Genomics最新文献

{"title":"Comparative effects of arecoline, caffeine, and nicotine on transcription level in the nucleus accumbens of mice.","authors":"Shaofang Huang, Xinran Wang, Feifan Zhou","doi":"10.1016/j.ygeno.2025.110986","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.110986","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"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":"","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, Mingxing Chu, Naominggaowa, Xiaoxu Zhang, Mingzhu Shan, Xiaoning Lu, Zhangyuan Pan, Jianning He","doi":"10.1016/j.ygeno.2025.110990","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.110990","url":null,"abstract":"<p><p>Horn is a defensive weapon of sheep, consisting of a horny sheath and a bony core. The KRT2 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 KRT2 gene using transcriptome sequencing data. Then, by comparing the protein sequences of 20 species, we identified 28 specific amino acid sites in Artiodactyla animals, constructed a phylogenetic tree of the KRT2 gene, and predicted its three-dimensional protein structure. Finally, whole genome sequencing data was used and mined 4 functional SNP sites of KRT2 gene, and use KASP assay to verify the loci. In addition, we explored the relationship between the KRT2 gene and the evolution of Artiodactyla animals, and predicted the possible mechanism by which the KRT2 gene affects the horn type of sheep.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"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":"","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, Wang Wei, Pan Yubiao, Huang Hua, Tong Hongyan","doi":"10.1016/j.ygeno.2024.110984","DOIUrl":"10.1016/j.ygeno.2024.110984","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"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":"","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, Lei Yu, Canlan Wu, Saisai Wei, Xiangwei Gao","doi":"10.1016/j.ygeno.2025.110987","DOIUrl":"10.1016/j.ygeno.2025.110987","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"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":"","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, Zhang Yuan, Wang Zhong, Guo Wei, Chen Jiajing, Ji Quan, Wang Yanfei, Li Ruiyang, Xu Houqiang, Chen Xiang","doi":"10.1016/j.ygeno.2024.110937","DOIUrl":"10.1016/j.ygeno.2024.110937","url":null,"abstract":"<p><p>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 (p < 0.05), followed by a stabilization of T levels and a significant decrease in LH levels (p < 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 TP53, PLK4, RPS9, PFN4, ACTB, CYP17A1, GPX4, CLDN1, AMH and DHH. Of these, the CYP17A1 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.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"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":"","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, Jiatian Xie, Fuyin Deng, Jinhua Cai, Sitai Chen, Xingrong Song, Shangzhou Xia, Qingyu Shen, Xinying Guo, Yamei Tang","doi":"10.1016/j.ygeno.2024.110976","DOIUrl":"10.1016/j.ygeno.2024.110976","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"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":"","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, Xiaoxu Yang, Qixi Wu","doi":"10.1016/j.ygeno.2025.110985","DOIUrl":"10.1016/j.ygeno.2025.110985","url":null,"abstract":"<p><p>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 (cis activity) to another cell lines (trans activity). We obtained enhancers cis activity maps and trans activity maps in two different cell lines. The cis and trans activity maps enabled us to identify cell type-specific active enhancers, with enrichment of motifs of differentially expressed TFs. Comparisons between the cis and trans 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.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"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":"","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, Hao Yuan, Xuanzeng Liu, Huihui Chang, Xuan Jing, Yimeng Nie, Yuan Huang","doi":"10.1016/j.ygeno.2024.110971","DOIUrl":"10.1016/j.ygeno.2024.110971","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid sequencing and identification for 18-STRs long amplicon panel using portable devices and nanopore sequencer.","authors":"Jiarong Zhang, Tingting Yang, Zihan Xie, Zilin Ren, Linyu Shi, Jiang-Wei Yan, Ming Ni","doi":"10.1016/j.ygeno.2024.110970","DOIUrl":"10.1016/j.ygeno.2024.110970","url":null,"abstract":"<p><p>STRs are the most commonly used forensic genetic markers for human identification. Nanopore sequencing has shown the advantages of high portability and large data throughput. Previous studies indicate it has great potential for profiling STRs based on the ligation library preparation method. However, this method, which requires more library preparation time and operations, is unsuitable for rapid STR profiling, particularly for field forensic applications. The transposase-based rapid library preparation method offers the possibility to perform human identification using portable instruments. However, the amplicons of conventional STR panels are too small and would be cut into scraps with rapid methods, making them impractical for genotyping. In this study, we developed an 18-STRs multiplex amplification panel with amplicons of ∼1.4 Kbp. The PCR conditions were optimized to be finished within 2 h and 12 min, and the PCR products could undergo rapid methods that involved random fragmentation. We found that, on average, 29.16 % of reads from the long-amplicon panel and rapid library kit covered the whole STR region, sufficient for downstream STR profiling analysis. We conducted a small validation experiment on 24 samples using portable instruments powered by a 1.5 kW‧h portable power source. The entire process took 10.5 h and we obtained enough data from 24 samples to perform trustworthy pairwise identification analysis using the STR profiles. The overall accuracy of the analysis was 95.36 %. In sum, the study evaluated and demonstrated the viability and potential of nanopore sequencing for forensic application in the field.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110970"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750463","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}

{"title":"Single-cell RNA sequencing reveals the heterogeneity of myofibroblasts in wound repair.","authors":"Miaonan Liu, Xiaoxuan Liu, Jingchi Zhang, Shaocong Liang, Yan Gong, Shengjun Shi, Xiaopeng Yuan","doi":"10.1016/j.ygeno.2024.110982","DOIUrl":"10.1016/j.ygeno.2024.110982","url":null,"abstract":"<p><p>Skin wound repair involves myofibroblasts crucial for tissue integrity. This study utilized single-cell RNA sequencing to explore myofibroblast diversity in various wound healing scenarios. Analysis of 89,148 cells from skin ulcers, keloids, and normal scars identified 13 cell clusters. Myofibroblast subcluster analysis unveiled 11 subsets, with subclusters 1 and 9 predominant in ulcers. Subcluster 1 exhibited heightened matrix metalloproteinase expression and involvement in bacterial response and angiogenesis, crucial in inflammation. Tissue validation confirmed subcluster 1 significance., while animal models supported upregulated CA12, TDO2, and IL-7R in chronic ulcers. These findings illuminate myofibroblast heterogeneity and their impact on wound healing, offering insights into potential therapeutic targets.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110982"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871887","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}