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Volume 4, Issue 6

Analysis of the long-read sequencing data using computational tools confirms the presence of 5-methylcytosine in the genome Open Access

Abstract

Modification of DNA bases plays important roles in the epigenetic regulation of eukaryotic gene expression. Among the different types of DNA methylation, 5-methylcytosine (5mC) is common in higher eukaryotes. Although bisulfite sequencing is the established detection method for this modification, newer methods, such as Oxford nanopore sequencing, have been developed as quick and reliable alternatives. An earlier study using sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) indicated the presence of 5mC at very low concentration in . More recently, a comprehensive study of the yeast genome found 40 5mC sites using the computational tool Nanopolish on nanopore sequencing output raw data. In the present study, we are trying to validate the prediction of the 5mC modifications in yeast with Nanopolish and two other nanopore software tools, Tombo and DeepSignal. Using publicly available genome sequencing data, we compared the open-access computational tools, including Tombo, Nanopolish and DeepSignal, for predicting 5mC. Our results suggest that these tools are indeed capable of predicting DNA 5mC modifications at a specific location from Oxford nanopore sequencing data. We also predicted that 5mC present in the genome might be located predominantly at the locus of chromosome 12.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): DNA methylation , long-read sequencing , Nanopore sequencing and third-generation sequencing
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2022-06-10
2024-04-26
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Analysis of the long-read sequencing data using computational tools confirms the presence of 5-methylcytosine in the Saccharomyces cerevisiae genome
Access Microbiology 4, 000363 (2022); https://doi.org/10.1099/acmi.0.000363
/content/journal/acmi/10.1099/acmi.0.000363
/content/journal/acmi/10.1099/acmi.0.000363
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