Genomics最新文献

{"title":"Decoding ferroptosis in alcoholic hepatitis: A bioinformatics approach to hub gene identification","authors":"Pan Tongtong ,&nbsp;Shen Yujuan ,&nbsp;Li Ting ,&nbsp;Yi Fangfang ,&nbsp;Wu Shijia ,&nbsp;Huang Yilun ,&nbsp;Zhang Huadong ,&nbsp;Zhang Qiongying ,&nbsp;Chen Yongping ,&nbsp;Chen Dazhi","doi":"10.1016/j.ygeno.2025.111009","DOIUrl":"10.1016/j.ygeno.2025.111009","url":null,"abstract":"<div><h3>Background</h3><div>Ferroptosis is associated with alcoholic hepatitis (AH); however, the underlying mechanisms remain unclear.</div></div><div><h3>Methods</h3><div>Changes in iron content and oxidative stress in AH patients and in vivo and in vitro models were analyzed. Iron homeostasis pathways in the livers of patients with AH were investigated using RNA sequencing. AH-associated ferroptosis-related genes (FRGs) were identified using weighted gene co-expression network analysis. Hub genes were identified using machine learning methods, and their diagnostic potential for AH was assessed. The correlation between FRGs and the immune microenvironment was analyzed, and the underlying regulatory mechanism was explored. FRG expression was validated in clinical samples and in vitro and in vivo models. The role of FRGs in AH-related ferroptosis was explored through gene-silencing experiments.</div></div><div><h3>Results</h3><div>Significant iron deposits and oxidative stress were detected in clinical samples and in vivo and in vitro AH models. Bioinformatics identified <em>GCLC</em>, <em>NQO1</em>, and <em>ULK1</em> as key FRGs linked to the immune microenvironment and AH-related pathogenic genes. A nomogram based on these FRGs accurately assessed AH risk, as validated using the calibration curve. A regulatory network involving 154 miRNAs and 136 transcription factors was mapped for FRGs. In AH patients, <em>NQO1</em> was upregulated in the liver, whereas <em>GCLC</em> and <em>ULK1</em> were downregulated. Silencing <em>GCLC</em> and <em>ULK1</em> reduced cell viability and increased oxidative stress and ferroptosis, whereas silencing <em>NQO1</em> had the opposite effect.</div></div><div><h3>Conclusions</h3><div>Therefore, <em>GCLC</em>, <em>NQO1</em>, and <em>ULK1</em> are key AH-related FRGs, potentially serving as targets for diagnosing and treating AH.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111009"},"PeriodicalIF":3.4,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046195","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":"Chromosome-level genome assembly and characterization of Kaixuan 016: A high-oleic peanut variety with improved agronomic traits developed through gamma-radiation-assisted breeding","authors":"Li Ren ,&nbsp;Li Deng ,&nbsp;Minjie Guo ,&nbsp;Wenzhao Dong ,&nbsp;Yuanjin Fang ,&nbsp;Xiangyu Tian ,&nbsp;Yang Li ,&nbsp;Junhua Yin ,&nbsp;Jianli Miao ,&nbsp;Zheng Zheng ,&nbsp;Shaowei Li ,&nbsp;Junping Hu ,&nbsp;Wenhao Liu ,&nbsp;Bingyan Huang ,&nbsp;Xinyou Zhang","doi":"10.1016/j.ygeno.2025.111010","DOIUrl":"10.1016/j.ygeno.2025.111010","url":null,"abstract":"<div><div>High-oleic peanuts are increasingly valued in agricultural production and consumer markets. Nevertheless, limited genomic information hinders the integration of genetic analyses and modern breeding strategies. This study details a chromosome-level genome assembly of Kaixuan 016, a high-oleic peanut variety developed through gamma-radiation-assisted breeding, exhibiting enhanced agronomic traits. Utilizing PacBio long-read sequencing and Hi-C technology, the assembly encompasses 2532.9 Mb, with a contig N50 of 11.48 Mb, structured into 20 pseudochromosomes. Repetitive elements comprise 72.26 % of the genome. Of the 69,845 protein-coding genes, 97 % are annotated in public databases. Phylogenetic analysis reveals divergence times of approximately 0.3 million years ago (Mya) for the A subgenome and 0.2 Mya for the B subgenome, with their initial divergence occurring around 2.6 Mya. Additionally, our study includes enrichment analyses on species-specific genes, along with expanded, contracted, and positively selected gene families engaged in vital metabolic and biosynthetic pathways such as photosynthesis, linoleic acid