Current Genomics最新文献

{"title":"Taxonomic Status and Phylogenetic Relationship of Family Charadriidae based on Complete Mitogenomes","authors":"Weiya Qian, Yizheng Liu, Keer Miao, Qing Chang, Chaochao Hu","doi":"10.2174/0113892029273517231017051819","DOIUrl":"https://doi.org/10.2174/0113892029273517231017051819","url":null,"abstract":"Background: The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Method: In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of nonsynonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Result: Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion: This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136316941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Prevalence of a c.5979dupA Variant in the Dysferlin Gene (DYSF) in Individuals from a Semiarid Region of Brazil","authors":"Isabella A. Motta, Maria Lucrécia A. Gouveia, Ana Paula M. Braga, Rafael S. Andrade, Mayra F.F. Montenegro, Sandra N. Gurgel, Keila M.F. Albuquerque, Priscilla A.N.G. Souto, Flávia P.B.F. Cardoso, Joseane S. Araujo, Mirella C.L. Pinheiro, Carlos E.P. da Silva, Pamella A.S. Gurgel, David Feder, Matheus M. Perez, Glaucia Luciano da Veiga, Beatriz C.A. Alves, Fernando L.A. Fonseca, Alzira A.S. Carvalho","doi":"10.2174/0113892029257856231013115036","DOIUrl":"https://doi.org/10.2174/0113892029257856231013115036","url":null,"abstract":"Background: Dysferlinopathies represent a group of limb girdle or distal muscular dystrophies with an autosomal-recessive inheritance pattern resulting from the presence of pathogenic variants in the dysferlin gene (DYSF). Objective: In this work, we describe a population from a small city in Brazil carrying the c.5979dupA pathogenic variant of DYSF responsible for limb girdle muscular dystrophy type 2R and distal muscular dystrophy. Methods: Genotyping analyses were performed by qPCR using customized probe complementary to the region with the duplication under analysis in the DYSF. Results: A total of 104 individuals were examined. c.5979dupA was identified in 48 (46.15%) individuals. Twenty-three (22%) were homozygotes, among whom 13 (56.5%) were female. A total of 91.3% (21) of homozygous individuals had a positive family history, and seven (30.4%) reported consanguineous marriages. Twenty-five (24%) individuals were heterozygous (25.8±16 years) for the same variant, among whom 15 (60%) were female. The mean CK level was 697 IU for homozygotes, 140.5 IU for heterozygotes and 176 IU for wild-type homo-zygotes. The weakness distribution pattern showed 17.3% of individuals with a proximal pattern, 13% with a distal pattern and 69.6% with a mixed pattern. Fatigue was present in 15 homozygotes and one heterozygote. Conclusion: The high prevalence of this variant in individuals from this small community can be explained by a possible founder effect associated with historical, geographical and cultural aspects.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135113544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pan-Cancer Analysis Identifies AIMP2 as a Potential Biomarker for Breast Cancer","authors":"Jie Qiu, Tao Zhou, Danhong Wang, Weimin Hong, Da Qian, Xiaozhen Liu, Xuli Meng","doi":"10.2174/0113892029255941231014142050","DOIUrl":"https://doi.org/10.2174/0113892029255941231014142050","url":null,"abstract":"Introduction:: Aminoacyl tRNA synthetase complex interacting with multifunctional protein 2 (AIMP2) is a significant regulator of cell proliferation and apoptosis. Despite its abnormal expression in various tumor types, the specific functions and effects of AIMP2 on tumor immune cell infiltration, proliferation, and migration remain unclear. background: AIMP2, Aminoacyl TRNA Synthetase Complex Interacting Multifunctional Protein 2, also known as JTV1, a multifunctional protein that forms a macromolecular complex with human aminoacyl tRNA synthetase, which consists of three non-enzymatic proteins, including p43, p38 and p18 proteins, of which p38 protein is AIMP2[1]. AIMP2 is necessary for the assembly and stability of aminoacyl tRNA synthetase complex[2]. Besides being important for efficient protein synthesis, additional physiological roles for AIMP2 have been discovered[3, 4]. For example, following DNA damage, AIMP2 is liberated from the ARS complex, phosphorylated in a JNK2-dependent pathway and translocated into the nucleus where it has been suggested to bind and sequester p53 from