Comparative Analysis of CpG Sites and Islands Distributed in Mitochondrial DNA of Model Organisms.

Animals (Basel)

Institute of Biological Bases of Animal Production, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland.

Published: April 2020

AI Article Synopsis

  • The study explores the under-researched area of mtDNA methylation across various species, seeking to clarify epigenetic modifications in mitochondrial DNA.
  • Researchers compared theoretical CpG (cytosine-guanine dinucleotide) localization in mtDNA reference sequences from 12 different model organisms, utilizing EMBOSS software and the newcpgseek algorithm to analyze CpG island parameters.
  • Results indicate that higher CpG site numbers are found in vertebrates compared to invertebrates, showing diverse distribution patterns that could influence mitochondrial gene expression, paving the way for future research on mtDNA methylation.

Article Abstract

The information about mtDNA methylation is still limited, thus epigenetic modification remains unclear. The lack of comprehensive information on the comparative epigenomics of mtDNA prompts comprehensive investigations of the epigenomic modification of mtDNA in different species. This is the first study in which the theoretical CpG localization in the mtDNA reference sequences from various species (12) was compared. The aim of the study was to determine the localization of CpG sites and islands in mtDNA of model organisms and to compare their distribution. The results are suitable for further investigations of mtDNA methylation. The analysis involved both strands of mtDNA sequences of animal model organisms representing different taxonomic groups of invertebrates and vertebrates. For each sequence, such parameters as the number, length, and localization of CpG islands were determined with the use of EMBOSS (European Molecular Biology Open Software Suite) software. The number of CpG sites for each sequence was indicated using the newcpgseek algorithm. The results showed that methylation of mtDNA in the analysed species involved mitochondrial gene expression. Our analyses showed that the CpG sites were commonly present in genomic regions including the D-loop, CYTB, ND6, ND5, ND4, ND3, ND2, ND1, COX3, COX2, COX1, ATP6, 16s rRNA, and 12s rRNA. The CpG distribution in animals from different species was diversified. Generally, the number of observed CpG sites of the mitochondrial genome was higher in the vertebrates than in the invertebrates. However, there was no relationship between the frequency of the CpG sites in the mitochondrial genome and the complexity of the analysed organisms. Interestingly, the distribution of the CpG sites for tRNA coding genes was usually cumulated in a larger CpG region in vertebrates. This paper may be a starting point for further research, since the collected information indicates possible methylation regions localized in mtDNA among different species including invertebrates and vertebrates.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222804PMC
http://dx.doi.org/10.3390/ani10040665DOI Listing

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