BMC Genomics最新文献

{"title":"Dexamethasone-induced whitening of rabbit brown adipose tissue: leptin resistance and mitochondrial dysfunction.","authors":"Xiaoqin Tang, Beibei Zhang, Puhang Xie, Yanpei Wei, Yanbo Qiu, Xiaohua Yi, Ziru Zhang, Muzi She, Xiuzhu Sun, Shuhui Wang","doi":"10.1186/s12864-025-11502-3","DOIUrl":"10.1186/s12864-025-11502-3","url":null,"abstract":"<p><strong>Background: </strong>Research on the effects of exogenous glucocorticoids on brown adipose tissue (BAT) is crucial for understanding how these hormones can induce metabolic disorders such as obesity. In this study, we explored the effects of glucocorticoids, specifically dexamethasone (Dex), on the metabolic transformation of BAT to white adipose tissue (WAT).</p><p><strong>Results: </strong>Our results indicate a significant whitening shift in BAT upon Dex treatment, characterized by increased lipid deposition, decreased mitochondrial density, a significant decline in cellular ATP content, and reduced expression of mitochondrial markers. We demonstrate the crucial role of leptin resistance in mediating mitochondrial function through the overexpression and inhibition of LEPR.</p><p><strong>Conclusions: </strong>Our results suggest the role of leptin resistance in regulating of mitochondrial biogenesis and energy metabolism in glucocorticoid-induced brown adipose whiteness.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"326"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751013","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 detection of runs of homozygosity in Ding'an pigs revealed candidate genes relating to meat quality traits.","authors":"Ziyi Wang, Deyou Pan, Xinfeng Xie, Ziqi Zhong, Feng Wang, Qian Xiao","doi":"10.1186/s12864-025-11501-4","DOIUrl":"10.1186/s12864-025-11501-4","url":null,"abstract":"<p><strong>Background: </strong>Ding'an (DA) pig, a native Chinese breed, is renowned for its excellent meat quality, disease resistance, high reproductive performance, and adaptability. Its meat quality traits hold significant economic value. However, its conservation population has been declining due to the impact of commercialized breeds and African swine fever, which is not conducive to its development and utilization.</p><p><strong>Results: </strong>This study utilized whole-genome resequencing data from 15 DA pigs to reveal their genetic characteristics and current resource status. We analyzed the length, number, and distribution patterns of Runs of Homozygosity (ROH) in DA pigs, as well as high-frequency ROH regions. The results identified 23,208,098 single nucleotide polymorphisms (SNPs), 4,497,242 insertion and deletion (InDels), 13,622 copy number variation (CNVs), and 399,934 structure variation (SVs). Further analysis revealed relatively high genetic diversity and low inbreeding levels in DA pigs. Through functional gene enrichment analysis of high-frequency ROH regions, we identified multiple candidate genes associated with specific traits in DA pigs, including meat quality (ANKRD1, CPNE5, MYOM1), fat deposition (OBSCN, MAPK4, PNPLA1, PACSIN1, GRM4), and skeletal muscle development (LRPPRC, WNT9A).</p><p><strong>Conclusions: </strong>This study conducted whole-genome sequencing and ROH analysis on DA pigs, revealing high genetic diversity and low inbreeding levels within the population. Through functional gene enrichment analysis of high-frequency ROH regions, we identified multiple candidate genes associated with meat quality, fat deposition, and skeletal muscle development. These findings not only enhance our understanding of the genetic mechanisms underlying the unique traits of DA pigs but also provide valuable insights for practical applications. Specifically, the identified candidate genes and genomic regions can guide conservation efforts to maintain genetic diversity and mitigate inbreeding risks. Meanwhile, these genetic insights can be integrated into breeding programs to improve meat quality and other economically important traits, thereby supporting the sustainable development and utilization of DA pigs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"316"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751015","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":"Metabolome and transcriptome analysis of anthocyanin biosynthesis reveal key metabolites and candidate genes in red-stemmed alfalfa (Medicago sativa).","authors":"Yaqian Zong, Zhili Zhao, Kai Zhou, Xinhui Duan, Bo Han, Chenggang He, Heping Huang, Hua Jiang","doi":"10.1186/s12864-025-11529-6","DOIUrl":"10.1186/s12864-025-11529-6","url":null,"abstract":"<p><strong>Background: </strong>Alfalfa (Medicago sativa L.) serves as a vital high-quality forage resource, especially in tropical and subtropical regions where there is a deficiency of protein-rich feed. The red pigmentation of stem of space mutated alfalfa was mainly caused by anthocyanin accumulation. However, investigations into the mechanisms governing anthocyanin biosynthesis in alfalfa stems have been scarce.