Mdm2-dependent ubiquitination[5]. AIMP2 has also been shown to be a substrate of E3 ligase Parkin[6]. Accumulation of AIMP2 as a result of Parkin mutation has been speculated to contribute to the characteristic dopaminergic cell death observed in Parkinson patients[7]. In addition, AIMP2 augments tumor necrosis factor-α-induced apoptotic signaling and exerts antiproliferative activities in TGF-β and Wnt pathways via distinct working mechanisms [8-10]. Therefore, we wonder that AIMP2 may play a crucial role in the occurrence and development of cancer. However, there are relatively few reseaches on AIMP2 in oncology. Current studies confirmed that AIMP2 may function as a multifunctional tumor suppressor[9, 11]. In this study, we analyzed the expression of AIMP2 and its relationship with the prognosis, Tumor Mutation Burden (TMB) and Microsatellite Instability (MSI) in 33 cancer types. In addition, we examined the correlation between AIMP2 and the immune microenvironment, immune-related antigens, and immune checkpoint genes. The results showed that AIMP2 was higher expressed in tumor tissue compared with normal tissue. Moreover, AIMP2 was associated with several tumor stages. Survival analysis showed that AIMP2 expression was strongly associated with OS in some cancer patients, where the high expression of AIMP2 was associated with a worse prognosis in five types of cancer. Then, we confirmed that the expression level of AIMP2 was associated with tumor immune infiltration and tumor microenvironment, especially in BRCA. Finally, si-RNA mediated knockdown of AIMP2 suppressed the proliferation and migration of BC cells in vitro. In conclusion, AIMP2 was found to be differentially expressed in the pan-cancer analysis and might play an important role in tumor immunity, which is expected to be a potential tumor prognostic marker, especially in BRCA. Method:: To assess AIMP","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"24 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135218841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the Concealed Transcriptomic Landscape of PTEN in Human Malignancies","authors":"Michaela A. Boti, Panagiotis G. Adamopoulos, Dido Vassilacopoulou, Andreas Scorilas","doi":"10.2174/0113892029265367231013113304","DOIUrl":"https://doi.org/10.2174/0113892029265367231013113304","url":null,"abstract":"Background: Phosphatase and tensin homolog, widely known as PTEN, is a major negative regulator of the PI3K/AKT/mTOR signaling pathway, involved in the regulation of a variety of important cellular processes, including cell proliferation, growth, survival, and metabolism. Since most of the molecules involved in this biological pathway have been described as key regulators in cancer, the study of the corresponding genes at several levels is crucial. Objective: Although previous studies have elucidated the physiological role of PTEN under normal conditions and its involvement in carcinogenesis and cancer progression, the transcriptional profile of PTEN has been poorly investigated. Methods: In this study, instead of conducting the “gold-standard” direct RNA sequencing that fails to detect less abundant novel mRNAs due to the decreased sequencing depth, we designed and implemented a multiplexed PTEN-targeted sequencing approach that combined both short- and longread sequencing. Results: Our study has highlighted a broad spectrum of previously unknown PTEN mRNA transcripts and assessed their expression patterns in a wide range of human cancer and non-cancer cell lines, shedding light on the involvement of PTEN in cell cycle dysregulation and thus tumor development. Conclusion: The identification of the described novel PTEN splice variants could have significant implications for understanding PTEN regulation and function, and provide new insights into PTEN biology, opening new avenues for monitoring PTEN-related diseases, including cancer.