Kowal Krzysztof, Tkaczyk Angelika, Ząbek Tomasz, Pierzchała Mariusz, Ślaska Brygida
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.
Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Animals (Basel). 2020 Apr 11;10(4):665. doi: 10.3390/ani10040665.
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.
关于线粒体DNA（mtDNA）甲基化的信息仍然有限，因此表观遗传修饰仍不清楚。由于缺乏关于mtDNA比较表观基因组学的全面信息，促使人们对不同物种中mtDNA的表观基因组修饰进行全面研究。这是第一项比较来自不同物种（12种）的mtDNA参考序列中理论CpG定位的研究。该研究的目的是确定模式生物mtDNA中CpG位点和岛的定位，并比较它们的分布。这些结果适用于对mtDNA甲基化的进一步研究。分析涉及代表无脊椎动物和脊椎动物不同分类群的动物模式生物的mtDNA序列的两条链。对于每个序列，使用EMBOSS（欧洲分子生物学开放软件套件）软件确定CpG岛的数量、长度和定位等参数。使用newcpgseek算法指出每个序列的CpG位点数量。结果表明，所分析物种中mtDNA的甲基化涉及线粒体基因表达。我们的分析表明，CpG位点普遍存在于包括D环、CYTB、ND6、ND5、ND4、ND3、ND2、ND1、COX3、COX2、COX1、ATP6、16s rRNA和12s rRNA的基因组区域。不同物种动物中的CpG分布是多样化的。一般来说，脊椎动物线粒体基因组中观察到的CpG位点数量比无脊椎动物中的要高。然而，线粒体基因组中CpG位点的频率与所分析生物的复杂性之间没有关系。有趣的是，脊椎动物中tRNA编码基因的CpG位点分布通常聚集在一个更大的CpG区域。本文可能是进一步研究的起点，因为所收集的信息表明在包括无脊椎动物和脊椎动物在内的不同物种中，mtDNA中可能存在甲基化区域。