</p><p><strong>Result: </strong>In this study, we conducted combined transcriptome and metabolome analyses on two types of alfalfa stems: space mutation red-stemmed alfalfa and non-space mutation green-stemmed alfalfa (control). Profiling of the anthocyanin metabolome unveiled 45 metabolites linked to anthocyanin biosynthesis, with cyanidin-3-O-glucoside, pelargonidin-3-O-arabinoside, delphinidin-3-O-(6-O-acetyl)-glucoside, and kaempferol-3-O-rutinoside identified as the primary anthocyanins of red-stemmed alfalfa. Transcriptome analysis revealed 72 differentially expressed genes related to anthocyanin biosynthesis pathways, of which 54 genes were highly expressed in red stems, including 12 PALs (phenylalanine ammonia-lyase), 22 4CLs (4-coumaroyl: CoA-ligase), eight CHSs (chalcone synthase), three F3Hs (flavanone 3-hydroxylase), two ANRs (anthocyanidin reductase), three DFRs (dihydroflavonol-4-reductase), three ANSs (anthocyanidin synthase), and one FLS (flavonol synthase) gene. These genes are likely pivotal for anthocyanin biosynthesis in red-stemmed. Co-expression analysis of differentially expressed genes and relative contents of differentially expressed anthocyanin showed that each anthocyanin was closely related to multiple genes, and anthocyanin accumulation process was regulated by multiple genes. The expressions of these genes were significantly positively correlated with the relative contents of cyanidin-3-O-glucoside, pelargonin-3-O-arabinoside, and kaempferol-3-O-rutin.</p><p><strong>Conclusion: </strong>Overall, the expression patterns of PAL, 4CL, CHS, F3H, ANR, DFR, ANS, and FLS structural genes in anthocyanin biosynthesis pathway were closely related to the composition and content of anthocyanins. Different anthocyanins' accumulation patterns may result in the different stem colors of alfalfa. These findings provide comprehensive insights into the molecular mechanisms for anthocyanin biosynthesis in red-stemmed alfalfa.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"323"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956477/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750064","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":"Whole-genome sequencing of extended spectrum beta lactamases (ESBLs)-producing Klebsiella pneumoniae (kp) isolates from selected hospitals in Malaysia.","authors":"Salawudeen Adamu, Mika'ila Bawa Ali, Mohd Nasir Mohd Desa, Hui-Min Neoh, Siti Norbaya Masri, Narcisse Joseph, Tengku Zetty Maztura Tengku Jamaluddin","doi":"10.1186/s12864-025-11215-7","DOIUrl":"10.1186/s12864-025-11215-7","url":null,"abstract":"<p><p>The resistance of ESBLs-producing Kp to various groups of antibiotics commonly used against infections they caused had become a global threat and required urgent attention. This study assessed the extended spectrum beta-lactamases (ESBLs)-producing Klebsiella pneumoniae isolates in terms of their genomic resistance. An analytical profile index (API) 20E kit was used to confirm a total of 100 clinical isolates of ESBL Klebsiella pneumoniae. The disc diffusion method was used to perform the antimicrobial susceptibility testing (AST), which was followed by the phenotypic detection of ESBLs. Six profiled representative ESBL positive strains were subjected to whole genome sequencing (WGS), multilocus sequence typing (MLST), and phylogenetic tree construction using the sequence data. The study showed that 46(46%) of the 100 isolates were positive for ESBL production and antibiotic susceptibility testing revealed significant resistance to β-lactam antibiotics including monobactam especially ampicillin/sulbactam (40%), cephalosporin groups (cefuroxime, cefotaxime, and ceftriaxone) stood at 51%, 49% and 48% respectively and aztreonam with 49%. The WGS analysis of the representative strains revealed genes encoding resistance to aminoglycoside (StrA4, StrB1, aac(3')-IIa, aac(6')-1b, aac(6')1b-cr-1, aadA16, aph(3')-VIa and aadA15), trimethoprim (dfrA14 and dfrA27), sulphonamide (sul1_11, sul2_2 and sul2_3), quinolone (QnrB40-1, QnrB10, QnrS2, OqxA and OqxB), tetracycline (tet(A)_4), fosfomycin (fosA3, floR2 and fosA7), macrolid (mph(A)_1), rifampicin (ARR-3), β-lactam (blaCTX-M-15_23, blaCTX-M-55, blaSHV-1_22, blaSHV11_18, blaSHV-11, blaSHV-1_1.1, blaSHV-11_3, blaSHV-11_19, blaTEM-1_1, blaTEM-1_5, blaOXA-51_10, blaOXA-30_1, blaNDM-1, blaLEN6, blaLEN8 and blaLEN21 were detected. The MLST analysis revealed two novel sequence types of representative strains (2 with ST NF^* and 12 with ST NF) and four other heterogeneous STs which include ST394, ST985, ST17 and ST11 while the phylogenetic tree of the strains showed closed clonal relationship and lineages with other reference isolates. In conclusion, the study's results showed a high prevalence of ESBL-producing Kp in the study area, and the representative strains' genomic contents demonstrated that ESBL-producing Kp in a clinical setting could serve as a reservoir for resistance genes and be the source of genetic transfer to other bacterial species. As a result, ongoing surveillance is required to monitor this endemic situation to prevent an epidemiological outbreak of K. pneumoniae- carrying ESBL.