metabolism, and fatty acid elongation<strong>—</strong>key processes for oleic acid accumulation in developing seeds. Comparative genomic analysis with the AT1–1 parent genome suggests that γ-radiation primarily induces structural variations in Kaixuan 016. Population analysis further differentiated Kaixuan 016 and its derivatives into two distinct clusters<strong>—</strong>Kainong and Jihua accessions, highlighting their superior agronomic traits. This high-quality genome assembly provides a vital resource for comparative genomic studies and facilitates the advancement of accelerated, genome-guided breeding efforts in high-oleic peanuts.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111010"},"PeriodicalIF":3.4,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143065041","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":"Multiple omics analysis reveals the regulation of SIRT4 on lipid deposition and metabolism during the differentiation of bovine preadipocytes","authors":"Hongming Ma ,&nbsp;Ying Lu ,&nbsp;Wei Chen ,&nbsp;Zhendong Gao,&nbsp;Dongwang Wu,&nbsp;Yuqing Chong,&nbsp;Jiao Wu,&nbsp;Dongmei Xi,&nbsp;Weidong Deng,&nbsp;Jieyun Hong","doi":"10.1016/j.ygeno.2025.111006","DOIUrl":"10.1016/j.ygeno.2025.111006","url":null,"abstract":"<div><div>The differentiation and lipid metabolism of preadipocytes are crucial processes in IMF deposition. Studies have demonstrated that <em>SIRT4</em> plays essential roles in energy metabolism and redox homeostasis, with its expression being coordinately regulated by multiple transcription factors associated with energy and lipid metabolism. In this study, the findings of multiple omics analysis reveal that <em>SIRT4</em> significantly up-regulates the expression of genes involved in adipogenesis and enhances the differentiation and lipid deposition of bovine preadipocytes. Furthermore, <em>SIRT4</em> profoundly influences the expression pattern of metabolites by increasing the abundance of substances involved in lipid synthesis while decreasing those that promote lipid oxidative decomposition. Additionally, <em>SIRT4</em> broadly up-regulates the expression levels of various lipid classes, including glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids. These findings not only provide a theoretical basis for molecular breeding and genetic improvement in beef cattle, but also offer potential therapeutic approaches for energy homeostasis disorders and obesity.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111006"},"PeriodicalIF":3.4,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058717","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":"CircPIK3C3 inhibits hepatocellular carcinoma progression and lenvatinib resistance by suppressing the Wnt/β-catenin pathway via the miR-452-5p/SOX15 axis","authors":"Feng Yuan ,&nbsp;Yongchang Tang ,&nbsp;Hao Liang ,&nbsp;Mingbo Cao ,&nbsp;Yupeng Ren ,&nbsp;Yuxuan Li ,&nbsp;Gaoyuan Yang ,&nbsp;Zhaozhong Zhong ,&nbsp;Zhiyong Xiong ,&nbsp;Zhiwei He ,&nbsp;Meihai Deng ,&nbsp;Zhicheng Yao","doi":"10.1016/j.ygeno.2025.110999","DOIUrl":"10.1016/j.ygeno.2025.110999","url":null,"abstract":"<div><h3>Introduction</h3><div>Resistance to lenvatinib limits the effectiveness of the targeted treatments for HCC. However, the exact mechanism behind this resistance remains elusive. Current research suggests that circular RNA (circRNA) is pivotal in mediating drug resistance during targeted treatments.</div></div><div><h3>Objectives</h3><div>To investigate the influence of circRNA on HCC progression and its resistance to lenvatinib.</div></div><div><h3>Methods</h3><div>We identified the crucial circRNA hsa_circ_0005711 (circPIK3C3) through bioinformatics. Study (in-vitro <em>and</em> in-vivo) on the expression of circPIK3C3 (measured by qRT-PCR) and its association with progress of HCC patients including lenvatinib resistance were performed. Techniques such as dual-luciferase reporter assays, RNA FISH, RAP, and AGO2-RIP were employed for discerning circPIK3C3's specific mechanisms related to progression of HCC and its lenvatinib resistance.