Genomics最新文献

{"title":"METTL14 facilitates the process of sexual reversal via m6A RNA methylation in Pelodiscus sinensis","authors":"Tong Zhou ,&nbsp;Guobin Chen ,&nbsp;Jizeng Cao ,&nbsp;Huizi Ji ,&nbsp;Guiwei Zou ,&nbsp;Hongwei Liang","doi":"10.1016/j.ygeno.2025.111030","DOIUrl":"10.1016/j.ygeno.2025.111030","url":null,"abstract":"<div><div>The Chinese soft-shelled turtle (<em>Pelodiscus sinensis, P. sinensis</em>) demonstrates noteworthy sexual dimorphism, where the males grow more rapidly and significantly larger than females under equivalent conditions. Estradiol (E2) administration can catalyze transformation from male to pseudo-female (PF), during which m6A RNA methylation undergoes considerable alterations. Nevertheless, the function of m6A methylation, specifically, the methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit gene (<em>METTL14</em>) during this sex reversal process remains unclear. Within this study, we characterized the <em>METTL14</em> gene, which was predominantly expressed within the ovary and demonstrated notable expression in PF individuals. Interference of <em>METTL14</em> results in altered expression of methylation-related genes, yielding elevated <em>RSPO1</em> expression and diminished <em>AMH</em> expression. Administration of E2 and <em>METTL14</em>-RNAi elicits 7994 differentially expressed genes (DEGs) during sexual differentiation, and KEGG enrichment analysis highlighted that <em>METTL14</em> profoundly affects embryonic development through pathways including steroid hormone biosynthesis, ovarian steroidogenesis, tryptophan metabolism, and Glycolysis/Gluconeogenesis. Gene set enrichment analysis (GSEA) indicated that METTL14-RNAi triggers reduced expression of steroid hormone biosynthesis and ovarian steroidogenesis pathways while increasing the PPAR signaling pathway. In conclusion, METTL14-RNAi results in significant up-regulation of <em>RSPO1</em> and down-regulation of <em>AMH</em>, inducing substantial alterations in pathways associated with hormone and metabolism. These findings propose that <em>METTL14</em> may play a facilitating role during E2-induced sex reversal in <em>P. sinensis</em>, offering a novel avenue for further exploration into all-male breeding.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111030"},"PeriodicalIF":3.4,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624202","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":"Gap-free genome assembly and comparative analysis reveal the evolution and lignin degradation mechanisms of Cylindrobasidium torrendii","authors":"Yang Yang ,&nbsp;Jian Chen ,&nbsp;Xuebo Hu","doi":"10.1016/j.ygeno.2025.111029","DOIUrl":"10.1016/j.ygeno.2025.111029","url":null,"abstract":"<div><div>The Physalacriaceae family comprises numerous saprophytic edible and medicinal fungi with significant ecological and economic importance. However, the lack of high-quality genomic data has hindered systematic studies of this family. Here, we report the chromosome-level genome assembly of <em>Cylindrobasidium torrendii</em>, a species identified in China, using a combination of Illumina, PacBio HiFi, and Hi-C sequencing technologies. The 33.67 Mb genome, featuring a GC content of 52.00 %, demonstrates enhanced continuity and completeness. Phylogenetic analysis based on 1685 single-copy orthologous gene families places <em>C. torrendii</em> in close evolutionary proximity to <em>Armillaria mellea</em> and <em>Gymnopus necrorhizus</em>, with a divergence time of 112.39 Mya. Comparative genomics reveals conserved syntenic blocks between chromosomes of <em>C. torrendii</em> and those of <em>Pleurotus ostreatus</em> and <em>Lentinula edodes</em>. Gene family analysis identified 980 expanded and 487 contracted gene families, with expanded genes significantly enriched in secondary metabolite biosynthesis pathways. CAZyme, P450, and laccase gene family comparisons highlighted the evolutionary dynamics of these gene families in <em>C. torrendii</em>. Transcriptomic analysis under fungal dark stress revealed significant upregulation of genes such as <em>CtoLAC7</em> and CAZymes (<em>GH</em> and <em>CE</em> families). This study provides a high-quality genomic resource and novel insights into the genetic and functional characteristics of <em>C. torrendii</em> and the <em>Physalacriaceae</em> family.