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"35 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135113985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete Chloroplast Genomes of Pterodon emarginatus Vogel and Pterodon pubescens Benth: Comparative and Phylogenetic Analyses","authors":"Juliana Borges Pereira Brito, Adriana Maria Antunes, Ramilla dos Santos Braga Ferreira, Mariana Pires de Campos Telles, Cíntia Pelegrineti Targueta de Azevedo Brito, Thannya Nascimento Soares","doi":"10.2174/0113892029244147231016050434","DOIUrl":"https://doi.org/10.2174/0113892029244147231016050434","url":null,"abstract":"Background: The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Objective: The species Pterodon emarginatus and P. pubescens, popularly known as white sucupira or faveira, are native to the Cerrado biome and have the potential for medicinal use and reforestation. They are sister species with evolutionary proximity. Methods: The chloroplast genomes of P. emarginatus and P. pubescens were sequenced on the Illumina MiSeq platform. The genomes were assembled based on the de novo strategy. We performed the annotation of the genes and the repetitive regions of the genomes. The nucleotide diversity and phylogenetic relationships were analyzed using the gene sequences of these species and others of the Leguminosae family, whose genomes are available in databases. Results: The complete chloroplast genome of P. emarginatus is 159,877 bp, and that of P. pubescens is 159,873 bp. The genomes of both species have circular and quadripartite structures. A total of 127 genes were predicted in both species, including 110 single-copy genes and 17 duplicated genes in the inverted regions. 141 microsatellite regions were identified in P. emarginatus and 140 in P. pubescens. The nucleotide diversity estimates of the gene regions in twenty-one species of the Leguminosae family were 0.062 in LSC, 0.086 in SSC, and 0.036 in IR. The phylogenetic analysis demonstrated the proximity between the genera Pterodon and Dipteryx, both from the clade Dipterygeae. Ten pairs of primers with potential for the development of molecular markers were designed. Conclusion: The genetic information obtained on the chloroplast genomes of P. emarginatus and P. pubescens presented here reinforces the similarity and evolutionary proximity between these species, with a similarity percentage of 99.8%.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"26 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135218842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome Sequencing and Organization of Three Geographically Different Isolates of Nucleopolyhedrovirus from the Gypsy Moth Reveal Significant Genomic Differences","authors":"Donus Gencer, Cihan Inan, Zeynep Bayramoglu, Remziye Nalcacioglu, Feifei Yin, Zheng Zhu, Jun Wang, Zhihong Hu, Lillian Pavlik, Basil Arif, Zihni Demirbag, Ismail Demir","doi":"10.2174/0113892029249830231014163829","DOIUrl":"https://doi.org/10.2174/0113892029249830231014163829","url":null,"abstract":"Background: The gypsy moth (Lymantria dispar L., Lepidoptera: Erebidae) is a worldwide pest of trees and forests. Lymantria dispar nucleopolyhedrovirus (LdMNPV) belongs to the Baculoviridae family and is an insect virus specific to gypsy moth larvae. In this study, we describe the complete genome sequences of three geographically diverse isolates, H2 (China), J2 (Japan), and T3 (Turkey), of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV). Method: The genomes of isolates H2, J2, and T3 were subjected to shotgun pyrosequencing using Roche 454 FLX and assembled using Roche GS De Novo Assembler. Comparative analysis of all isolates was performed using bioinformatics methods. Results: The genomes of LdMNPV-H2, J2, and T3 were 164,746, 162,249, and 162,614 bp in size, had GC content of 57.25%, 57.30%, and 57.46%, and contained 162, 165, and 164 putative open reading frames (ORFs ≥ 150 nt), respectively. Comparison between the reference genome LdMNPV-5/6 (AF081810) and the genomes of LdMNPV-H2, J2, and T3 revealed differences in gene content. Compared with LdMNPV-5/6, ORF5, 6, 8, 10, 31, and 67 were absent in LdMNPVH2, ORF5, 13, and 66 were absent in LdMNPV-J2, and ORF10, 13, 31, and 67 were absent in LdMNPV-T3. In addition, the gene encoding the mucin-like protein (ORF4) was split into two parts in isolates H2 and T3 and designated ORF4a and ORF4b. Phylogenetic analysis grouped isolates H2 and J2 in a different cluster than isolate T3, which is more closely related to the Turkish and Polish isolates. In addition, H2 was found to be closely related to a South Korean LdMNPV isolate. Conclusion: This study provided a more detailed overview of the relationships between different geographic LdMNPV isolates. The results showed remarkable differences between groups at the genome level.