</div></div><div><h3>Results</h3><div>Study (in-vitro <em>and</em> in-vivo) revealed that circPIK3C3 exhibited reduced expression and lenvatinib resistance in HCC, which was intimately tied to patient outcomes. Moreover, circPIK3C3 elevated SOX15 expression while suppressing the signaling pathway related to Wnt/β-catenin via inhibition of miR-452-5p through a competitive endogenous RNA (ceRNA) network. This, in turn, mitigated HCC progression and its resistance to lenvatinib.</div></div><div><h3>Conclusion</h3><div>CircPIK3C3 is instrumental in the disease progression and resistance to Lenvatinib in HCC. It presents a potential therapeutic avenue for patients with lenvatinib-resistant HCC and could serve as a valuable molecular marker for forecasting lenvatinib resistance in HCC patients.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110999"},"PeriodicalIF":3.4,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037758","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":"Chromosome-level de novo genome unveils the evolution of Gleditsia sinensis and thorns development","authors":"Dandan Xiao ,&nbsp;Jiahao Liu ,&nbsp;Jing Wang ,&nbsp;Xiaoqian Yang ,&nbsp;Yuzhang Yang ,&nbsp;Ruen Yu ,&nbsp;Chun Wang ,&nbsp;Hongbo Gao ,&nbsp;Yanwei Wang ,&nbsp;Yanping Liu ,&nbsp;Dingchen Fan ,&nbsp;Furong Lin","doi":"10.1016/j.ygeno.2025.111004","DOIUrl":"10.1016/j.ygeno.2025.111004","url":null,"abstract":"<div><div><em>Gleditsia sinensis</em> Lam. (<em>G. sinensis</em>) as an important species within the Leguminosae family, has been utilized in Chinese medicine for centuries, and its thorns serve as a chief medicinal ingredient. The absence of a comprehensive genome database has hindered its in-depth research. In this investigation, a chromosome-level de novo genome assembly of <em>G. sinensis</em> ‘Yulin No.1’ was achieved, which harbors a 786.13 Mb sized genome with 36,408 protein-coding genes and experiences two WGD events. The comparative and evolutionary analysis unveiled the close phylogenetic relationship between <em>G. sinensis</em> and eight other Leguminosae species. The WGCNA and gene family analysis further indicated that <em>GsinMYB</em> was involved in the development of thorns. This investigation offered a high-level genome of <em>G. sinensis</em>, facilitating comparisons in Leguminosae species evolution and functional elucidation. It also provided key insights for further research on the molecular regulation mechanisms of thorn development in plants and the molecular breeding of <em>G. sinensis</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111004"},"PeriodicalIF":3.4,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037810","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":"Chromosome-scale genomes of ecologically and economically important rabbitfish Siganus guttatus and Siganus oramin","authors":"Lin Xian ,&nbsp;Sunil Kumar Sahu ,&nbsp;Xiaolin Huang ,&nbsp;Chao Li ,&nbsp;Yu Liang ,&nbsp;Yan Ou-Yang ,&nbsp;Huayang Guo ,&nbsp;Bo Liu ,&nbsp;Kecheng Zhu ,&nbsp;Baosuo Liu ,&nbsp;Nan Zhang ,&nbsp;Tengfei Zhu ,&nbsp;Qiye Li ,&nbsp;Dianchang Zhang","doi":"10.1016/j.ygeno.2025.111007","DOIUrl":"10.1016/j.ygeno.2025.111007","url":null,"abstract":"<div><div><em>Siganus guttatus</em> and <em>Siganus oramin</em> are two major species that are naturally distributed along the Eastern Pacific coast and possess considerable ecological and economic value. Here, we present the construction and comparative analysis of the chromosome-level genomes of these two <em>Siganus</em> species. Employing a hybrid assembly strategy, we partitioned and independently assembled the PacBio, Illumina and Hi-C reads of <em>S. guttatus</em> and <em>S. oramin,</em> resulting in chromosome-level genomes. The assembly sizes (N50 size, BUSCO completeness) of the two genomes were 642.4 M (25.76 M, 98.26 %) and 502.8 M (16.98 M, 98.8 %) for <em>S. guttatus</em> and <em>S. oramin</em>, respectively, exhibiting high contiguity and integrity. This study marks the first successful assembly of chromosome-level genomes in <em>Siganus</em> species, along with an initial exploration of their dietary habits and habitats through comparative genomics analysis. These findings offer essential resources for comparative genomics and molecular evolution research.