BMC Genomics最新文献

{"title":"JSNMFuP: a unsupervised method for the integrative analysis of single-cell multi-omics data based on non-negative matrix factorization.","authors":"Bai Zhang, Mengdi Nan, Liugen Wang, Hanwen Wu, Xiang Chen, Yongle Shi, Yibing Ma, Jie Gao","doi":"10.1186/s12864-025-11462-8","DOIUrl":"https://doi.org/10.1186/s12864-025-11462-8","url":null,"abstract":"<p><p>With the rapid advancement of sequencing technology, the increasing availability of single-cell multi-omics data from the same cells has provided us with unprecedented opportunities to understand the cellular phenotypes. Integrating multi-omics data has the potential to enhance the ability to reveal cellular heterogeneity. However, data integration analysis is extremely challenging due to the different characteristics and noise levels of different molecular modalities in single-cell data. In this paper, an unsupervised integration method (JSNMFuP) based on non-negative matrix factorization is proposed. This method integrates the information extracted from the latent variables of each omic through a consensus graph. High-dimensional geometrical structure is captured in the original data and biologically-related feature links across modalities are incorporated into the model using regularization terms. JSNMFuP can be utilized for data visualization and clustering, facilitating marker characterization and gene ontology enrichment analysis, providing rich biological insights for downstream analysis. The application on real datasets shows that JSNMFuP has superior performance in cell clustering. The factors are interpretable, making it an effective method for analyzing cell heterogeneity using single-cell multi-omics data.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"274"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of the P4ATPase gene family and its response to biotic and abiotic stress in soybean (Glycine max L.).","authors":"Jingjing Wei, Gaoyang Zhang, Huanhuan Lv, Saidi Wang, Xingyu Liu, Yanli Qi, Zhongke Sun, Chengwei Li","doi":"10.1186/s12864-025-11468-2","DOIUrl":"https://doi.org/10.1186/s12864-025-11468-2","url":null,"abstract":"<p><strong>Background: </strong>Soybean is an important legume crop and has significant agricultural and economic value. P4-ATPases (aminophospholipid ATPases, ALAs), one of the classes of P-type ATPases, can transport or flip phospholipids across membranes, creating and maintaining lipid asymmetry and playing crucial roles in plant growth and development. To date, however, the ALA gene family and its expression patterns under abiotic and biotic stresses have not been studied in the soybean genome.</p><p><strong>Results: </strong>A total of 27 GmALA genes were identified in the soybean genome and these genes were unevenly distributed on 15 chromosomes and classified into five groups based on phylogenetic analysis. The GmALAs family had diverse intron-exon patterns and a highly conserved motif distribution. A total of eight domains were found in GmALAs, and all GmALAs had conserved PhoLip_ATPase_C, phosphorylation and transmembrane domains. Cis-acting elements in the promoter demonstrated that GmALAs are associated with cellular development, phytohormones, environmental stress and photoresponsiveness. Analysis of gene duplication events revealed 24 orthologous gene pairs in soybean and synteny analysis revealed that GmALAs had greater collinearity with AtALAs than with OsALAs. Evolutionary constraint analyses suggested that GmALAs have undergone strong selective pressure for purification during the evolution of soybeans. Tissue-specific expression profiles revealed that GmALAs were differentially expressed in roots, stems, seeds, flowers, nodules and leaves. The expression pattern of these genes appeared to be diverse in the different developmental tissues. Combined transcriptome and qRT-PCR data confirmed the differential expression of GmALAs under abiotic (dehydration, saline, low temperature, ozone, light, wounding and phytohormones) and biotic stresses (aphid, fungi, rhizobia and rust pathogen).</p><p><strong>Conclusion: </strong>In summary, genome-wide identification and evolutionary and expression analyses of the GmALAs gene family in soybean were conducted. Our work provides an important theoretical basis for further understanding GmALAs in biological functional studies.