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"322"},"PeriodicalIF":3.5,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750521","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":"Integrative genomic analysis reveals shared loci for reproduction and production traits in Yorkshire pigs.","authors":"Ran Wei, Zhenyang Zhang, He Han, Jian Miao, Pengfei Yu, Hong Cheng, Wei Zhao, Xiaoliang Hou, Jianlan Wang, Yongqi He, Yan Fu, Zhen Wang, Qishan Wang, Zhe Zhang, Yuchun Pan","doi":"10.1186/s12864-025-11416-0","DOIUrl":"10.1186/s12864-025-11416-0","url":null,"abstract":"<p><strong>Background: </strong>Improving reproductive performance in Yorkshire pigs, a key maternal line in three-way crossbreeding systems, remains challenging due to low heritability and historical selection pressures favoring production traits. Identifying pleiotropic genetic variants that influence both reproduction and production traits is crucial for understanding their genetic interplay and enhancing molecular breeding strategies.</p><p><strong>Results: </strong>Genome-wide association studies (GWAS) using 2,764 individuals identified 264,660 significant loci associated with reproduction traits and 12,460 loci for production traits, with 73 independent signals, including genes such as SCLT1 and CAPN9. A total of 465,047 independent loci were identified, resulting in a genome-wide significance threshold of <math><mrow><mn>2.15</mn> <mo>×</mo> <msup><mrow><mn>10</mn></mrow> <mrow><mo>-</mo> <mn>6</mn></mrow> </msup> </mrow> </math> . Genetic correlations analysis between reproduction and production traits across parities revealed varying trends, including a strengthening negative correlation between mean litter weight (MLW) and backfat thickness (BFT) with increasing parity (P1: <math><msub><mi>r</mi> <mi>g</mi></msub> </math> =-0.0376; P2: <math><msub><mi>r</mi> <mi>g</mi></msub> </math> =-0.1371; P3: <math><msub><mi>r</mi> <mi>g</mi></msub> </math> =-0.1475). Given 1062 shared significant loci between MLW and BFT, local genetic correlation was calculated within the corresponding genomic regions, resulting in a weak correlation of 0.014. Transcriptome-wide association studies (TWAS) leveraging data from the PigGTEx project, which includes 9,530 RNA-sequencing samples across 34 tissues, revealed 2,143 significant genes, with 31 linked to total number of piglets born (TNB) and 133 to number of piglets born alive (NBA). These results highlight the importance of these genes in reproductive performance, with SCLT1 being notably significant in reproductive tissues. For MLW, integrating results from multiple analyses revealed CENPE as a strong candidate gene, exhibiting significant association and colocalization. Validation in an independent population (n = 300) showed that incorporating the top 0.2% of significant single nucleotide polymorphisms (SNPs) in the GFBLUP model improved predictive accuracy, increasing from 0.0168 to 0.0242 for MLW.</p><p><strong>Conclusion: </strong>This study provides new insights into the pleiotropic genetic architecture underlying reproduction and production traits in Yorkshire pigs. Genetic correlations, shared loci, and candidate genes inform breeding program design. The increased accuracy of genomic selection using these significant loci highlights their practical utility in improving breeding efficiency. These findings suggest opportunities for refining selection strategies, although further research is warranted to fully realize their potential for enhancing breeding programs.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"310"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742228","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 provides new insights into the resistance of pepper to Phytophthora capsici infection.","authors":"Fengyan Shi, Xiuxue Wang, Meijun Wei, Xi Zhang, Zhidan Wang, Xiaochun Lu, Chunlei Zou","doi":"10.1186/s12864-025-11498-w","DOIUrl":"10.1186/s12864-025-11498-w","url":null,"abstract":"<p><strong>Background: </strong>Phytophthora blight is a highly destructive soil-borne disease caused by Phytophthora capsici Leonian, which threatens pepper production. The molecular mechanism of pepper resistance to phytophthora blight is unclear, and the excavation and functional analysis of resistant genes are the bases and prerequisites for phytophthora blight-resistant breeding. We aimed to analyze the expression patterns of key genes in the plant-pathogen interaction metabolic pathway and propose a working model of the pepper defense signal network against Phytophthora capsici infection.