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111007"},"PeriodicalIF":3.4,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037813","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":"Single-cell transcriptome reveals three types of adipocytes associated with intramuscular fat content in pigs","authors":"Jing Xu ,&nbsp;Hao Peng ,&nbsp;Renzhuo Kuang ,&nbsp;Zheyu Han ,&nbsp;Honghong Zhou ,&nbsp;Mingyang Hu ,&nbsp;YaPing Guo ,&nbsp;Zhixiang Xu ,&nbsp;Daoyuan Wang ,&nbsp;Ruixian Ma ,&nbsp;Daisuke Takao ,&nbsp;Mengjin Zhu ,&nbsp;Fenge Li ,&nbsp;Yunxia Zhao","doi":"10.1016/j.ygeno.2025.110998","DOIUrl":"10.1016/j.ygeno.2025.110998","url":null,"abstract":"<div><div>Intramuscular fat is an essential component of muscle tissue, and understanding its contribution to skeletal muscle fat infiltration and meat quality, together with the underlying genetic mechanisms, is a major topic in pig husbandry. However, the composition of cell types and gene expression profiles essential for this purpose remain largely unexplored. Here, we performed single-cell transcriptome analysis on muscle tissue from adult pigs and identified 15 cell types, including three previously uncharacterized types of adipocytes: Adipocyte 1, Adipocyte 2, and Aregs. Phenotypic analysis showed their proportions correlated closely with intramuscular fat content. Based on integrated analysis of ATAC-seq with RNA-seq data, Adipocyte 1 and Aregs have gene expression profiles and transcription factor (TF) motif enrichment typical of adipocytes. On the other hand, myogenic TF motifs were enriched in marker gene promoters in Adipocyte 2, suggesting that these cells originate from muscle cells. Moreover, the marker gene promoters and lineage-specific TF expression in these three adipocyte types were conserved between pigs and humans. These findings provide deep insights towards understanding the complexity of mammalian intramuscular adipocyte types and the gene regulation underlying their organization and function.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 110998"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037821","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":"Transcriptomics reveals the regulatory mechanisms of circRNA in the muscle tissue of cows with ketosis postpartum","authors":"Tao Tang ,&nbsp;Jing Zhou ,&nbsp;Meigui Wang ,&nbsp;Siqi Xia ,&nbsp;Wenqiang Sun ,&nbsp;Xianbo Jia ,&nbsp;Jie Wang ,&nbsp;Songjia Lai","doi":"10.1016/j.ygeno.2025.111008","DOIUrl":"10.1016/j.ygeno.2025.111008","url":null,"abstract":"<div><div>The transition period from late pregnancy to early lactation in dairy cows involves significant metabolic changes to cope with the challenges related to energy metabolism. Muscle tissue, as the largest energy-metabolizing tissue in dairy cows, plays a crucial role in energy metabolism. Furthermore, circular RNAs (circRNAs) have been shown to play key roles in various biological events. However, the regulatory mechanisms of energy metabolism and muscle cells mediated by circRNAs in the muscle tissue of ketotic dairy cows remain unclear. Here, we identified a total of 5103 circRNAs in the muscle tissue of ketosis-affected cows. Among these, compared to healthy cows, 57 circRNAs were differentially expressed in the muscle tissue of ketosis-affected cows, with 39 upregulated and 18 downregulated. Functional enrichment analysis based on the source genes of circRNAs indicated that circ-30,628 is closely related to carbon metabolism, and circ-CoQ₂ is associated with mitochondrial energy metabolism. Given the sponge effect of circRNAs on miRNAs, we further predicted the network relationships of downstream miRNAs and mRNAs of circ-30,628 and circ-CoQ₂, and found that their downstream target genes are involved in signaling pathways such as MAPK, Wnt, FoxO, and autophagy, which is associated with the proliferation, differentiation, energy metabolism, oxidative stress, and mitochondrial function of muscle cells. In summary, these findings provide a theoretical basis for understanding the functions of circRNAs regulating energy metabolism in the muscle tissue of ketosis-affected cows, thereby reducing the accumulation of ketone bodies to prevent the occurrence of ketosis in dairy cows.