Genomics最新文献

{"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 (H₂S) 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 H₂S, 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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"title":"Genomic insights and phylogenetics of the mitochondrial genome of Cryptocarya","authors":"Jiepeng Huang ,&nbsp;Di Zhang ,&nbsp;Shiting Yang ,&nbsp;Yanyu Liu ,&nbsp;Jurong Ma ,&nbsp;Maojuan Zhou ,&nbsp;Yunhong Tan ,&nbsp;Yu Song","doi":"10.1016/j.ygeno.2025.111018","DOIUrl":"10.1016/j.ygeno.2025.111018","url":null,"abstract":"<div><div>The tropical genus <em>Cryptocarya</em> is known for its valuable timber and the constituents in these trees show potential for medicinal properties. However, the phylogenetic relationships among species in Asia remain unclear. Here, we report the first mitochondrial genome for <em>Cryptocarya kwangtungensis</em>, consisting of 758,020 bp, including 43 protein-coding genes, 23 tRNA genes and three rRNA genes, with 234 simple sequence repeats, and 1275 dispersed repeats, 35 homologous DNA fragments between the mitogenome and the plastome. Comparative genomic analysis indicated frequent recombination events among the sequences of five magnoliids mitogenomes and only five conserved clustered genes. Further phylogenetic analyses based on 91 mitochondrial regions and nuclear ribosomal cistron sequences of 21 species compound three well-resolved congruent groups for the <em>Cryptocarya</em> species in Asia, both of which support the genus divide into three clades, suggesting that the mitogenome sequence can provide strongly supported relationships within the genus in the family Lauraceae.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111018"},"PeriodicalIF":3.4,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491642","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":"Navigating gene editing in porcine embryos: Methods, challenges, and future perspectives","authors":"Julieta G. Hamze ,&nbsp;Josep M. Cambra ,&nbsp;Sergio Navarro-Serna ,&nbsp;Cristina A. Martinez-Serrano","doi":"10.1016/j.ygeno.2025.111014","DOIUrl":"10.1016/j.ygeno.2025.111014","url":null,"abstract":"<div><div>Gene editing technologies, particularly CRISPR/Cas9, have emerged as transformative tools in genetic modification, significantly advancing the use of porcine embryos in biomedical and agricultural research. This review comprehensively examines the various methodologies for gene editing and delivery methods, such as somatic cell nuclear transfer (SCNT), microinjection, electroporation, and lipofection. This review, focuses on the advantages or limitations of using different biological sources (<em>in vivo- vs. in vitro</em> oocytes/embryos). Male germ cell manipulation using sperm-mediated gene transfer (SMGT) and testis-mediated gene transfer (TMGT) represent innovative approaches for producing genetically modified animals. Although these technologies have revolutionized the genetic engineering field, all these strategies face challenges, including high rates of off-target events and mosaicism. This review emphasizes the need to refine these methods, with a focus on reducing mosaicism and improving editing accuracy. Further advancements are essential to unlocking the full potential of gene editing for both agricultural applications and biomedical innovations.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111014"},"PeriodicalIF":3.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143422675","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":"Molecular mapping and development of SSR markers associated with Chilli leaf curl virus resistance in chilli (Capsicum annuum L.)","authors":"K. Sai Timmarao ,&nbsp;Naresh Ponnam ,&nbsp;D.C. Lakshmanareddy ,&nbsp;M. Krishna Reddy ,&nbsp;V. Venkataravanappa ,&nbsp;P. Roshini ,&nbsp;Mahebub Shaik ,&nbsp;B.P. Manoj ,&nbsp;K. Madhavi Reddy","doi":"10.1016/j.ygeno.2025.111015","DOIUrl":"10.1016/j.ygeno.2025.111015","url":null,"abstract":"<div><div>Chilli leaf curl virus (ChLCV), caused by whiteflies transmitted begomoviruses, poses a significant threat to chilli cultivation and production all over the world. Exploring host plant resistance and identification of associated molecular markers will accelerate resistance breeding. QTL-seq analysis was employed in the IHR4615(R) × IHR2451(S) F₂ population to identify QTLs associated with ChLCV-Raichur isolate resistance. A significant QTL was mapped on chromosome 6 associated with ChLCV-Raichur isolate resistance. Defense-related genes were predicted within the identified locus. Further refining of the identified locus with simple sequence repeats (SSR) markers led to the identification of two SSR markers IHR-LCV-SSR-76 and IHR-LCV-SSR-165 associated with the ChLCV-Raichur isolate resistance with 89.50 and 72.50 % prediction efficacy, respectively in IHR4615(R) × IHR2451(S) F₂ population. These markers are located at 7 cM and 17.65 cM genetic distances from the resistant gene. These markers were further validated in another resistant source-based F₂ population of IHR4392(S) × IHR4597(R). The developed and validated molecular markers can be explored in marker-assisted breeding programs aiming at developing resistant cultivars/ F₁ hybrids of chilli.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111015"},"PeriodicalIF":3.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425250","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}