iRNA-m7G: Identifying N7-methylguanosine Sites by Fusing Multiple Features

Chen, Wei; Feng, Pengmian; Song, Xiaoming; Lv, Hao; Lin, Hao

doi:10.1016/j.omtn.2019.08.022

Cited by 85 publications

(67 citation statements)

References 43 publications

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“…The lipo2000 was mixed with the pcDNA-Opa1 plasmid or siRNAs and incubated for 30 min at room temperature (Imber et al, 2019). The serum-containing medium in the six-well plate was removed and gently rinsed with phosphate buffered saline (PBS) before adding 1.6 mL of serum-free medium containing pcDNA-Opa1 plasmid or siRNAs and cultured in a 5% CO 2 incubator at 37 • C. The solution was changed after 6 h (Chen et al, 2019).…”

Section: Transfection Of Sirnas and Opa1 Plasmidsmentioning

confidence: 99%

RETRACTED: Oxidized LDL Causes Endothelial Apoptosis by Inhibiting Mitochondrial Fusion and Mitochondria Autophagy

Zheng¹,

Lu²

2020

Front. Cell Dev. Biol.

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Oxidized low-density lipoprotein (ox-LDL)-induced endothelial dysfunction is an initial step toward atherosclerosis development. Mitochondria damage correlates with ox-LDL-induced endothelial injury through an undefined mechanism. We explored the role of optic atrophy 1 (Opa1)-related mitochondrial fusion and mitophagy in ox-LDL-treated endothelial cells, focusing on mitochondrial damage and cell apoptosis. Oxidized low-density lipoprotein treatment reduced endothelial cell viability by increasing apoptosis. Endothelial cell proliferation and migration were also impaired by ox-LDL. At the molecular level, mitochondrial dysfunction was induced by ox-LDL, as demonstrated by decreased mitochondrial membrane potential, increased mitochondrial reactive oxygen species production, augmented mitochondrial permeability transition pore openings, and elevated caspase-3/9 activity. Mitophagy and mitochondrial fusion were also impaired by ox-LDL. Opa1 overexpression reversed this effect by increasing endothelial cell viability and decreasing apoptosis. Interestingly, inhibition of mitophagy or mitochondrial fusion through transfection of siRNAs against Atg5 or Mfn2, respectively, abolished the protective effects of Opa1. Our results illustrate the role of Opa1-related mitochondrial fusion and mitophagy in sustaining endothelial cell viability and mitochondrial homeostasis under ox-LDL stress.

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Section: Transfection Of Sirnas and Opa1 Plasmidsmentioning

confidence: 99%

RETRACTED: Oxidized LDL Causes Endothelial Apoptosis by Inhibiting Mitochondrial Fusion and Mitochondria Autophagy

Zheng¹,

Lu²

2020

Front. Cell Dev. Biol.

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“…ML algorithms have been widely applied in various fields, 63 , 64 , 65 , 66 , 67 such as post-replication DNA modification site predictions, particularly 4mC, 6mA, and 5-hydroxymethylcytosine sites. 2 , 56 , 68 Table 2 summarizes the existing 4mC prediction methods that utilize a wide range of ML algorithms, feature encodings, and different approaches.…”

Section: Methodsmentioning

confidence: 99%

Empirical Comparison and Analysis of Web-Based DNA N4-Methylcytosine Site Prediction Tools

Manavalan

Hasan

Basith

et al. 2020

Molecular Therapy - Nucleic Acids

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DNA N 4 -methylcytosine (4mC) is a crucial epigenetic modification involved in various biological processes. Accurate genome-wide identification of these sites is critical for improving our understanding of their biological functions and mechanisms. As experimental methods for 4mC identification are tedious, expensive, and labor-intensive, several machine learning-based approaches have been developed for genome-wide detection of such sites in multiple species. However, the predictions projected by these tools are difficult to quantify and compare. To date, no systematic performance comparison of 4mC tools has been reported. The aim of this study was to compare and critically evaluate 12 publicly available 4mC site prediction tools according to species specificity, based on a huge independent validation dataset. The tools 4mCCNN ( Escherichia coli ), DNA4mC-LIP ( Arabidopsis thaliana ), iDNA-MS ( Fragaria vesca ), DNA4mC-LIP and 4mCCNN ( Drosophila melanogaster ), and four tools for Caenorhabditis elegans achieved excellent overall performance compared with their counterparts. However, none of the existing methods was suitable for Geoalkalibacter subterraneus , Geobacter pickeringii , and Mus musculus , thereby limiting their practical applicability. Model transferability to five species and non-transferability to three species are also discussed. The presented evaluation will assist researchers in selecting appropriate prediction tools that best suit their purpose and provide useful guidelines for the development of improved 4mC predictors in the future.

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“…K-fold cross-validation method could effectively utilize limited data, and the evaluation results are as close as possible to the model's performance on the test set. Therefore, we used this method to evaluate the model's performance (Wei et al, 2018 ; Chen et al, 2019a , b ; Dao et al, 2019 ). For single label system, there are several common evaluation indexes to measure the predictive performance of the predictor, including Sensitivity (Sn), Accuracy (Acc), Specificity (Sp) and Matthew's correlation coefficient (MCC), which can be defined as following,…”

Section: Methodsmentioning

confidence: 99%

iPromoter-5mC: A Novel Fusion Decision Predictor for the Identification of 5-Methylcytosine Sites in Genome-Wide DNA Promoters

Zhang

Xiao

2020

Front. Cell Dev. Biol.

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The hypomethylation of the whole cancer genome and the hypermethylation of the promoter of specific tumor suppressor genes are the important reasons for the rapid proliferation of cancer cells. Therefore, obtaining the distribution of 5-methylcytosine (5mC) in promoters is a key step to further understand the relationship between promoter methylation and mRNA gene expression regulation. Large-scale detection of DNA 5mC through wet experiments is still time-consuming and laborious. Therefore, it is urgent to design a method for identifying the 5mC site of genome-wide DNA promoters. Based on promoter methylation data of the small cell lung cancer (SCLC) from the database named cancer cell line Encyclopedia (CCLE), we built a fusion decision predictor called iPromoter-5mC for identifying methylation modification sites in promoters using deep neural network (DNN). One-Hot Encoding (One-hot) was used to encode the promoter samples for the classification. The method achieves average AUC of 0.957 on the independent testing dataset, indicating that our predictor is robust and reliable. A user-friendly web-server called iPromoter-5mC could be freely accessible at http://www. jci-bioinfo.cn/iPromoter-5mC, which will provide simple and effective means for users to study promoter 5mC modification. The source code of the proposed methods is freely available for academic research at https://github.com/zlwuxi/iPromoter-5mC.

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iRNA-m7G: Identifying N7-methylguanosine Sites by Fusing Multiple Features

Cited by 85 publications

References 43 publications

RETRACTED: Oxidized LDL Causes Endothelial Apoptosis by Inhibiting Mitochondrial Fusion and Mitochondria Autophagy

RETRACTED: Oxidized LDL Causes Endothelial Apoptosis by Inhibiting Mitochondrial Fusion and Mitochondria Autophagy

Empirical Comparison and Analysis of Web-Based DNA N4-Methylcytosine Site Prediction Tools

iPromoter-5mC: A Novel Fusion Decision Predictor for the Identification of 5-Methylcytosine Sites in Genome-Wide DNA Promoters

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