Genomics最新文献

{"title":"Hepatic and intestinal insights into the molecular mechanisms of dietary Antarctic krill-induced body color differentiation in Plectropomus leopardus","authors":"Jiayi Wu ,&nbsp;Mengya Wang ,&nbsp;Xin Gao ,&nbsp;Mingyi Wang ,&nbsp;Chaofan Jin ,&nbsp;Da Zheng ,&nbsp;Jiangping Yan ,&nbsp;Zhenmin Bao ,&nbsp;Bo Wang ,&nbsp;Jingjie Hu","doi":"10.1016/j.ygeno.2025.110989","DOIUrl":"10.1016/j.ygeno.2025.110989","url":null,"abstract":"<div><div>Antarctic krill (<em>Euphausia superba</em>), which is rich in astaxanthin, has been widely utilized as a dietary supplement in fish aquaculture. Our study was to feed juvenile leopard coral grouper (<em>Plectropomus leopardus</em>) a diet containing 50 % Antarctic krill, revealing significant body color differentiation between a reddened group (BKR) and a non-reddened group (BKB), followed by comparative analysis with the control group (BCon) without krill supplementation. Histological analysis and carotenoid content in the liver and intestine were differentially regulated in color-differentiated individuals. Transcriptomic profiling revealed differentially expressed genes (DEGs) among color-differentiated individuals, with up-regulated DEGs in BKR being linked to carotenoid uptake, metabolism, and transport. Key DEGs (<em>acss2l</em>, <em>insig1</em>, <em>fabp7</em>, and <em>bco1</em>) were validated through qRT-PCR and FISH. Additionally, WGCNA identified potential gene regulatory networks in the liver and intestine that were responsive to the body coloration. This study elucidates the molecular mechanisms by which Antarctic krill influences carotenoid-based body coloration, offering new insights into the application of Antarctic krill in aquaculture.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110989"},"PeriodicalIF":3.4,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanistic insights into GLP-1 receptor agonist-induced weight loss through ceRNA network analysis","authors":"Wenxin Li ,&nbsp;Xinyu Zhang ,&nbsp;Jiamin Song ,&nbsp;Ling Yang ,&nbsp;Dong Wang ,&nbsp;Guoyue Yuan ,&nbsp;Li Zhao","doi":"10.1016/j.ygeno.2025.110988","DOIUrl":"10.1016/j.ygeno.2025.110988","url":null,"abstract":"<div><h3>Background</h3><div>GLP-1 receptor agonists (GLP-1RA) have been extensively utilized in the management of body weight in individuals with obesity. Circular RNA (circRNA), a class of covalently closed RNA molecules, has garnered increasing attention for its potential role in the pathogenesis of obesity. However, the specific mechanisms through which circRNA contributes to GLP-1RA-induced weight loss remains elusive.</div></div><div><h3>Methods</h3><div>High-throughput sequencing analyzed epididymal adipose tissue from obese mice under high-fat, and GLP-1RA intervention (600 μg/kg/d). The functions of differentially expressed (DE) genes were enriched and analyzed. The circRNA-miRNA-mRNA interaction network was constructed in Cytoscape, and KEGG pathway gene enrichment was validated via western blotting.</div></div><div><h3>Results</h3><div>A total of 644 DEcircRNAs, 186 DEmiRNAs, and 3474 DEmRNAs were identified. Based on ceRNA score calculations, network diagrams were constructed. Gene Ontology (GO) analysis revealed that DERNAs were linked to lipid and fatty acid metabolism. DE genes within ceRNA pairs were enriched in lipid metabolism pathways, especially the PI3K-Akt and AMPK signaling pathways. GLP-1RA induced the phosphorylation of AKT and AMPK, which subsequently led to a reduction of SREBP-1, ACC, and FAS.</div></div><div><h3>Conclusion</h3><div>GLP-1RA might activate PI3K-Akt and AMPK signaling pathways to combat obesity through the ceRNA network of circRNAs.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110988"},"PeriodicalIF":3.