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Comprehensive expression genome-wide association study of long non-coding RNAs in four porcine tissues.
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-04 DOI: 10.1016/j.ygeno.2025.111026
Liyan Deng, Marta Gòdia, Martijn F L Derks, Barbara Harlizius, Samin Farhangi, Zhonglin Tang, Martien A M Groenen, Ole Madsen
{"title":"Comprehensive expression genome-wide association study of long non-coding RNAs in four porcine tissues.","authors":"Liyan Deng, Marta Gòdia, Martijn F L Derks, Barbara Harlizius, Samin Farhangi, Zhonglin Tang, Martien A M Groenen, Ole Madsen","doi":"10.1016/j.ygeno.2025.111026","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111026","url":null,"abstract":"<p><strong>Background: </strong>Long non-coding RNAs (lncRNAs), a type of non-coding RNA molecules, are known to play critical regulatory roles in various biological processes. However, the functions of the majority of lncRNAs remain largely unknown, and little is understood about the regulation of lncRNA expression. In this study, high-throughput DNA genotyping and RNA sequencing were applied to investigate genomic regions associated with lncRNA expression, commonly referred to as lncRNA expression quantitative trait loci (eQTLs). We analyzed the liver, lung, spleen, and muscle transcriptomes of 100 three-way crossbred sows to identify lncRNA transcripts, explore genomic regions that might influence lncRNA expression, and identify potential regulators interacting with these regions.</p><p><strong>Result: </strong>We identified 6380 lncRNA transcripts and 3733 lncRNA genes. Correlation tests between the expression of lncRNAs and protein-coding genes were performed. Subsequently, functional enrichment analyses were carried out on protein-coding genes highly correlated with lncRNAs. Our correlation results of these protein-coding genes uncovered terms that are related to tissue specific functions. Additionally, heatmaps of lncRNAs and protein-coding genes at different correlation levels revealed several distinct clusters. An expression genome-wide association study (eGWAS) was conducted using 535,896 genotypes and 1829, 1944, 2089, and 2074 expressed lncRNA genes for liver, spleen, lung, and muscle, respectively. This analysis identified 520,562 significant associations and 6654, 4525, 4842, and 7125 eQTLs for the respective tissues. Only a small portion of these eQTLs were classified as cis-eQTLs. Fifteen regions with the highest eQTL density were selected as eGWAS hotspots and potential mechanisms of lncRNA regulation in these hotspots were explored. However, we did not identify any interactions between the transcription factors or miRNAs in the hotspots and the lncRNAs, nor did we observe a significant enrichment of regulatory elements in these hotspots. While we could not pinpoint the key factors regulating lncRNA expression, our results suggest that the regulation of lncRNAs involves more complex mechanisms.</p><p><strong>Conclusion: </strong>Our findings provide insights into several features and potential functions of lncRNAs in various tissues. However, the mechanisms by which lncRNA eQTLs regulate lncRNA expression remain unclear. Further research is needed to explore the regulation of lncRNA expression and the mechanisms underlying lncRNA interactions with small molecules and regulatory proteins.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111026"},"PeriodicalIF":3.4,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572693","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}
引用次数: 0
16S rDNA sequencing reveal synergistic effects of silkworm feces and earthworms on nutrient-poor soil microbial community structure and function in Guangxi.