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"277"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and characterization of the TmSnRK2 family proteins related to chicoric acid biosynthesis in Taraxacum mongolicum.","authors":"Qun Liu, Zhiqing Wu, Changyang Yu, Xiwu Qi, Hailing Fang, Xu Yu, Li Li, Yang Bai, Dongmei Liu, Zequn Chen, Guoyin Kai, Chengyuan Liang","doi":"10.1186/s12864-025-11460-w","DOIUrl":"https://doi.org/10.1186/s12864-025-11460-w","url":null,"abstract":"<p><strong>Background: </strong>Taraxacum mongolicum is rich in phenolic acids and is widely utilized in food and medicine globally. Our previous research demonstrated that the abscisic acid (ABA) hormone significantly enhances chicoric acid accumulation in T. mongolicum. SNF1-related protein kinase 2s (SnRK2s) are extensively involved in ABA signaling and have the potential to regulate the biosynthesis of phenolic acids.</p><p><strong>Results: </strong>In this study, liquid chromatography-mass spectrometry (LC-MS) and transcriptomic analyses revealed that the TmbZIP1-Tm4CL1 pathway plays a crucial role in the transcriptional regulation of chicoric acid biosynthesis. Seven TmSnRK2s were identified in T. mongolicum and classified into three groups. Analysis of the TmSnRK2s promoters (2000 bp in length) indicated that the three most prevalent stress-related elements were ABA, methyl jasmonate (MeJA), and light. ABA treatments (0 h, 2 h, 4 h, 8 h, and 24 h) showed that all seven TmSnRK2s were significantly modulated by ABA, with the exception of SnRK2.7. TmSnRK2.2, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 were localized in both the cytoplasm and nucleus, whereas TmSnRK2.1 and TmSnRK2.5 were exclusively observed in the cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays indicated that TmSnRK2.1, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 interact with TmbZIP1. The motifs 'Q(S/G)(V/D)(D/E)(I/L)××I(I/V)×EA' and 'D×(D/ED××D)' are identified as the core sites that facilitate the binding of TmSnRK2s to TmbZIP1. Dual-luciferase reporter assays demonstrated that TmSnRK2.3 and TmSnRK2.6 enhance the stability of TmbZIP1 binding to proTm4CL1.</p><p><strong>Conclusion: </strong>These findings enhance our understanding of the specific roles of certain members of the TmSnRK2 family in the biosynthesis pathway of chicoric acid.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"276"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abnormal DNA methylation of EBF1 regulates adipogenesis in chicken.","authors":"Xiaohuan Chao, Lijin Guo, Meiling Hu, Mao Ye, Zhexia Fan, Kang Luan, Jiahao Chen, Chunlei Zhang, Manqing Liu, Bo Zhou, Xiquan Zhang, Zhenhui Li, Qingbin Luo","doi":"10.1186/s12864-025-11464-6","DOIUrl":"https://doi.org/10.1186/s12864-025-11464-6","url":null,"abstract":"<p><strong>Background: </strong>DNA methylation influences gene expression and is involved in numerous biological processes, including fat production. It is involved in lipid generation in numerous animal species, including poultry. However, the effect of DNA methylation on adipogenesis in chickens remains unclear.</p><p><strong>Results: </strong>A total of 12 100-day-old chickens were divided into high and low-fat groups based on their abdominal fat ratios. Subsequently, genome-wide bisulfite sequencing (WGBS) was performed on their abdominal fat, and 1877 differentially methylated region (DMR) genes were identified, among which SLC45A3, EBF1, PLA2G15, and ACAD9 were associated with lipid metabolism. Interestingly, EBF1 showed a lower level of DNA methylation and higher mRNA expression in the low-fat group, as determined by comprehensive RNA-seq analysis. Cellular verification showed that EBF1 expression was upregulated by 5-azacytidine (5-Aza) and downregulated by betaine. EBF1 facilitated the differentiation of immortalized chicken preadipocyte 1 (ICP-1) through the PPAR-γ pathway, thereby affecting chicken adipogenesis.</p><p><strong>Conclusion: </strong>A combination of WGBS and RNA-seq analyses revealed 48 DMGs in the abdominal fat tissue of chickens. Notably, the DNA methylation status of EBF1 was inversely related to its mRNA expression. Mechanistically, DNA methylation regulates EBF1 expression, which in turn mediates the differentiation of ICP-1 through the PPARγ pathway. This study provides a theoretical framework for investigating the effects of DNA methylation on adipogenesis in chickens.