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative effects of arecoline, caffeine, and nicotine on transcription level in the nucleus accumbens of mice","authors":"Shaofang Huang ,&nbsp;Xinran Wang ,&nbsp;Feifan Zhou","doi":"10.1016/j.ygeno.2025.110986","DOIUrl":"10.1016/j.ygeno.2025.110986","url":null,"abstract":"<div><div>Though widely consumed, current research on the neural mechanisms of arecoline, caffeine, and nicotine remains limited, and the similarities and differences of these substances on the nervous system are still not clear. This study used RNA-seq to analyze the gene expression in the nucleus accumbens (NAc) of mice, and compared the behavioral changes through open field and conditioned place preference (CPP), exploring the effects of different psychoactive substances at transcriptional and behavioral levels. Gene Ontology enrichment analysis revealed that nicotine and caffeine significantly alter biological processes related to synaptic function, and KEGG pathway analysis showed that the differentially expressed genes in the nicotine-treated group were significantly more enriched in pathways related to substance dependence, with arecoline showing the least enrichment. Furthermore, only acute caffeine treatment significantly increased mouse activity, and only nicotine induced CPP. These results provided a scientific basis for evaluating arecoline, caffeine, and nicotine on the nervous system.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110986"},"PeriodicalIF":3.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tissue-specific expression, functional analysis, and polymorphism of the KRT2 gene in sheep horn","authors":"Hao Yang ,&nbsp;Mingxing Chu ,&nbsp;Naominggaowa ,&nbsp;Xiaoxu Zhang ,&nbsp;Mingzhu Shan ,&nbsp;Xiaoning Lu ,&nbsp;Zhangyuan Pan ,&nbsp;Jianning He","doi":"10.1016/j.ygeno.2025.110990","DOIUrl":"10.1016/j.ygeno.2025.110990","url":null,"abstract":"<div><div>Horn is a defensive weapon of sheep, consisting of a horny sheath and a bony core. The <em>KRT2</em> gene is related to keratinization of the epidermis, so it is likely to be one of the contributor genes affecting horn type in sheep. In this study, we first analyzed the species-specific and tissue-specific expression of the <em>KRT2</em> gene using transcriptome sequencing data. Then, by comparing the protein sequences of 20 species, we identified 28 specific amino acid sites in <em>Artiodactyla</em> animals, constructed a phylogenetic tree of the <em>KRT2</em> gene, and predicted its three-dimensional protein structure. Finally, whole genome sequencing data was used and mined 4 functional SNP sites of <em>KRT2</em> gene, and use KASP assay to verify the loci. In addition, we explored the relationship between the <em>KRT2</em> gene and the evolution of <em>Artiodactyla</em> animals, and predicted the possible mechanism by which the <em>KRT2</em> gene affects the horn type of sheep.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110990"},"PeriodicalIF":3.4,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142962016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ARF3 as a novel biomarker and target in acute myeloid leukemia: Insights from pan-cancer analysis","authors":"Yang Wenli ,&nbsp;Wang Wei ,&nbsp;Pan Yubiao ,&nbsp;Huang Hua ,&nbsp;Tong Hongyan","doi":"10.1016/j.ygeno.2024.110984","DOIUrl":"10.1016/j.ygeno.2024.110984","url":null,"abstract":"<div><div>Acute myeloid leukemia is a malignant hematologic disorder characterized by the excessive proliferation and accumulation of immature myeloid cells. This abnormality disrupts normal hematopoiesis, leading to symptoms such as anemia, increased susceptibility to infections and bleeding. ADP-ribosylation factors (ARFs) are critical in various cellular functions, including vesicular trafficking, membrane dynamics, cytoskeleton organization, signal transduction, endocytosis, exocytosis, and maintaining organelle integrity. Among ARF family members, ARF3 has garnered relatively less attention compared to other members like ARF1 and ARF6, leaving its role less understood. In this study, we found that the higher expression of ARF3 is correlated with poorer prognosis in AML patients. Silencing ARF3 in AML cells interrupted cell cycle progression and promote cell death as well as inhibit leukemogenesis in vivo. Mechanically, ARF3 knockdown suppressed AML progression by inhibiting PI3K/Akt signaling pathway. Our results indicate that ARF3 is linked to poor outcomes in AML patients and can serve as a potential therapeutic target for AML treatment.