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111029"},"PeriodicalIF":3.4,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604483","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":"Integrated analysis of single-cell and bulk RNA sequencing identifies APOC1 as a biomarker and therapeutic target for G0/G1 cell cycle arrest in cholangiocarcinoma","authors":"Qinlei Wang ,&nbsp;Zhaowei Sun ,&nbsp;Maobing Wang ,&nbsp;Chuan Feng ,&nbsp;Menshou Chen ,&nbsp;Haoran Li ,&nbsp;Jingyun Guo ,&nbsp;Bingyuan Zhang ,&nbsp;Kai Ma ,&nbsp;Miao Liu ,&nbsp;Jinzhong Pang ,&nbsp;Yujie Feng","doi":"10.1016/j.ygeno.2025.111028","DOIUrl":"10.1016/j.ygeno.2025.111028","url":null,"abstract":"<div><div>Cholangiocarcinoma is characterized by its high malignancy, frequent recurrence and insensitivity to conventional radiotherapy and chemotherapy. This resistance may be associated with the presence of cells in the G0/G1 arrest phase within the cancer. Cancer cells in the G0/G1 phase are resistant to therapies targeting actively dividing cells, allowing them to evade conventional adjuvant treatments and survive. When conditions become favorable, these quiescent cells can re-enter the cell cycle, proliferate and potentially contribute to cancer recurrence. However, the biomarkers for identifying cells in the G0/G1 arrest phase within cholangiocarcinoma and the molecular mechanisms inducing G0/G1 arrest remain unclear. In our study, we first identified APOC1 as a characteristic gene for G0/G1 phase arrest in cholangiocarcinoma through bulk RNA sequencing (bulkRNA-seq). We then used single-cell RNA sequencing(scRNA-seq) for cell cycle inference and localized the expression peaks of APOC1 to verify its active cell cycle phase. Our experiments demonstrated that APOC1 can induce G0/G1 phase arrest in cholangiocarcinoma cells by inhibiting the Wnt/β-catenin signaling pathway, thereby suppressing cell proliferation, migration and invasion. This suggests that APOC1 may serve as a key regulatory factor and an important biomarker for cells in the G0/G1 phase of cholangiocarcinoma.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111028"},"PeriodicalIF":3.4,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596673","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":"Identification of blacklist regions in cattle and pig genomes","authors":"Mei Kong ,&nbsp;Jingwen Dou ,&nbsp;Hong Liu ,&nbsp;Jing Xu ,&nbsp;Zhuqing Zheng ,&nbsp;Aishao Shangguan ,&nbsp;Zhenshuang Tang ,&nbsp;Xiaolong Qi ,&nbsp;Saixian Zhang ,&nbsp;Yue Xiang ,&nbsp;Yuhua Fu ,&nbsp;Xiaoyong Du ,&nbsp;Xinyun Li ,&nbsp;Liangliang Fu ,&nbsp;Zhonglin Tang ,&nbsp;Jingjin Li","doi":"10.1016/j.ygeno.2025.111027","DOIUrl":"10.1016/j.ygeno.2025.111027","url":null,"abstract":"<div><div>Cattle and pigs are important farm animals and biomedical models for studying human development and diseases. Accurate annotation of their cis-regulatory elements is essential for advancing breeding strategies and biological research. Identifying these elements typically relies on ChIP-seq data, which profiles histone modifications and transcription factors. Although some large-scale ChIP-seq projects have decoded functional genomes in cattle and pigs, no comprehensive blacklist identification has been performed. In this study, we systematically identified and evaluated blacklist regions in cattle and pig genomes using the ENCODE pipeline. We annotated 126.8 Mb and 99.9 Mb of blacklist regions in cattle and pigs, respectively. We found that removing these blacklist regions is a critical quality control measure that can enhance the reliability of ChIP-seq analysis. Overall, our results provide a valuable resource for farm animal research, and we propose eliminating these problematic regions to reduce abnormally high signals and improve downstream analyses.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111027"},"PeriodicalIF":3.4,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580538","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":"Comprehensive expression genome-wide association study of long non-coding RNAs in four porcine tissues","authors":"Liyan Deng ,&nbsp;Marta Gòdia ,&nbsp;Martijn F.L. Derks ,&nbsp;Barbara Harlizius ,&nbsp;Samin Farhangi ,&nbsp;Zhonglin Tang ,&nbsp;Martien A.M. Groenen ,&nbsp;Ole Madsen","doi":"10.1016/j.ygeno.2025.111026","DOIUrl":"10.1016/j.ygeno.2025.111026","url":null,"abstract":"<div><h3>Background</h3><div>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.</div></div><div><h3>Result</h3><div>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.</div></div><div><h3>Conclusion</h3><div>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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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 ,&nbsp;Jinmei Wei ,&nbsp;Delong Guan ,&nbsp;Yuhan Peng ,&nbsp;Jing Song ,&nbsp;Feng Qian","doi":"10.1016/j.ygeno.2025.111025","DOIUrl":"10.1016/j.ygeno.2025.111025","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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}

{"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}