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"275"},"PeriodicalIF":3.5,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution and amplification of the trehalose-6-phosphate synthase gene family in Theaceae.","authors":"Zaibao Zhang, Tao Xiong, Kejia Li, Kexin Huang, Chunxia Liao, Guangqu Liu","doi":"10.1186/s12864-025-11475-3","DOIUrl":"https://doi.org/10.1186/s12864-025-11475-3","url":null,"abstract":"<p><strong>Background: </strong>Trehalose-6-phosphate synthase (TPS) is an essential enzyme involved in the production of trehalose, and the genes associated with TPS are crucial for various processes such as growth, development, defense mechanisms, and resistance to stress. However, there has been no documentation regarding the evolution and functional roles of the TPS gene family within Theaceae.</p><p><strong>Results: </strong>Here, we uncovered the lineage-specific evolution of TPS genes in Theaceae. A total of 102 TPS genes were discovered across ten Theaceae species with sequenced genomes. Consistent with the previous classification, our phylogenetic analysis indicated that the TPS genes in Theaceae can be categorized into two primary subfamilies and six distinct clades (I, II-1, II-2, II-3, II-4, II-5), with clade I containing a greater number of introns compared to those found in clade II. Segmental duplication served as the main catalyst for the evolution of TPS genes within Theaceae, and numerous TPS genes exhibited inter-species synteny among various Theaceae species. Most of the TPS genes were ubiquitously expressed, and expression divergence of TPS paralogous pairs was observed. The cis-acting elements found in TPS genes indicated their involvement in responses to phytohormones and stress.</p><p><strong>Conclusion: </strong>This research enhanced our understanding of the lineage-specific evolution of the TPS gene family in Theaceae and offered important insights for future functional analyses.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"273"},"PeriodicalIF":3.5,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Short-term heat exposure affects thermogenesis and mitophagy in goat brown adipocytes.","authors":"Yulong Song, Die Li, Duo Su, Tingting Jiang, Longrui Li, Siyuan Zhan, Tao Zhong, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang, Linjie Wang","doi":"10.1186/s12864-025-11467-3","DOIUrl":"https://doi.org/10.1186/s12864-025-11467-3","url":null,"abstract":"<p><strong>Background: </strong>Brown adipose tissue (BAT) has a significant impact in newborn goats on maintaining body temperature through non-shivering thermogenesis in response to cold exposure. However, the roles of heat treatment on BAT thermogenesis are still limited.</p><p><strong>Results: </strong>This study focused on the effects of short-term heat exposure on goat brown adipocytes. We found that the content of mitochondria and the proteins of UCP1 and PGC1α were increased after 12 h of heat exposure. Additionally, the triglyceride (TG) content was significantly decreased after 1, 2, 6 h of heat exposure. Furthermore, RNA-seq analysis of brown adipocytes after 12 h of heat exposure identified 1091 differentially expressed genes (DEGs). The KEGG enrichment analysis were mainly enriched in thermogenesis, fatty acid metabolism and mitophagy. In addition, we found that the amount of mitophagosomes and expression levels of mitophagy-related protein (LC3BII/LC3BI, BNIP3, and BECN) were elevated after 12 h of heat treatment.</p><p><strong>Conclusion: </strong>These findings collectively indicate that heat exposure enhances the thermogenic capacity and mitophagy level of goat brown adipocytes. Our study provides evidence that heat exposure facilitates adaptive thermogenesis in goat brown adipocytes.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"272"},"PeriodicalIF":3.5,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An mRNA expression atlas for the duck with public RNA-seq datasets.","authors":"Qiuyu Tao, Anqi Huang, Jingjing Qi, Zhao Yang, Shihao Guo, Yinjuan Lu, Xinxin He, Xu Han, Shuaixue Jiang, Mengru Xu, Yuan Bai, Tao Zhang, Shenqiang Hu, Liang Li, Lili Bai, HeHe Liu","doi":"10.1186/s12864-025-11385-4","DOIUrl":"https://doi.org/10.1186/s12864-025-11385-4","url":null,"abstract":"<p><strong>Background: </strong>Ducks are globally important poultry species and a major source of farm animal products, including meat, eggs, and feathers. A thorough understanding of the functional genomic and transcriptomic sequences is crucial for improving production efficiency.