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110984"},"PeriodicalIF":3.4,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142931315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ribosome profiling reveals dynamic translational landscape following X-ray irradiation","authors":"Jingyu Hou ,&nbsp;Lei Yu ,&nbsp;Canlan Wu ,&nbsp;Saisai Wei ,&nbsp;Xiangwei Gao","doi":"10.1016/j.ygeno.2025.110987","DOIUrl":"10.1016/j.ygeno.2025.110987","url":null,"abstract":"<div><div>X-ray irradiation induces widespread changes in gene expression. Positioned at the bottom of the central dogma, translational regulation responds swiftly to environmental stimuli, fine-tuning protein levels. However, the global view of mRNA translation following X-ray exposure remains unclear. In this study, we systematically investigated X-ray-induced translational alternation using ribosome profiling. Our study revealed a temporary translation inhibition in HEK293T cells following X-ray treatment. A subset of mRNAs experienced translational upregulation by bypassing upstream open reading frames (uORFs). The upregulated genes were enriched in the MAPK signaling pathway, such as MAPKBP1. Suppression of MAPKBP1 inhibited X-ray-induced cell apoptosis. Furthermore, we identified the induction of novel peptides encoded by small open reading frames (smORFs) within long non-coding RNAs (lncRNAs) upon X-ray treatment. Overall, our findings provide a comprehensive overview of the translational landscape within eukaryotic cells following X-ray treatment, offering new insights into DNA damage response.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110987"},"PeriodicalIF":3.4,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Key role of CYP17A1 in Leydig cell function and testicular development in Qianbei Ma goats","authors":"Tang Wen ,&nbsp;Zhang Yuan ,&nbsp;Wang Zhong ,&nbsp;Guo Wei ,&nbsp;Chen Jiajing ,&nbsp;Ji Quan ,&nbsp;Wang Yanfei ,&nbsp;Li Ruiyang ,&nbsp;Xu Houqiang ,&nbsp;Chen Xiang","doi":"10.1016/j.ygeno.2024.110937","DOIUrl":"10.1016/j.ygeno.2024.110937","url":null,"abstract":"<div><div>Reproductive traits are vital economic parameters in goat production, and boosting the reproductive capacity of breeding rams is crucial for enhancing the profitability of goat farming. Currently, research on the reproductive performance of Qianbei Ma goats mainly centers on investigating mechanisms associated with prolificacy and estrous ovulation in ewes, with limited emphasis on ram reproductive aspects. This study used scanning electron microscopy and enzyme-linked immunosorbent assay (ELISA) to profile the morphology of testis and the dynamic changes of Luteinizing Hormone (LH), Follicle-Stimulating Hormone (FSH), and Testosterone (T) in serum at different developmental stages of Qianbei Ma goats. Meanwhile, transcriptome sequencing technology was used to investigate the mRNA expression patterns in testicular tissues at different developmental stages: newborn (0 M), puberty (6 M), sexual maturity (12 M), and physical maturity (18 M). The results showed that the diameter, circumference, and area of the testicular seminiferous tubules gradually increased with age. The levels of T and LH in serum significantly increased from 0 to 6 months after birth (<em>p</em> &lt; 0.05), followed by a stabilization of T levels and a significant decrease in LH levels (<em>p</em> &lt; 0.05). Meanwhile, FSH shows a decreasing trend between 0 and 18 months after birth. A total of 26,437 differentially expressed genes were identified in 6 comparison groups, which involve various biological processes such as immunity, growth, metabolism, development, and reproduction, and are significantly enriched in signaling pathways related to testicular development and spermatogenesis. WGCNA analysis identified 6 regions significantly associated with testicular development and spermatogenesis, and selected 320 genes for constructing a PPI network. Ten candidate genes related to testicular development and spermatogenesis were identified, including <em>TP53</em>, <em>PLK4</em>, <em>RPS9</em>, <em>PFN4</em>, <em>ACTB</em>, <em>CYP17A1, GPX4</em>, <em>CLDN1</em>, <em>AMH</em> and <em>DHH</em>. Of these, the <em>CYP17A1</em> gene promotes interstitial cell proliferation, and promotes T synthesis. This study provides a theoretical basis and data support for promoting efficient breeding of goats and early breeding of excellent male goats.