</p><p><strong>Results: </strong>The 'ZCM334' pepper material used in this study is a high-generation inbred line that is immune to Phytophthora capsici and shows no signs of infection after inoculation. Comparative transcriptome analysis of the roots of 'ZCM334' and the susceptible material 'Early Calwonder' revealed significant differences in their gene expression profiles at different stages after inoculation. Most differentially expressed genes were significantly enriched in the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, plant-pathogen interaction, and fatty acid degradation metabolic pathways. Some defense genes and transcription factors significant in pepper resistance to phytophthora blight were identified, including PR1, RPP13, FLS2, CDPK, CML, MAPK, RLP, RLK, WRYK, ERF, MYB, and bHLH, most of which were regulated after inoculation. A working model was constructed for the defense signal network of pepper against Phytophthora capsici.</p><p><strong>Conclusions: </strong>These data provide a valuable source of information for improving our understanding of the potential molecular mechanisms by which pepper plants resist infection by Phytophthora capsici. The identification of key genes and metabolic pathways provides avenues for further exploring the immune mechanism of 'ZCM334' resistance to phytophthora blight.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"311"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742232","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 and comparative evolution of 14-3-3 gene family members in five Brassicaceae species.","authors":"Jingya Zhao, Shengqin Liu, Hui Ren, Owusu Edwin Afriyie, Mengzhu Zhang, Dachao Xu, Xianzhong Huang","doi":"10.1186/s12864-025-11513-0","DOIUrl":"https://doi.org/10.1186/s12864-025-11513-0","url":null,"abstract":"<p><strong>Background: </strong>The 14-3-3 proteins are highly conserved regulatory eukaryotic proteins, which are crucial in growth, development, and stress responses. However, systematic characterization of the 14-3-3 gene family in Brassicaceae species and their evolutionary relationships have not been comprehensively reported.</p><p><strong>Results: </strong>This study conducted genome-wide identification, structural characteristics, and comparative evolutionary analysis of 14-3-3 gene family members in Arabidopsis thaliana, A. lyrata, A. pumila, Camelina sativa, and Brassica oleracea using comparative genomics. Overall, a total of 108 14-3-3 genes, which were phylogenetically classified into ε and non-ε groups were identified in the five species, with the non-ε members exhibiting more similar exon-intron structures and conserved motif patterns. Collinearity analysis revealed that the Brassicaceae 14-3-3 gene family members underwent varying degrees of expansion following whole-genome duplication (WGD) events. Notably, the number of 14-3-3 gene family members between A. lyrata and A. thaliana remained similar despite the former having approximately 1.66-fold larger genome size. In contrast, the number of 14-3-3 gene family members in A. pumila and C. sativa increased in proportionately to their genome size, while gene members in the more distantly related species to A. thaliana, B. oleracea, showed irregular expansion patterns. Selection pressure analysis revealed that 14-3-3 homologs in all the five species underwent purifying selection, with the group ε members experiencing relatively weaker purifying selection. Cloning of ApGRF6-2 gene from A. pumila indicated that the ApGRF6-2 protein was localized in the cell membrane and cytoplasm, while ectopic overexpression of ApGRF6-2 in A. thaliana could promote early flowering by upregulating the expression of floral meristem identity genes.</p><p><strong>Conclusion: </strong>This study provides a comprehensive and systematic identification of the 14-3-3 gene family members in five Brassicaceae species using updated genome sequences, and the results could form a basis for further validation of functional and molecular mechanisms of 14-3-3 genes in plant growth, development, abiotic stress responses, as well as flowering regulation.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"309"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742224","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":"Integrative analysis of transcriptome and metabolism reveals functional roles of redox homeostasis in low light and salt combined stress in Leymus chinensis.","authors":"Jikai Li, Suyang Fang, Hailing Zhang, Zubair Iqbal, Chen Shang, Weibo Han, Kai Huang, Xiangshen Meng, Muyuan Dai, Zhiheng Lu, Bingnan Guo, Mingnan Qu","doi":"10.1186/s12864-025-11526-9","DOIUrl":"10.1186/s12864-025-11526-9","url":null,"abstract":"<p><p>Salt stress is one of the major limiting factors of Leymus chinensis (named sheepgrass) growth, which accelerates inhibitive effects that are particularly concomitant with low light regimes (LL-Salt). However, little is known about physiological and molecular mechanisms under such