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111008"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037890","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":"Transcriptome analysis reveals potential medicinal ingredient synthesis in ornamental Dendrobium","authors":"Runyang Zhou ,&nbsp;Xi Peng ,&nbsp;Yao Teng ,&nbsp;Sian Liu ,&nbsp;Yingdan Yuan","doi":"10.1016/j.ygeno.2025.111003","DOIUrl":"10.1016/j.ygeno.2025.111003","url":null,"abstract":"<div><div><em>Dendrobium</em> is divided into ornamental and medicinal varieties due to ornamental and medicinal values. However, current research mainly focuses on medicinal <em>Dendrobium</em>, with less study on the medicinal value of ornamental <em>Dendrobium</em>. We analyzed the microstructures, active components of the stems from twelve ornamental <em>Dendrobium</em>, and explored the biosynthetic networks of these active components based on transcriptome sequencing. This study found the <em>Dendrobium</em> with the highest content of polysaccharide, alkaloid, and flavonoid was <em>Dendrobium aphyllum</em> (53.89 %), <em>Dendrobium thyrsiflorum</em> (2.11 %) and <em>Dendrobium loddigesii</em> (7.21 %). Further research revealed 9 DEGs associated with polysaccharide biosynthesis were highly expressed in <em>D. aphyllum</em>; 4 DEGs related to alkaloid biosynthesis were highly expressed in <em>D. thyrsiflorum</em>; 8 DEGs associated with flavonoid biosynthesis were highly expressed in <em>D. loddigesii</em>. This study revealed the potential medicinal value of ornamental <em>Dendrobium</em> and the synthetic mechanisms of its medicinal components, providing a foundation for the medical applications of ornamental <em>Dendrobium</em>.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111003"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037830","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 analysis of the transcriptome-wide m6A Methylome in sheep testicular development","authors":"Binpeng Xi ,&nbsp;Zengkui Lu ,&nbsp;Rui Zhang ,&nbsp;Shengguo Zhao ,&nbsp;Jianye Li ,&nbsp;Xuejiao An ,&nbsp;Yaojing Yue","doi":"10.1016/j.ygeno.2025.111005","DOIUrl":"10.1016/j.ygeno.2025.111005","url":null,"abstract":"<div><div>N6-methyladenosine (m6A) modification of RNA is a critical post-transcriptional modification, that dynamically contributes to testicular development and spermatogenesis. Nevertheless, the investigation into the role of m6A in testicular development of sheep remains insufficient. Herein, we conducted a comprehensive analysis of the m6A transcriptome landscape in the testes of F1 hybrid Southdown × Hu sheep across M0 (0 months old, newborn), M3 (3 months old, sexually immature), M6 (6 months old, sexually mature), and Y1 (1 years old, adult). By profiling the m6A signatures across the transcriptome, we observed distinct differences in m6A modification patterns during sheep testicular development. Our cross-analysis of m6A and mRNA expression revealed that the expression of 743 genes and their m6A modification were concurrent. Notably, the combined analysis of the two comparative groups, M0 vs. M6 and M0 vs. Y1, exhibited a positive correlation, with 30 candidate genes each located within the largest protein-protein interaction network. Intriguingly, eight key hub genes (<em>VEGFA</em>, <em>HDAC9</em>, <em>ZBTB40</em>, <em>KDM5B</em>, <em>MTRR</em>, <em>EAPS1</em>, <em>TSSK3</em>, and <em>BMP4</em>) were identified to be associated with the regulation of sheep testicular development and spermatogenesis. These findings contribute to a deeper understanding of the dynamic role of m6A modification in sheep testicular biology. This study to map RNA m6A modification in sheep testes at different ages, providing novel insights into m6A topology and the molecular mechanisms associated with spermatogenesis in Southdown × Hu sheep F1 hybrids and laying the foundation for further investigations of mammalian spermatogenesis.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 2","pages":"Article 111005"},"PeriodicalIF":3.4,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143037762","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}