Genomics最新文献_第6页

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets 母体日粮纤维含量的差异影响胎儿和仔猪基因表达模式和染色质可及性。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-13 DOI: 10.1016/j.ygeno.2025.110995

Smahane Chalabi , Linda Loonen , Jos Boekhorst , Houcheng Li , Lingzhao Fang , Peter W. Harrison , Wassim Lakhal , Jerome Lluch , Alexey Sokolov , Sarah Djebali , Andrea Rau , Elisabetta Giuffra , Jerry Wells

{"title":"Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets","authors":"Smahane Chalabi , Linda Loonen , Jos Boekhorst , Houcheng Li , Lingzhao Fang , Peter W. Harrison , Wassim Lakhal , Jerome Lluch , Alexey Sokolov , Sarah Djebali , Andrea Rau , Elisabetta Giuffra , Jerry Wells","doi":"10.1016/j.ygeno.2025.110995","DOIUrl":"10.1016/j.ygeno.2025.110995","url":null,"abstract":"<div><div>This study investigates the impact of maternal gestation diets with varying fiber contents on gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post weaning. High-fiber maternal diets, enriched with sugar beet pulp or pea internal fiber, were compared to a low-fiber maternal diet to evaluate their effects on liver and muscle tissues. The findings demonstrate that maternal high-fiber diets significantly alter chromatin accessibility, predicted transcription factor activity and transcriptional landscape in both fetuses and piglets. A gene set enrichment analysis revealed over-expression of gene ontology terms related to metabolic processes and under-expression of those linked to immune responses in piglets from sows given the high-fiber diets during gestation. This suggests better metabolic health and immune tolerance of the fetus and offspring, in line with the documented epigenetic effects of short chain fatty acids on immune and metabolic pathways. A deconvolution analysis of the bulk RNA-seq data was performed using cell-type specific markers from a single cell transcriptome atlas of adult pigs. These results confirmed that the transcriptomic and chromatin accessibility data do not reflect different cell type compositions between maternal diet groups but rather phenotypic changes triggered by maternal nutrition in shaping the epigenetic and transcriptional environment of fetus and offspring. Our findings have implications for improving animal health and productivity as well as broader implications for human health, suggesting that optimizing maternal diet with high-fiber content could enhance metabolic health and immune function in the formative years after birth and potentially to adulthood.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110995"},"PeriodicalIF":3.4,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003624","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}

引用次数: 0

Decoding gene expression dynamics during seed development in sesame (Sesamum indicum L.) through RNA-Seq analysis 通过RNA-Seq分析解码芝麻种子发育过程中的基因表达动态。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-12 DOI: 10.1016/j.ygeno.2025.110997

Bantayehu Bekele , Mebeaselassie Andargie , Miguel Gallach , Dereje Beyene , Kassahun Tesfaye

{"title":"Decoding gene expression dynamics during seed development in sesame (Sesamum indicum L.) through RNA-Seq analysis","authors":"Bantayehu Bekele , Mebeaselassie Andargie , Miguel Gallach , Dereje Beyene , Kassahun Tesfaye","doi":"10.1016/j.ygeno.2025.110997","DOIUrl":"10.1016/j.ygeno.2025.110997","url":null,"abstract":"<div><div>Sesame (<em>Sesamum indicum</em> L., 2n = 2× = 26) from the Pedaliaceae family is primarily grown for its high oil content, rich in unsaturated fatty acids like linoleic acid (LA) and alpha-linolenic acid (ALA). However, the molecular mechanisms of sesame oil accumulation remain poorly understood. This study analyzed transcriptomes at two seed development stages: Young Stage (YS, pods 1.5–2.5 cm) and Mature Stage (MS, brown pods >2.5 cm), to explore regulatory mechanisms and identify key genes involved in lipid biosynthesis.</div><div>From 25,173 genes, 18,820 with expression values >10 CPM in at least 70 % of replicates were included in differential expression (DE) analysis. Active expression (LFC > 0) was observed in 9372 and 9448 genes at YS and MS, respectively. DEGs were annotated, revealing roles in various biological processes, (e.g., mRNA metabolic process, reproduction-related developmental processes, seed development), molecular functions (e.g., aminoacyltransferase activity, ubiquitin-like protein and ubiquitin-protein transferase activities), and cellular components (e.g., peroxisome, microbody, lipid droplet).</div><div>KEGG analysis highlighted genes involved in fatty acid synthesis (e.g., <em>fabG</em>, <em>fabZ</em>), TAG biosynthesis (<em>DGAT1</em>, <em>GPAT</em>), and alpha-linolenic acid metabolism (<em>AOS</em>, <em>LCAT3</em>). Key genes upregulated at MS included <em>SIN_1025205</em> (protein transport), <em>SIN_1006853</em> (acetylajmalan esterase), and <em>SIN_1003267</em> (gamma-cadinene synthase). The study generated a valuable transcriptome dataset and gene list for seed development and lipid biosynthesis, which will be validated through functional studies. An interactive webpage is provided for data exploration.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110997"},"PeriodicalIF":3.4,"publicationDate":"2025-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983286","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}

