Comparisons of Distribution of CpG Islands Through the Sex-Chromosomes Between Rat (Rattus norvegicus) and Swine (Sus scrofa)

CpG islands are the developed key genomic features in epigenetic research. The role of DNA methylation can be discovered by characterizing their methylation state. By mapping of DNA methylation in various cell types, it was clear the lack of methylation in the majority of CpG islands, but numerous cases were found of differentially methylated, or even constitutively methylated regions that are well defined as CpG islands based on their sequence content (Dindot et al., 2009). Antequera and Bird (1993) suggested that mammalian promoters belong to two different categories in terms of base composition and DNA methylation. The region is devoid of methylation that has a higher G+C content than the genome average, while the rest have a methylation pattern and base composition indistinguishable from bulk DNA. Regulatory regions are made up of a variable number of short modules to which activators and repressors bind in such a way that their integrated contributions result in the correct expression of the gene. Despite the sequence diversity among promoters, genes transcribed by RNA polymerase II can be classified in two different and mutually exclusive groups according to the distribution of CpG dinucleotides across their 5’ ends. The frequency of CpGs is the same as the genome average, which is roughly one of every 100 nucleotides. Genes belonging to the other group are surrounded by a region ~ 1 kb long where the frequency of CpGs is approximately 10 times higher than the genome average. CpG involves transcriptional regulation and their potential use as markers to localize genes in genome sequences. The contrast between the island and non-island DNA is so sharp because CpGs occur at the expected frequency at CpG islands based on their G+C content, whereas CpGs in bulk DNA is 20% of their expected frequency, due to the spontaneous deamination (Suzuki and Bird (2008), Illingworth et al. (2008), Futscher (2002) ).

The present study aims to identify CpG islands using a comparative biocomputational approach. The sequence of in X Chr and Y Chr Rattus norvegicus and Sus scrofa will be downloaded from NCBI Genome (https://www.ncbi.nlm.nih.gov/genome). The downloaded chromosome sequences were subjected to notepad++ for further modification. Then the sequences were subjected to Perl code for predicting the statistical data. The statistical data were subjected to an R programming environment for further cleaning and getting the predicted data.

The average island length of Rattus norvegicus in the X-chromosome is 596.19 and Sus scrofa has an average island length of 580.44 it means Rattus norvegicus has a greater average island length as compared to Sus scrofa as shown in the table. Variation in island length is more in both species. The standard error of the CpG island of the X-chromosome of Rattus norvegicus is 3.68 and in Sus scrofa the value is2.02. It means Rattus norvegicus has a greater variation in their genome. Island number varies in both species. X-chromosome of Rattus norvegicus island number is 4465 and in Sus scrofa the value is 13539. It means Sus scrofa has more island number as compared to Rattus norvegicus. Average G+C concentration is close to each other in both species. In the X-chromosome of Sus scrofa, the value is54.5 and the case of the Rattus norvegicus value is 53.03. The average CpG concentration is close to each other as shown in Table 1. The value of average CpG concentration in Rattus norvegicus is 4.94 and in the case of Sus scrofa it is 5.13. It means there is a small difference in the value of both species. The average ratio (Observed CpG/Expected CpG) is 0.73 in Rattus norvegicus in the case of Sus scrofa 0.7. It means the value of the average ratio of Rattus norvegicus is greater than the value of Sus scrofa. We have got the minimum island length which is the same in both species. Both species have a similar value that is 500. The maximum island length value of Sus scrofa is 5639 and in the case of Rattus norvegicus that is 4484. It means Sus scrofa has a maximum island length as compared to Rattus norvegicus.

The average island length of Rattus norvegicus in Y-chromosome is 560.46 and Sus scrofa has an average island length of 567.28 it means Sus scrofa has a greater average island length as compared to Rattus norvegicus as shown in the table. Variation in island length is more in both species. The standard error of the CpG island of Y-chromosome of Rattus norvegicus is 12.67 and in Sus scrofa the value is 4.55. It means Rattus norvegicus has a greater variation in their genome. Island number varies in both species. Y-chromosome of Rattus norvegicus island number is 110 and in Sus scrofa the value is 1820. It means Sus scrofa has more island number as compared to Rattus norvegicus. Average G+C concentration is close to each other in both species. In the Y-chromosome of Sus scrofa the value is 53.86 and in the case of the Rattus norvegicus value is 52.7. The average CpG concentration is close to each other as shown in Table 2. The value of average CpG concentration in Rattus norvegicus is 4.73 and in the case of Sus scrofa, it is 4.96. It means there is a small difference in the value of both species. The average ratio (Observed CpG/Expected CpG) is 0.7 in Rattus norvegicus in the case of Sus scrofa 0.7. We have got the minimum island length which is the same in both species. Both species have a similar value that is 500. The maximum island length value of Sus scrofa is 2650 and in the case of Rattus norvegicus, that is 1059. It means Sus scrofa has a maximum island length as compared to Rattus norvegicus.

In prokaryotes it is associated with restriction-modification systems, targeting short palindromic or nearly palindromic sites. DNA methylation is used as a signal for the regulation of a particular DNA protein interaction. Methylation systems typically comprise of a DNA methylase and one or more DNA binding proteins which will overlap the target methylation site on DNA, subsequently blocking methylation of that site.The laboratory rat (Rattus norvegicus) have incalculable benefits to human health it is mostly used in experimental medicine and drug production. The diploid number chromosome is 42 in Rattus norvegicus and has an autosomal complement consisting of seven pairs of metacentrics, three pairs of submetacentric, and 10 pairs of acrocentrics. The X-chromosome is an acrocentric of medium size and the Y is the smallest acrocentric of the complement (Duncan and Van Peenen 1971). Rattus norvegicus, has multiple copies of Sry Y-chromosome while the maximum mammals have only a single copy (Turner et al. 2007). Pigs (Sus scrofa) have been domesticated in the old world since antiquity. Pig provides valuable products to humans; including fertilizer, leather, pork, and a variety of medicines an indigenous pig has a diploid number of chromosomes (2n) of 38, which includes 18 pairs of autosomes and one pair of allosomes or sex-chromosomes. First, 5 pairs of autosomes are submetacentric, the next 2 pairs are subtelocentric, a subsequent 5 pairs are metacentrics, the remaining six pairs are telocentric and sex-chromosomes are metacentrics in nature. The first chromosome was the longest pair and a thirteenth pair was the second largest, while a Y-chromosome was the smallest in the karyotype of the pig (Vishnu et al. 2015).