LL-Salt in sheepgrass. This study aims to uncover the key reprogrammed metabolic pathways induced by LL-Salt through an integrated analysis of transcriptome and metabolism. Results suggested that the growth of sheepgrass seedlings was dramatically inhibited with a ranging of 8 to 20% reduction in F_v/F_m in LL-Salt combined treatments. Catalase activities were increased by 40% in LL but significantly decreased in salt stress, ranging from 15 to 46%. Both transcriptome and metabolism analysis reveal that carbon metabolism pathways were significantly enriched in the differentially expressed genes with downregulation by both LL and salt stress treatment. Metabolites involved in the photorespiration pathway, including serine and glycolate, were downregulated in LL while upregulated in salt stress treatment, with the same pattern of expression levels of a photorespiration regulatory gene, glycolate oxidase. Collectively, we found that serval antioxidant redox pathways, including photorespiration, GSG/GSSH redox, and ABA signaling, participated in response to LL and salt combined events and highlighted the roles of cellular redox homeostasis in LL-Salt response in sheepgrass.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"312"},"PeriodicalIF":3.5,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742226","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":"Aromatase reduces sperm motility by down-regulating the expression of proteins related to ATP synthesis in seminal plasma extracellular vesicles.","authors":"Xuliang Luo, Yan Guo, Xuelian Li, Zi Mei, Haobo Zhou, Ping Qiu, Haoxin Wang, Yan Chen, Yanzhang Gong","doi":"10.1186/s12864-025-11500-5","DOIUrl":"https://doi.org/10.1186/s12864-025-11500-5","url":null,"abstract":"<p><strong>Background: </strong>Aromatase, encoded by Cyp19a1, is the rate limiting enzyme in biosynthesis of estrogens, and excessive aromatase can reduce the semen quality in roosters. Seminal plasma extracellular vesicles (SPEV) are nanoscale vesicles that carry and transmit signaling molecules, thereby affecting semen quality. Currently it is still unclear whether SPEV are involved in the process of that aromatase affects the quality semen in chicken. To clarify this issue, lentivirus carrying Cyp19a1 (LV-CYP19A1) for over-expression of aromatase was constructed and injected to testis of 35-week-old roosters. Semen quality and seminal plasma hormone were measured, and SPEV were also extracted and proteome sequencing was performed after treatment of LV-CYP19A1.</p><p><strong>Results: </strong>The results indicated that semen volume, fertility, sperm motility, testosterone (T) levels were significantly decreased, and estradiol (E₂) levels were significantly increased in LV-CYP19A1 group than those in control group (P < 0.05). Through proteomic analysis of SPEV, we identified 966 differentially expressed proteins (DEPs) in the comparison of LV-CYP19A1 group and control group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) items of DEPs are mainly enriched in ATP synthesis coupled electron transport, flagellated sperm motility, regulation of steroid biosynthetic process, and PI3K-Akt signaling pathway. Furthermore, 8 proteins including ENO4, APOB, SDHA, SDHB, UQCRC1, VIN, PITGB3 and FXN were identified as key proteins in SPEV involving in the process of aromatase regulated rooster semen quality.</p><p><strong>Conclusions: </strong>Our results reveal that aromatase can down-regulate the protein expression related to regulation of ATP synthesis and metabolism, and sperm motility in SPEV, thereby reducing semen quality in roosters.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"305"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742190","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":"Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.","authors":"Dingwen Su, Moritz Peters, Volker Soltys, Yingguang Frank Chan","doi":"10.1186/s12864-025-11442-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11442-y","url":null,"abstract":"<p><p>A common objective across ATAC-seq and ChIP-seq analyses is to identify differential signals across contrasted conditions. However, in differential analyses, the impact of copy number variation is often overlooked. Here, we demonstrated copy number differences among samples could drive, if not dominate, differential signals. To address this, we propose a pipeline featuring copy number normalization. By comparing the averaged signal per gene copy, it effectively segregates differential signals driven by copy number from other factors. Further applying it to Down syndrome unveiled distinct dosage-dependent and -independent changes on chromosome 21. Thus, we recommend copy number normalization as a general approach.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"306"},"PeriodicalIF":3.5,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742194","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}