引用次数: 0

Further insights into the molecular mechanisms underlying tobacco straw cultivation of Pleurotus ostreatus by comparative transcriptome analyses 通过比较转录组分析进一步了解平菇烟草秸秆栽培的分子机制。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-10 DOI: 10.1016/j.ygeno.2025.110992

Xinran Li, Liu Luo, Xuying Wang , Miao Zhu

{"title":"Further insights into the molecular mechanisms underlying tobacco straw cultivation of Pleurotus ostreatus by comparative transcriptome analyses","authors":"Xinran Li, Liu Luo, Xuying Wang , Miao Zhu","doi":"10.1016/j.ygeno.2025.110992","DOIUrl":"10.1016/j.ygeno.2025.110992","url":null,"abstract":"<div><div>Cultivation of edible mushrooms on straw can significantly reduce production costs, provide notable environmental and ecological benefits. However, the molecular mechanisms via which mushrooms utilize straw are not well understood. We conducted a comparative transcriptomic analysis of oyster mushrooms cultivated on two different biomass substrates, namely, corncob and tobacco straw at various developmental stages. The results revealed that the biomass substrates induced distinct transcriptomic changes during mycelium and fruiting body development. Straw affected the metabolism of pyruvate and acetyl-CoA, with significant downregulation of pyruvate decarboxylase expression, and upregulation of acetyl-CoA hydrolase during mycelial growth. Genes associated with cell wall and carbohydrate metabolism were significantly upregulated, and the PLD-PA-mTOR pathway was activated during the fruiting body development stage in mushrooms grown on straw. These findings reveal the transcriptomic adaptations of oyster mushrooms to tobacco straw, and enhance our understanding of the molecular mechanisms underlying biomass conversion by edible fungi using straw.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110992"},"PeriodicalIF":3.4,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968968","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}

引用次数: 0

Identification of aberrant plasma vesicles containing AAK1 and CCDC18-AS1 in adolescents with major depressive disorder and preliminary exploration of treatment efficacy 青少年重度抑郁障碍中含有AAK1和CCDC18-AS1的异常血浆囊泡的鉴定及治疗效果的初步探讨

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-09 DOI: 10.1016/j.ygeno.2025.110993

Yifan Xu , Rong Zhang , Xinzhe Du , Yangxi Huang , Yao Gao , Yujiao Wen , Dan Qiao , Ning Sun , Zhifen Liu

{"title":"Identification of aberrant plasma vesicles containing AAK1 and CCDC18-AS1 in adolescents with major depressive disorder and preliminary exploration of treatment efficacy","authors":"Yifan Xu , Rong Zhang , Xinzhe Du , Yangxi Huang , Yao Gao , Yujiao Wen , Dan Qiao , Ning Sun , Zhifen Liu","doi":"10.1016/j.ygeno.2025.110993","DOIUrl":"10.1016/j.ygeno.2025.110993","url":null,"abstract":"<div><h3>Background</h3><div>Major depressive disorder (MDD) during adolescence significantly jeopardizes both mental and physical health. However, the etiology underlying MDD in adolescents remains unclear.</div></div><div><h3>Methods</h3><div>A total of 74 adolescents with MDD and 40 health controls (HCs) who underwent comprehensive clinical and cognitive assessments were enrolled. Differential expression analysis was conducted on plasma extracellular vesicles (EVs) carrying long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray analysis. Two possible lncRNA-miR-mRNA networks were established and candidate regulatory axes were generated using the StarBase, miRDB, and TargetScan bioinformatics databases. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the candidate molecules and signaling axes in a clinical cohort.</div></div><div><h3>Results</h3><div>A total of 3752 dysregulated lncRNAs and 1789 dysfunctional mRNAs were identified. Two candidate regulatory axes (AC156455.1/miR-126-5p/AAK1 and CCDC18-AS1/miR-6835-5p/CCND2) with potential connections with MDD were selected. The candidate molecules exhibit differential expression patterns among adolescents with MDD and HCs, as well as before and after treatment with sertraline in adolescents with MDD. Furthermore, AAK1, CCDC18-AS1, and miR-6835-5p expressions exhibited significant differences between the response and non-response groups. Baseline expression of CCDC18-AS1, miR-6835-5p, and CCND2 could predict the therapeutic effect of sertraline, which may be associated with reducing suicidal ideation and improving cognitive function.</div></div><div><h3>Conclusion</h3><div>Our study may provide insights into the understanding of the underlying pathological mechanisms in adolescents with MDD.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110993"},"PeriodicalIF":3.4,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969795","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}