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-03 DOI: 10.1016/j.ygeno.2025.111025
Fuzhi Lu, Jinmei Wei, Delong Guan, Yuhan Peng, Jing Song, Feng Qian
{"title":"16S rDNA sequencing reveal synergistic effects of silkworm feces and earthworms on nutrient-poor soil microbial community structure and function in Guangxi.","authors":"Fuzhi Lu, Jinmei Wei, Delong Guan, Yuhan Peng, Jing Song, Feng Qian","doi":"10.1016/j.ygeno.2025.111025","DOIUrl":"https://doi.org/10.1016/j.ygeno.2025.111025","url":null,"abstract":"<p><p>This study evaluates the synergistic effects of silkworm feces and earthworms on nutrient-poor acidic red soils in Guangxi, China. Using 16S rDNA amplicon sequencing, soil samples from untreated fields, silkworm feces, earthworm gut contents, and soils treated with silkworm feces combined with three earthworm densities (50, 80, and 110 worms/kg) were compared. The earthworm gut microbiome increased in diversity in a density-dependent manner, while treated soils displayed enhanced microbial richness-with the 80 worms/kg treatment showing the highest diversity (605 genera). Random Forest analysis identified key bacterial genera, and co-occurrence networks pinpointed potential keystone taxa. PICRUSt2 predicted enrichment of pathways for xenobiotic biodegradation, carbohydrate metabolism, and secondary metabolite biosynthesis. These findings demonstrate that integrating silkworm feces with an optimal earthworm density improves soil microbial diversity and function, offering insights for sustainable organic waste management and soil health.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"111025"},"PeriodicalIF":3.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566820","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}
引用次数: 0
Genetic variation underlying nitrogen-deficiency tolerance in Gossypium hirsutum during the seedling stage 幼苗期 Gossypium hirsutum 耐缺氮性的遗传变异。
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111019
Xing Lv , Yuxin Song , Huifeng Ke, Zhengwen Sun, Yan Zhang, Xingfen Wang, Zhiying Ma, Qishen Gu
{"title":"Genetic variation underlying nitrogen-deficiency tolerance in Gossypium hirsutum during the seedling stage","authors":"Xing Lv ,&nbsp;Yuxin Song ,&nbsp;Huifeng Ke,&nbsp;Zhengwen Sun,&nbsp;Yan Zhang,&nbsp;Xingfen Wang,&nbsp;Zhiying Ma,&nbsp;Qishen Gu","doi":"10.1016/j.ygeno.2025.111019","DOIUrl":"10.1016/j.ygeno.2025.111019","url":null,"abstract":"<div><div>As over-fertilization leads to environmental concerns, selecting high yield cotton cultivars with a high nitrogen use efficiency (NUE) has become crucially important. However, the genetic effects underlying NUE traits remain unclear. In this study, a genome-wide association study (GWAS) was performed using 2.65 million high-quality single-nucleotide polymorphisms (SNPs) based on three NUE related traits at the seedling stage of 419 core accessions in four environments. A total of 21 novel loci were detected, of which, the novel peak on D10 chromosome was consistently detected for multiple traits and selected to analyze. We further identified and validated a novel candidate gene <em>GhERF4</em> by RNA-seq, RT-qPCR, virus-induced gene silencing (VIGS) and overexpression methods, and the results suggest that <em>GhERF4</em> plays a negative role in the regulation of N-deficiency tolerance. The identified SNPs and candidate genes provide new insights into understanding the molecular mechanism and breeding varieties in N-efficient tolerance.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111019"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500282","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
Molecular regulation of cardiomyocyte functions by exogenous hydrogen sulphide in Atlantic salmon (Salmo salar)
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111017
Carlo C. Lazado , Thinh Hoang Nhan , Vibeke Voldvik , Erik Burgerhout , Arvind Y.M. Sundaram , Torstein Tengs , Tone-Kari K. Østbye , Øivind Andersen
{"title":"Molecular regulation of cardiomyocyte functions by exogenous hydrogen sulphide in Atlantic salmon (Salmo salar)","authors":"Carlo C. Lazado ,&nbsp;Thinh Hoang Nhan ,&nbsp;Vibeke Voldvik ,&nbsp;Erik Burgerhout ,&nbsp;Arvind Y.M. Sundaram ,&nbsp;Torstein Tengs ,&nbsp;Tone-Kari K. Østbye ,&nbsp;Øivind Andersen","doi":"10.1016/j.ygeno.2025.111017","DOIUrl":"10.1016/j.ygeno.2025.111017","url":null,"abstract":"<div><div>Hydrogen sulphide (H<sub>2</sub>S) is known to regulate various physiological processes, but its role in fish cardiac function, especially at the molecular level, is poorly understood. This study examined the molecular functions of exogenous H<sub>2</sub>S, using sodium hydrosulphide (NaHS) as a donor, on Atlantic salmon cardiomyocytes. NaHS concentrations of 10 to 160 μM showed limited cytotoxicity and no impact on cell proliferation, though higher doses increased ATP activity. Menadione and NaHS administered separately or sequentially differentially regulated the expression of antioxidant response and sulphide detoxification genes. Transcriptomic analysis over 24, 48, 72, and 120 h revealed differential gene expression related to metabolic recovery. Enriched Gene Ontology terms at 24 h included processes like cell signalling and lipid metabolism, shifting to lipid metabolism and ribosomal processes by 48 h. By 120 h, xenobiotic metabolism and RNA synthesis were prominent. The study highlights NaHS-induced metabolic adjustments, particularly in lipid metabolism, in Atlantic salmon cardiomyocytes.