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110937"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-resolution dissection of human cell type-specific enhancers in cis and trans activities","authors":"Meng Wang,&nbsp;Xiaoxu Yang,&nbsp;Qixi Wu","doi":"10.1016/j.ygeno.2025.110985","DOIUrl":"10.1016/j.ygeno.2025.110985","url":null,"abstract":"<div><div>The spatiotemporal-specific gene expression is regulated by cell type-specific regulatory elements. Here we selected the H3K4me1-associated DNA sequences as candidate enhancers in two different human cell lines and performed ChIP-STARR-seq to quantify the cell-type-specific enhancer activities with high-resolution. We investigated how the activity landscape of enhancers would change when transferred from native cells (<em>cis</em> activity) to another cell lines (<em>trans</em> activity). We obtained enhancers <em>cis</em> activity maps and <em>trans</em> activity maps in two different cell lines. The <em>cis</em> and <em>trans</em> activity maps enabled us to identify cell type-specific active enhancers, with enrichment of motifs of differentially expressed TFs. Comparisons between the <em>cis</em> and <em>trans</em> activity maps revealed general consistent regulatory property with different levels of activity in two cell lines, suggesting sequence intrinsic regulatory properties remain similar in different types of cells. This study provides a new perspective on sequence intrinsic enhancer activities in different types of cells.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110985"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expansion of peripheral cytotoxic CD4+ T cells in Alzheimer's disease: New insights from multi-omics evidence","authors":"Jiongxue Chen ,&nbsp;Jiatian Xie ,&nbsp;Fuyin Deng ,&nbsp;Jinhua Cai ,&nbsp;Sitai Chen ,&nbsp;Xingrong Song ,&nbsp;Shangzhou Xia ,&nbsp;Qingyu Shen ,&nbsp;Xinying Guo ,&nbsp;Yamei Tang","doi":"10.1016/j.ygeno.2024.110976","DOIUrl":"10.1016/j.ygeno.2024.110976","url":null,"abstract":"<div><div>The significance of the adaptive immune response in Alzheimer's disease (AD) is increasingly recognized. We analyzed scRNA-Seq data from AD patients, revealing a notable rise in CD4 cytotoxic T cells (CD4-CTLs) in peripheral blood mononuclear cells (PBMCs), validated in vivo and in vitro. This rise correlates with cognitive decline in AD patients. We also identified transcription factors TBX21 and MYBL1 as key drivers of CD4-CTL expansion. Further analyses indicate these cells are terminally differentiated, showing clonal expansion, metabolic changes, and unique communication patterns. Mendelian randomization identified risk genes SRGN and ITGB1, suggesting their genetic regulation in CD4-CTLs may contribute to AD. To summarize, our findings characterize the expansion of CD4-CTLs in the PBMCs of AD patients, providing valuable understanding into the possible mechanisms involved in the expansion of CD4-CTLs in AD.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110976"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary dynamics of repetitive elements and their relationship with genome size in Acrididae","authors":"Lina Zhao ,&nbsp;Hao Yuan ,&nbsp;Xuanzeng Liu ,&nbsp;Huihui Chang ,&nbsp;Xuan Jing ,&nbsp;Yimeng Nie ,&nbsp;Yuan Huang","doi":"10.1016/j.ygeno.2024.110971","DOIUrl":"10.1016/j.ygeno.2024.110971","url":null,"abstract":"<div><div>It is widely accepted that repetitive elements (REs) represent the primary mechanism driving genome size variation across eukaryotes. The observed genome sizes and REs of 59 species within the Acrididae were obtained and characterized. The genome sizes observed ranged from 6.60 pg to 19.35 pg, while the proportion of REs varied from 57.92 % to 83.58 %. The primary contributors were identified as LTR (2.34 % ∼ 20.98 %) and LINEs (6.70 % ∼ 16.33 %). The results of ancestral reconstruction indicated that the proportion of REs in ancestral nodes was 69.53 %, which suggests that they have undergone extensive genome expansion or contraction. A significant positive correlation was identified between the proportion of REs and genome size. Transposable elements were found to account for approximately 41 % of the observed variation in genome size. Moreover, the LTR was identified as the most significant RE type in relation to genome size expansion within the Acrididae.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110971"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}