引用次数: 0

Hepatic and intestinal insights into the molecular mechanisms of dietary Antarctic krill-induced body color differentiation in Plectropomus leopardus 南极磷虾诱导的豹斑电鼠体色分化的肝脏和肠道分子机制。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-05 DOI: 10.1016/j.ygeno.2025.110989

Jiayi Wu , Mengya Wang , Xin Gao , Mingyi Wang , Chaofan Jin , Da Zheng , Jiangping Yan , Zhenmin Bao , Bo Wang , Jingjie Hu

{"title":"Hepatic and intestinal insights into the molecular mechanisms of dietary Antarctic krill-induced body color differentiation in Plectropomus leopardus","authors":"Jiayi Wu , Mengya Wang , Xin Gao , Mingyi Wang , Chaofan Jin , Da Zheng , Jiangping Yan , Zhenmin Bao , Bo Wang , 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}

引用次数: 0

Mechanistic insights into GLP-1 receptor agonist-induced weight loss through ceRNA network analysis 通过ceRNA网络分析GLP-1受体激动剂诱导体重减轻的机制。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-04 DOI: 10.1016/j.ygeno.2025.110988

Wenxin Li , Xinyu Zhang , Jiamin Song , Ling Yang , Dong Wang , Guoyue Yuan , Li Zhao

{"title":"Mechanistic insights into GLP-1 receptor agonist-induced weight loss through ceRNA network analysis","authors":"Wenxin Li , Xinyu Zhang , Jiamin Song , Ling Yang , Dong Wang , Guoyue Yuan , 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}

引用次数: 0

Comparative effects of arecoline, caffeine, and nicotine on transcription level in the nucleus accumbens of mice 槟榔碱、咖啡因和尼古丁对小鼠伏隔核转录水平的影响。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-04 DOI: 10.1016/j.ygeno.2025.110986

Shaofang Huang , Xinran Wang , Feifan Zhou

{"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":"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}

引用次数: 0

Tissue-specific expression, functional analysis, and polymorphism of the KRT2 gene in sheep horn 羊角KRT2基因的组织特异性表达、功能分析及多态性研究。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-04 DOI: 10.1016/j.ygeno.2025.110990

Hao Yang , Mingxing Chu , Naominggaowa , Xiaoxu Zhang , Mingzhu Shan , Xiaoning Lu , Zhangyuan Pan , Jianning He

引用次数: 0

ARF3 as a novel biomarker and target in acute myeloid leukemia: Insights from pan-cancer analysis ARF3作为急性髓系白血病的新生物标志物和靶点：来自泛癌症分析的见解。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-03 DOI: 10.1016/j.ygeno.2024.110984

Yang Wenli , Wang Wei , Pan Yubiao , Huang Hua , Tong Hongyan

{"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":"<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}

引用次数: 0

Ribosome profiling reveals dynamic translational landscape following X-ray irradiation 核糖体分析揭示x射线照射后HEK293T细胞的动态翻译景观。

IF 3.4 2区生物学

Genomics Pub Date : 2025-01-02 DOI: 10.1016/j.ygeno.2025.110987

Jingyu Hou , Lei Yu , Canlan Wu , Saisai Wei , Xiangwei Gao

{"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":"<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}

引用次数: 0