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111017"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509311","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
GnRHR inhibits the malignant progression of triple-negative breast cancer by upregulating FOS and IFI44L
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111021
Caiping Chen , Li Xue , Chao Han , Wanxin Wu , Ning Lu , Xiang Lu
{"title":"GnRHR inhibits the malignant progression of triple-negative breast cancer by upregulating FOS and IFI44L","authors":"Caiping Chen ,&nbsp;Li Xue ,&nbsp;Chao Han ,&nbsp;Wanxin Wu ,&nbsp;Ning Lu ,&nbsp;Xiang Lu","doi":"10.1016/j.ygeno.2025.111021","DOIUrl":"10.1016/j.ygeno.2025.111021","url":null,"abstract":"<div><div>Gonadotropin-releasing hormone receptor (GnRHR) has been identified as a factor that hinders the malignant advancement of triple-negative breast cancer (TNBC). Nevertheless, the specific molecular mechanism responsible for this impact remains unclear. This study demonstrates that GnRHR exhibits low expression levels in TNBC, which correlates with an unfavorable prognosis for patients. GnRHR promotes the expression of FOS, subsequently enhancing IFI44L transcription and expression, thereby inhibiting TNBC cell proliferation, migration, and invasion. Goserelin reduced the growth rate of TNBC tumors in nude mice, resulting in elevated levels of GnRHR, FOS, and IFI44L in tumor tissues, while the expression of Ki67, vimentin, and N-cadherin decreased. Overall, our results reveal that GnRHR suppresses the malignant progression of TNBC by upregulating FOS and IFI44L. Goserelin slows down the proliferation of TNBC tumors in vivo through the GnRHR/FOS/IFI44L pathway, which may present a new therapeutic approach for the management of TNBC.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111021"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143500339","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
Global effect of copper excess and deficiency in Saccharomyces cerevisiae proficient or deficient in nonsense-mediated mRNA decay
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111020
Xinyi Zhang , Sunday Olaniyan , Xiayan Li , Bernd Zechmann , Mary Lauren Benton , Bessie Kebaara
{"title":"Global effect of copper excess and deficiency in Saccharomyces cerevisiae proficient or deficient in nonsense-mediated mRNA decay","authors":"Xinyi Zhang ,&nbsp;Sunday Olaniyan ,&nbsp;Xiayan Li ,&nbsp;Bernd Zechmann ,&nbsp;Mary Lauren Benton ,&nbsp;Bessie Kebaara","doi":"10.1016/j.ygeno.2025.111020","DOIUrl":"10.1016/j.ygeno.2025.111020","url":null,"abstract":"<div><div>The highly conserved nonsense-mediated mRNA decay (NMD) pathway was initially identified as an mRNA surveillance pathway. NMD is now also known to have multiple functions including precise regulation of gene expression. In <em>Saccharomyces cerevisiae</em>, about 5–10 % of the transcriptome is regulated by the NMD pathway. Previous studies found environmental condition-specific regulation of transcripts by NMD in <em>S. cerevisiae</em>. In this study, we examined the effect varying copper levels have on global regulation of mRNAs by NMD. Specifically, the consequences of copper excess and deficiency on cellular ultrastructure and transcriptomes of <em>S. cerevisiae</em> cells with a functional and non-functional NMD pathway was investigated. Copper excess or deficiency resulted in enlarged vacuoles in yeast cells relative to cells grown in normal growth conditions. Additionally, yeast cells with a functional NMD pathway had dilated endoplasmic reticulum (ER) when exposed to elevated copper levels. In elevated copper levels dilated ER were not observed in cells with a non-functional NMD pathway. Furthermore, copper deficiency led to widespread changes in gene expression relative to the normal growth and elevated copper conditions. Significant enrichments for Molecular function (MF) included transmembrane transporter activity and helicase activity for transcripts upregulated in complete minimal (CM) only. For transcripts upregulated in both CM and 100 μM copper, significant enrichments for MF were found in structural constituent of cell wall, ferric-chelate reductase (NADPH) activity, metal ion and DNA binding. Transcripts upregulated specifically in low copper were greatly enriched for categories related to RNA binding and RNA metabolic processes.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111020"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491654","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