</p><p><strong>Result: </strong>This study constructed the largest duck mRNA expression atlas among all waterfowl species to date. The atlas encompasses 1,257 tissue samples across 30 tissue types, representing all major organ systems. Using advanced clustering analysis, we established co-expression network clusters to describe the transcriptional features in the duck mRNA expression atlas and, when feasible, assign these features to unique tissue types or pathways. Additionally, we identified 27 low-variance, highly expressed housekeeping genes suitable for gene expression experiments. Furthermore, in-depth analysis revealed potential sex-biased gene expression patterns within tissues and specific gene expression profiles in meat-type and egg-type ducks, providing valuable resources to understand the genetic basis of sex differences and particular phenotypes. This research elucidates the biological processes affecting duck productivity.</p><p><strong>Conclusion: </strong>This study presents the most extensive gene expression atlas for any waterfowl species to date. These findings are of significant value for advancing duck biological research and industrial applications.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"268"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single nucleotide polymorphism-based analysis of linkage disequilibrium and runs of homozygosity patterns of indigenous sheep in the southern Taklamakan desert.","authors":"Zhi-Peng Han, Lu-Lu Zhang, Xiao-Peng Li, Li-Jun Zhu, Xue-Chen Zhang, Wen Zhou, Shudong Liu","doi":"10.1186/s12864-025-11445-9","DOIUrl":"https://doi.org/10.1186/s12864-025-11445-9","url":null,"abstract":"<p><p>Runs of Homozygosity (ROH) are homozygous genomic fragments inherited from parents to offspring. ROH can be used to indicate the level of inbreeding, as well as to identify possible signatures of artificial or natural selection. Indigenous sheep populations on the southern edge of the Taklimakan Desert have evolved unique genetic traits adapted to extreme desert environments. In an attempt to better understand the adaptive mechanisms of these populations under harsh conditions, we used Illumina® Ovine SNP50K BeadChip to perform a genomic characterization of three recognized breeds (Duolang: n = 36, Hetian: n = 84, Qira black: n = 189) and one ecotypic breed (Kunlun: n = 27) in the region. Additionally, we assessed genomic inbreeding coefficients through ROH analysis, revealing insights into the inbreeding history of these populations. Subsequently, we retrieved candidate genes associated with economic traits in sheep from ROH islands in each breed. To better understand the autozygosity and distribution of ROH islands in these indigenous sheep breeds relative to international breeds, we also included three commercial mutton breeds (Poll Dorset: n = 108, Suffolk: n = 163, Texel: n = 150). The study revealed that among seven sheep breeds, Hetian exhibited the shortest linkage disequilibrium (LD) decay distance, while Kunlun demonstrated the highest LD levels. A total of 10,916 ROHs were obtained. The number of ROHs per breed ranged from 34 (Kunlun) to 2,826 (Texel). The length of ROH was mainly 1-5 Mb (63.54%). Furthermore, 991 candidate genes specific to indigenous sheep breeds were identified, including those associated with heat tolerance, adaptability, energy metabolism, reproduction, and immune response. These findings elucidate the genetic adaptation of indigenous sheep in the Taklimakan Desert, uncovering distinctive characteristics of indigenous sheep formation, and advocating for the conservation and genetic enhancement of local sheep populations.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"267"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The involvement of PsTCP genes in hormone-mediated process of bud dormancy release in tree peony (Paeonia suffruticosa).","authors":"Qianqian Wang, Bole Li, Zefeng Qiu, Jiayi Ying, Xuyichen Jin, Zeyun Lu, Junli Zhang, Xia Chen, Xiangtao Zhu","doi":"10.1186/s12864-025-11439-7","DOIUrl":"https://doi.org/10.1186/s12864-025-11439-7","url":null,"abstract":"<p><strong>Background: </strong>The complete dormancy release determines the quality of bud break, flowering and fruiting. While in tree peony (Paeonia suffruticosa Andr.), the insufficient accumulation of cold temperatures results in incomplete dormancy release and poor flowering quality.