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135218848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modulation of Plant MicroRNA Expression: Its Potential Usability in Wheat (Triticum aestivum L.) Improvement","authors":"Louie Cris Lopos, Urbashi Panthi, Igor Kovalchuk, Andriy Bilichak","doi":"10.2174/0113892029264886231016050547","DOIUrl":"https://doi.org/10.2174/0113892029264886231016050547","url":null,"abstract":"Abstract: Wheat, a crucial crop for the pursuit of food security, is faced with a plateauing yield projected to fall short of meeting the demands of the exponentially increasing human population. To raise global wheat productivity levels, strong efforts must be made to overcome the problems of (1) climate change-induced heat and drought stress and (2) the genotype-dependent amenability of wheat to tissue culture, which limits the success of recovering genetically engineered plants, especially in elite cultivars. Unfortunately, the mainstream approach of genetically engineering plant protein-coding genes may not be effective in solving these problems as it is difficult to map, annotate, functionally verify, and modulate all existing homeologs and paralogs within wheat’s large, complex, allohexaploid genome. Additionally, the quantitative, multi-genic nature of most agronomically important traits furthers the complications faced by this approach. miRNAs are small, noncoding RNAs (sncRNAs) that repress gene expression at the post-transcriptional level, regulating various aspects of plant growth and development. They are gaining popularity as alternative targets of genetic engineering efforts for crop improvement due to their (1) highly conserved nature, which facilitates reasonable prediction of their gene targets and phenotypic effects under different expression levels, and (2) the capacity to target multiple genes simultaneously, making them suitable for enhancing complex and multigenic agronomic traits. In this mini-review, we will discuss the biogenesis, manipulation, and potential applications of plant miRNAs in improving wheat’s yield, somatic embryogenesis, thermotolerance, and drought-tolerance in response to the problems of plateauing yield, genotype-dependent amenability to tissue culture, and susceptibility to climate change-induced heat and drought stress.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"34 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135315837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants","authors":"Amarinder Singh Thind, Somdatta Sinha","doi":"10.2174/0113892029264990231013112156","DOIUrl":"https://doi.org/10.2174/0113892029264990231013112156","url":null,"abstract":"Background: Viruses have high mutation rates, facilitating rapid evolution and the emergence of new species, subspecies, strains and recombinant forms. Accurate classification of these forms is crucial for understanding viral evolution and developing therapeutic applications. Phylogenetic classification is typically performed by analyzing molecular differences at the genomic and sub-genomic levels. This involves aligning homologous proteins or genes. However, there is growing interest in developing alignment-free methods for whole-genome comparisons that are computationally efficient. Methods: Here we elaborate on the Chaos Game Representation (CGR) method, based on concepts of statistical physics and free of sequence alignment assumptions. We adopt the CGR method for classification of the closely related clades/lineages A and B of the SARS-Corona virus 2019 (SARS-CoV-2), which is one of the fastest evolving viruses. Results: Our study shows that the CGR approach can easily yield the SARS-CoV-2 phylogeny from the available whole genomes of lineage A and lineage B sequences. It also shows an accurate classification of eight different strains and the newly evolved XBB variant from its parental strains. Compared to alignment-based methods (Neighbour-Joining and Maximum Likelihood), the CGR method requires low computational resources, is fast and accurate for long sequences, and, being a K-mer based approach, allows simultaneous comparison of a large number of closely-related sequences of different sizes. Further, we developed an R pipeline CGRphylo, available on GitHub, which integrates the CGR module with various other R packages to create phylogenetic trees and visualize them. Conclusion: Our findings demonstrate the efficacy of the CGR method for accurate classification and tracking of rapidly evolving viruses, offering valuable insights into the evolution and emergence of new SARS-CoV-2 strains and recombinants.