Genome-wide identification of Tegillarca granosa ATP-binding cassette (ABC) transporter family related to arsenic toxicity 在全基因组范围内鉴定与砷毒性相关的粒尾藻ATP结合盒(ABC)转运体家族
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111024
Jinmu Kim , Hyeon Jin Kim , Eunkyung Choi , Jung Jun Park , Minjoo Cho , Soyun Choi , Hyejin Kim , Jung Sick Lee , Hyun Park
{"title":"Genome-wide identification of Tegillarca granosa ATP-binding cassette (ABC) transporter family related to arsenic toxicity","authors":"Jinmu Kim ,&nbsp;Hyeon Jin Kim ,&nbsp;Eunkyung Choi ,&nbsp;Jung Jun Park ,&nbsp;Minjoo Cho ,&nbsp;Soyun Choi ,&nbsp;Hyejin Kim ,&nbsp;Jung Sick Lee ,&nbsp;Hyun Park","doi":"10.1016/j.ygeno.2025.111024","DOIUrl":"10.1016/j.ygeno.2025.111024","url":null,"abstract":"<div><div>Arsenic is a widespread environmental contaminant recognized for its high mobility and potential toxicity. Arsenic levels at Suncheon Bay, one of the primary <em>Tegillarca granosa</em> culturation sites in South Korea, were identified as higher than the habitat's threshold effect level (TEL). After 12 and 48 h of arsenic exposure, a total of 939 and 842 DEGs were identified in the gill and mantle, respectively. Detoxification genes were identified based on DEG analysis, and out of 10 ABCA3 genes in <em>T. granosa</em>, seven ABCA3 genes in total were up- and/or downregulated in two tissues. The metabolic and the cell adhesion molecules KEGG pathways were the most enriched among the commonly identified up- and downregulated genes. The ‘metabolic process’ gene ontology term was highly enriched with upregulated DEGs. We then identified 74 ATP-binding cassette (ABC) genes in the <em>T. granosa</em> genome, which has seven subfamilies (A to G), with gene expansion found in the ABCC and ABCA subfamilies. Although the precise mechanisms of arsenic-induced gene dysregulation remain unknown, our findings suggest that ABCA3 genes might participate in arsenic active transport and play an important role in arsenic detoxification.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111024"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143520339","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
MEF2A promoter methylation negatively regulates mRNA transcription and affects myoblast physiological function in cattle
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111016
Jinkui Sun , Xiang Chen , Yong Ruan , Jiali Xu , Houqiang Xu
{"title":"MEF2A promoter methylation negatively regulates mRNA transcription and affects myoblast physiological function in cattle","authors":"Jinkui Sun ,&nbsp;Xiang Chen ,&nbsp;Yong Ruan ,&nbsp;Jiali Xu ,&nbsp;Houqiang Xu","doi":"10.1016/j.ygeno.2025.111016","DOIUrl":"10.1016/j.ygeno.2025.111016","url":null,"abstract":"<div><div>This study investigates the regulatory effects of methylation in the promoter region of the bovine MEF2A gene on its transcription levels and the impact on bovine myoblasts. Transcription levels and promoter methylation status of MEF2A in the same tissues of calves and adult cattle were assessed using qRT-PCR and BSP methods. The results indicated that MEF2A expression levels in calves were significantly lower than those in adult cattle (<em>P</em> &lt; 0.05), while the methylation rate of MEF2A was significantly higher in calves (<em>P</em> &lt; 0.05), suggesting a correlation between high methylation levels and reduced gene expression. Subsequently, MEF2A overexpression and interference vectors were transfected into bovine myoblasts to examine the effects of altered MEF2A expression on its promoter methylation status. The findings revealed that MEF2A overexpression significantly reduced the methylation rate (<em>P</em> &lt; 0.01), whereas MEF2A interference increased the methylation rate (<em>P</em> &lt; 0.01), aligning with the expression trends of DNMT1. Furthermore, bovine myoblasts were treated with varying concentrations of the methylation inhibitor 5-Aza-dC to evaluate changes in MEF2A promoter methylation and mRNA levels. The effects on cell cycle progression, apoptosis, and other growth parameters were assessed using flow cytometry, ELISA, and qRT-PCR. Results showed that a concentration of 1 μM 5-Aza-dC effectively reduced MEF2A promoter methylation and significantly upregulated MEF2A expression, leading to accelerated cell cycle progression and increased secretion levels of GH and INS, all differences being statistically significant (<em>P</em> &lt; 0.01). Additionally, 1 μM of 5-Aza-dC promoted apoptosis, with qRT-PCR results for relevant genes supporting this finding. In conclusion, methylation of the MEF2A promoter negatively regulates its mRNA transcription levels, thereby impacting the growth and development of Guanling cattle myoblasts. These results provide valuable insights for the genetic improvement of cattle through marker-assisted selection.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111016"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537063","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