</p><p><strong>Results: </strong>In order to investigate if phytohormone can replace the chilling requirement in south China and other similar regions, the roles of fluridone (Flu), gibberellin (GA₃), and their combination in the bud dormancy release process were analyzed. It demonstrated that the application of exogenous GA₃ and the mixture significantly expedited the dormancy release of tree peony at 23℃. Furthermore, the endogenous hormone levels provided evidence for the substantial impact of exogenous GA₃ on dormancy release, highlighting its potential involvement in the chilling-independent pathway of dormancy release. Transcriptome sequencing and analysis of expression profiles were conducted to identify the crucial genes implicated in the dormancy release mechanism of tree peony. Among numerous genes from diverse gene families, the particularly interesting were TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS-like genes (PsTCP3, PsTCP4, and PsTCP14), which had significant expression levels during the dormancy release process under different treatments. They were divided into two distinct sub-families based on their different domains. Specifically, PsTCP14 was classified under Class I, while PsTCP3 and PsTCP4 were classified under Class II. The analysis of expression patterns revealed a significant accumulation of the three PsTCPs in buds undergoing dormancy release, with clear upregulation observed in response to GA₃ and the mixture treatments. Additionally, the analysis of promoter activity demonstrated the sensitivity of PsTCP4 and PsTCP14 to GA₃ and Flu.</p><p><strong>Conclusion: </strong>The application of exogenous GA₃ has been shown to effectively expedite the release of dormancy in tree peony through a pathway that is not dependent on chilling. Further research found that PsTCP genes might play a crucial role in this process. These findings contribute to the understanding of the molecular mechanism of PsTCPs in the hormone-mediated and temperature-independent release of bud dormancy in tree peony.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 1","pages":"266"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.","authors":"Shuangquan Zhang, Anjun Ma, Xuping Xie, Zhichao Lian, Yan Wang","doi":"10.1186/s12864-025-11399-y","DOIUrl":"https://doi.org/10.1186/s12864-025-11399-y","url":null,"abstract":"<p><strong>Background: </strong>Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent years, convolutional neural networks (CNNs) have succeeded in TF-DNA binding prediction, but existing DL methods' accuracy needs to be improved and convolution function in TF-DNA binding prediction should be further explored.</p><p><strong>Results: </strong>We develop a cascaded convolutional neural network model named CacPred to predict TF-DNA binding on 790 Chromatin immunoprecipitation-sequencing (ChIP-seq) datasets and seven ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode, and single ligation) datasets. We compare CacPred to six existing DL models across nine standard evaluation metrics. Our results indicate that CacPred outperforms all comparison models for TF-DNA binding prediction, and the average accuracy (ACC), matthews correlation coefficient (MCC), and the area of eight metrics radar (AEMR) are improved by 3.3%, 9.2%, and 6.4% on 790 ChIP-seq datasets. Meanwhile, CacPred improves the average ACC, MCC, and AEMR of 5.5%, 16.8%, and 12.9% on seven ChIP-nexus datasets. To explain the proposed method, motifs are used to show features CacPred learned. In light of the results, CacPred can find some significant motifs from input sequences.</p><p><strong>Conclusions: </strong>This paper indicates that CacPred performs better than existing models on ChIP-seq data. Seven ChIP-nexus datasets are also analyzed, and they coincide with results that our proposed method performs the best on ChIP-seq data. CacPred only is equipped with the convolutional algorithm, demonstrating that pooling processing of the existing models leads to losing some sequence information. Some significant motifs are found, showing that CacPred can learn features from input sequences. In this study, we demonstrate that CacPred is an effective and feasible model for predicting TF-DNA binding. CacPred is freely available at https://github.com/zhangsq06/CacPred .</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":"26 Suppl 2","pages":"264"},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}