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

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

Molecular Differences in Mitochondrial Genomes (Mitogenomes) of Dogs with Recurrent and Multiple Tumours and Their Reference to the Human Mitochondrial Genome

The aim of this study was to identify molecular defects caused by mutations in mitochondrial DNA in cases of recurrent and multiple canine tumours. We presented molecular differences in the mtDNA genome for two tumours observed in different body parts of five dogs and throughout time in the case of the recurrence. Mitochondrial DNA was sequenced on an Illumina MiSeq sequencer using a 600-cycle kit in a paired-end mode targeting at least 100x coverage. The sequences obtained were subjected to bioinformatic analyses in order to determine mutation and polymorphic sites within the analysed mtdna genome in the tumour tissue. The total amount of changes: single nucleotide polymorphisms (SNPs), indels, mutations, and heteroplasmy detected in this study was 329. Ten polymorphisms were found in all analysed samples: ins.2679_2680g (tRNA-Leu (UUR)), m.5367c>t (COX1), m.5444t>C (COX1), m.6065a>G (COX1), m.8368c>T (ATP6), m.8807g>A (COX3), ins.9913_9914tg (ND4L), m.13299t>A (ND5), m.15814c>T, and m.16418A>G (control region). Interestingly, the highest number of differences in the mtdna genome was observed between non-cancerous pyogranuloma tissue and epithelioma glandulae sebacei. The mutations in the non-cancerous tissue were mainly found in positions where polymorphisms were observed in blood and tumour tissue. The lowest number of changes was observed for the youngest analysed dog, which may indicate that some changes appeared in the mitogenomes with age. There were fewer heteroplasmic alterations in the larger than smaller tumour, which may suggest that the tumour growth is enhanced by genomic instability. The changes in the protein-coding genes were mostly synonymous, and nonsynonymous changes did not lead to alterations in protein properties. New mutations were observed in the post-recurrence tumours in comparison with the pre-recurrent tissue and blood

Mitochondrial DNA Changes in Respiratory Complex I Genes in Brain Gliomas

Mitochondria are organelles necessary for oxidative phosphorylation. The interest in the role of mitochondria in the process of carcinogenesis results from the fact that a respiratory deficit is found in dividing cells, especially in cells with accelerated proliferation. The study included tumor and blood material from 30 patients diagnosed with glioma grade II, III and IV according to WHO (World Health Organization). DNA was isolated from the collected material and next-generation sequencing was performed on the MiSeqFGx apparatus (Illumina). The study searched for a possible relationship between the occurrence of specific mitochondrial DNA polymorphisms in the respiratory complex I genes and brain gliomas of grade II, III and IV. The impact of missense changes on the biochemical properties, structure and functioning of the encoded protein, as well as their potential harmfulness, were assessed in silico along with their belonging to a given mitochondrial subgroup. The A3505G, C3992T, A4024G, T4216C, G5046A, G7444A, T11253C, G12406A and G13604C polymorphisms were assessed as deleterious changes in silico, indicating their association with carcinogenesis

Effects of Dietary n–3 and n–6 Polyunsaturated Fatty Acids in Inflammation and Cancerogenesis

The dietary recommendation encourages reducing saturated fatty acids (SFA) in diet and replacing them with polyunsaturated fatty acids (PUFAs) n–3 (omega–3) and n–6 (omega–6) to decrease the risk of metabolic disturbances. Consequently, excessive n–6 PUFAs content and high n–6/n–3 ratio are found in Western-type diet. The importance of a dietary n–6/n–3 ratio to prevent chronic diseases is linked with anti-inflammatory functions of linolenic acid (ALA, 18:3n–3) and longer-chain n–3 PUFAs. Thus, this review provides an overview of the role of oxylipins derived from n–3 PUFAs and oxylipins formed from n–6 PUFAs on inflammation. Evidence of PUFAs’ role in carcinogenesis was also discussed. In vitro studies, animal cancer models and epidemiological studies demonstrate that these two PUFA groups have different effects on the cell growth, proliferation and progression of neoplastic lesions