ELF5 gene promotes milk lipid synthesis in goat mammary epithelial cells by transcriptomic analysis
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111023
Cunxia Ma, Yuzhu Guo, Tongtong Tu, Shuangshuang Cui, Jintao Zhong, Yunhai Zhang, Ning Song, Hongyu Liu
{"title":"ELF5 gene promotes milk lipid synthesis in goat mammary epithelial cells by transcriptomic analysis","authors":"Cunxia Ma,&nbsp;Yuzhu Guo,&nbsp;Tongtong Tu,&nbsp;Shuangshuang Cui,&nbsp;Jintao Zhong,&nbsp;Yunhai Zhang,&nbsp;Ning Song,&nbsp;Hongyu Liu","doi":"10.1016/j.ygeno.2025.111023","DOIUrl":"10.1016/j.ygeno.2025.111023","url":null,"abstract":"<div><div>E74-like factor 5 (ELF5) is an Ets transcription factor of epithelial development, while the function of <em>ELF5</em> gene in goat milk fat synthesis remains to be elucidated. In goat mammary epithelial cells, we performed RNA sequencing and analyzed differentially expressed genes (DEGs) after <em>ELF5</em> gene overexpression. <em>ELF5</em> gene significantly up-regulated the synthesis of triglyceride, total cholesterol, free fatty acid, and lipid droplets. We obtained 929 DEGs after <em>ELF5</em> gene overexpression in GMECs. Among the DEGs, <em>SPP1</em>, <em>ELOVL1</em>, <em>PNPLA2</em>, <em>FOXO1</em>, <em>PTGS2</em>, <em>SEMA6A</em>, <em>ACSL5</em>, and <em>GPNMB</em> genes that are related to lipid metabolism were identified. Enrichment analysis showed MAPK and FoxO signaling pathways were up-regulated by <em>ELF5</em> gene overexpression in GMECs. These findings offer evidence that <em>ELF5</em> gene could be a candidate gene for the regulation of milk lipid synthesis in goats, and provide molecular targets for the breeding of goats with high milk fat.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111023"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143512240","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
Genome-wide identification of light-harvesting chlorophyll a/b-binding (LHC) gene family in tomato and functional analysis of SlLhcb1.11 and SlELIP1 under cold stress
IF 3.4 2区 生物学
Genomics Pub Date : 2025-03-01 DOI: 10.1016/j.ygeno.2025.111022
Fanyi Meng , Mengqiu Ma , Shanshan Li , Pan Liang , Yunfei Liang , Hongyan Shi , Shudi Huang , Huai Su , Yilin Deng , Muhammad Asif Akram , Xiaoxia Shen , Ru Feng , Xiangqiang Zhan , Fang Ma
{"title":"Genome-wide identification of light-harvesting chlorophyll a/b-binding (LHC) gene family in tomato and functional analysis of SlLhcb1.11 and SlELIP1 under cold stress","authors":"Fanyi Meng ,&nbsp;Mengqiu Ma ,&nbsp;Shanshan Li ,&nbsp;Pan Liang ,&nbsp;Yunfei Liang ,&nbsp;Hongyan Shi ,&nbsp;Shudi Huang ,&nbsp;Huai Su ,&nbsp;Yilin Deng ,&nbsp;Muhammad Asif Akram ,&nbsp;Xiaoxia Shen ,&nbsp;Ru Feng ,&nbsp;Xiangqiang Zhan ,&nbsp;Fang Ma","doi":"10.1016/j.ygeno.2025.111022","DOIUrl":"10.1016/j.ygeno.2025.111022","url":null,"abstract":"<div><div>Light-harvesting chlorophyll a/b-binding (LHC) proteins, as the antenna complex, collect and transfer light energy to the reaction centers of PSII. They are crucial for abiotic stress responses, especially in the photoprotection under cold stress. However, members of the <em>LHC</em> gene family in tomato (<em>Solanum lycopersicum</em> L.) have not yet been identified. In this study, a total of 39 SlLHC proteins containing the chlorophyll a/b binding domain or light-harvesting-like domain were identified, and classified into four subfamilies: Lhc, Lil, PsbS, and FCII. Further qRT-PCR analysis showed <em>SlLhcb1.11</em> was inhibited and <em>SlELIP1</em> was induced at low temperature (4 °C). Subsequently, the result of VIGS experiment showed that silencing <em>SlLhcb1.11</em> or <em>SlELIP1</em> genes resulted in lighter leaf color, reduced chlorophyll content, compromised photosynthesis, and decreased cold tolerance in tomato plants. These findings offer novel insights into the structure and function of <em>SlLHC</em> genes, thereby contributing to genetic resources for the development of cold-tolerant tomato germplasm.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111022"},"PeriodicalIF":3.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531302","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
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