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"56 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135315919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deacetylation of Histones and Non-histone Proteins in Inflammatory Diseases and Cancer Therapeutic Potential of Histone Deacetylase Inhibitors","authors":"Ezgi Man, Serap EVRAN","doi":"10.2174/0113892029265046231011100327","DOIUrl":"https://doi.org/10.2174/0113892029265046231011100327","url":null,"abstract":"abstract: Epigenetic changes play an important role in the pathophysiology of autoimmune diseases such as allergic asthma, multiple sclerosis, lung diseases, diabetes, cystic fibrosis, atherosclerosis, rheumatoid arthritis, and COVID-19. There are three main classes of epigenetic alterations: post-translational modifications of histone proteins, control by non-coding RNA and DNA methylation. Since histone modifications can directly affect chromatin structure and accessibility, they can regulate gene expression levels. Abnormal expression and activity of histone deacetylases (HDACs) have been reported in immune mediated diseases. Increased acetylated levels of lysine residues have been suggested to be related to the overexpression of inflammatory genes. This review focuses on the effect of HDAC modifications on histone and non–histone proteins in autoimmune diseases. Furthermore, we discuss the potential therapeutic effect of HDAC inhibitors (HDACi) used in these diseases.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135322662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DLC-ac4C: A Prediction Model for N4-acetylcytidine Sites in Human mRNA Based on DenseNet and Bidirectional LSTM Methods","authors":"Jianhua Jia, Xiaojing Cao, Zhangying Wei","doi":"10.2174/0113892029270191231013111911","DOIUrl":"https://doi.org/10.2174/0113892029270191231013111911","url":null,"abstract":"Introduction: N4 acetylcytidine (ac4C) is a highly conserved nucleoside modification that is essential for the regulation of immune functions in organisms. Currently, the identification of ac4C is primarily achieved using biological methods, which can be time-consuming and laborintensive. In contrast, accurate identification of ac4C by computational methods has become a more effective method for classification and prediction Aim: To the best of our knowledge, although there are several computational methods for ac4C locus prediction, the performance of the models they constructed is poor, and the network structure they used is relatively simple and suffers from the disadvantage of network degradation. This study aims to improve these limitations by proposing a predictive model based on integrated deep learning to better help identify ac4C sites. Methods: In this study, we propose a new integrated deep learning prediction framework, DLCac4C. First, we encode RNA sequences based on three feature encoding schemes, namely C2 encoding, nucleotide chemical property (NCP) encoding, and nucleotide density (ND) encoding. Second, one-dimensional convolutional layers and densely connected convolutional networks (DenseNet) are used to learn local features, and bi-directional long short-term memory networks (Bi-LSTM) are used to learn global features. Third, a channel attention mechanism is introduced to determine the importance of sequence characteristics. Finally, a homomorphic integration strategy is used to limit the generalization error of the model, which further improves the performance of the model. Results: The DLC-ac4C model performed well in terms of sensitivity (Sn), specificity (Sp), accuracy (Acc), Mathews correlation coefficient (MCC), and area under the curve (AUC) for the independent test data with 86.23%, 79.71%, 82.97%, 66.08%, and 90.42%, respectively, which was significantly better than the prediction accuracy of the existing methods. Conclusion: Our model not only combines DenseNet and Bi-LSTM, but also uses the channel attention mechanism to better capture hidden information features from a sequence perspective, and can identify ac4C sites more effectively.","PeriodicalId":10803,"journal":{"name":"Current Genomics","volume":"48 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135779408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}