Abstract
DNA N4-Methylcytosine is a genetic modification process which has an essential role in changing different biological processes such as DNA conformation, DNA replication, DNA stability, cell development and structural alteration in DNA. Due to its negative effects, it is important to identify the modified 4mC sites. Further, methylcytosine may develop anywhere at cytosine residue, however, clonal gene expression patterns are most likely transmitted just for cytosine residues in strand-symmetrical sequences. For this reason many different experiments are introduced but they proved not to be viable choice due to time limitation and high expenses. Therefore, to date there is still need for an efficient computational method to deal with 4mC sites identification. Keeping it in mind, in this research we have proposed an efficient model for Fragaria vesca (F. vesca) and Rosa chinensis (R. chinensis) genome. The proposed iRG-4mC tool is developed based on neural network architecture with two encoding schemes to identify the 4mC sites. The iRG-4mC predictor outperformed the existing state-of-the-art computational model by an accuracy difference of 9.95% on F. vesca (training dataset), 8.7% on R. chinesis (training dataset), 6.2% on F. vesca (independent dataset) and 10.6% on R. chinesis (independent dataset). We have also established a webserver which is freely accessible for the research community.
Highlights
DNA modification consisting of methylation and demethylation plays a crucial role in gene regulation
We evaluated the iRG-4mC tool on four datasets, where two datasets were for F. vesca genome and the other two are for R. chinensis
Getting inspired from the importance of N4-methylcytosine sites identification, we have proposed an identification computational tool named as iRG-4mC
Summary
DNA modification consisting of methylation and demethylation plays a crucial role in gene regulation. Research demonstrates that DNA modification exhibits the property to modify DNA protein interactions, chromatin structure, stability and conformation [3,4]. It has a role in the regulation of a few activities such as cell development, chromosome stability and genomic imprinting [5,6,7]. Host DNA present in exogenous pathogenic DNA of prokaryotes can be detected by 6mA and 4mC [11], where 4mC perform error correction and regulation of DNA replication [12,13]. 5mC plays an essential role in various activities of eukaryotes, such as gene imprinting, regulation, and transposon suppression. 6mA and 4mC can only be identified using high sensitive techniques [15]
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