation with exercise. Co-expression network analysis (WGCNA) identified modules enriched for endoplasmic reticulum protein processing and stress responses (<em>PLAA</em>, <em>RAD23</em>, <em>ERN1</em>), alongside intensified ribosome and RNA biogenesis, reflecting an elevated demand for protein synthesis and quality control. Functional enrichment (WebGestalt,) highlighted among others ribosome biogenesis, core metabolic pathways, RNA transport. These insights contribute to understanding the genetic and molecular mechanisms underpinning avian navigation and performance, providing a foundation for further research into flight-related neurophysiology.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111188"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145878055","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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