Identification of Transition Bias in Oxidized Low Density Lipoprotein Receptor 1 Gene in Buffalo

Introduction events in particular, across the generations of a species have recently been identified as potential targets for Since transitions (T C, A G) have been observed evolutionary studies [5]. Recently transition bias was to occur at higher frequencies than transversions (T A, observed in the bovine genome where in, they T G, C A, C G) in most of the DNA sequences [1], evaluated 15,110 SNPs and concluded that 69.8% of the phenomenon is commonly termed as transition the total SNPs turned out to be transitions [6]. Shabir et bias. The nature of nucleotide substitutions not only aid al and Jawale [7,8] reported nine SNPs in Intron I of in the comprehension of species evolution at DNA-Oxidized Low Density Lipoprotein Receptor 1 (OLR1) sequence level but also help in calculating the evoluti-gene in four breeds of Indian buffalo. onary distance between the species. The transition/ The present study was aimed at exploring transversion mutation rate biases are predicted to differ nucleotide substitution pattern in intron-1 of OLR1 significantly among the genes [2]. One of the other gene of buffalo, using a comparative analysis of 24 important features of such substitutions is their different nucleotide substitution models. association with the type and intensity of natural selection, the sustenance of high allelic diversity in Materials and Methods Major Histocompatibility Complexes (MHC's) being a Sequence data: 52 OLR1 (Intron I) sequences of four prime archetype [3]. The evolutionary studies primarily buffalo species viz. Surti, Jaffarabadi, Mehsana and entail the study of genetic distances in mitochondrial Banni, previously deposited in NCBI (Accession DNA [4], however, differential genomic nucleotide numbers: GQ478023 to GQ478042 & GQ415420 to substitutions and SNPs in population have also been GQ415451) were aligned in MEGA 5.0. The pattern of demonstrated to help in understanding their evolution. nucleotide substitution, maximum likelihood estimate The alterations in Intronic regions, intron gain/loss of transition/transversion bias and maximum likelihood fits using 24 different nucleotide substitutions models available in MEGA 5.0 were analyzed in OLR1 (IntronI) in four breeds of buffalo viz. Jaffarabadi, Abstract Background and aim: Though transition bias has been previously demonstrated in cattle, however, there has not been any study that has explored transition bias in buffalo nuclear genome. The aim of the present study was to evaluate the nucleotide substitution pattern in the Intron I of Oxidised Low Density Lipoprotein Receptor 1 (OLR1) gene in four breeds of Indian buffalo using 24 …


Introduction
events in particular, across the generations of a species have recently been identified as potential targets for Since transitions (T C, A G) have been observed evolutionary studies [5].Recently transition bias was to occur at higher frequencies than transversions (T A, observed in the bovine genome where in, they T G, C A, C G) in most of the DNA sequences [1], evaluated 15,110 SNPs and concluded that 69.8% of the phenomenon is commonly termed as transition the total SNPs turned out to be transitions [6].Shabir et bias.The nature of nucleotide substitutions not only aid al and Jawale [7,8] reported nine SNPs in Intron I of in the comprehension of species evolution at DNA-Oxidized Low Density Lipoprotein Receptor 1 (OLR1) sequence level but also help in calculating the evolutigene in four breeds of Indian buffalo.onary distance between the species.The transition/ The present study was aimed at exploring transversion mutation rate biases are predicted to differ nucleotide substitution pattern in intron-1 of OLR1 significantly among the genes [2].One of the other gene of buffalo, using a comparative analysis of 24 important features of such substitutions is their different nucleotide substitution models.association with the type and intensity of natural selection, the sustenance of high allelic diversity in

Major Histocompatibility Complexes (MHC's) being a
Sequence data: 52 OLR1 (Intron I) sequences of four prime archetype [3].The evolutionary studies primarily buffalo species viz.Surti, Jaffarabadi, Mehsana and entail the study of genetic distances in mitochondrial Banni, previously deposited in NCBI (Accession DNA [4], however, differential genomic nucleotide numbers: GQ478023 to GQ478042 & GQ415420 to substitutions and SNPs in population have also been GQ415451) were aligned in MEGA 5.0.The pattern of demonstrated to help in understanding their evolution.
nucleotide substitution, maximum likelihood estimate The alterations in Intronic regions, intron gain/loss of transition/transversion bias and maximum likelihood fits using 24 different nucleotide substitutions models available in MEGA 5.0 were analyzed in OLR1 (IntronI) in four breeds of buffalo viz.Jaffarabadi, Surti, Mehsana and Banni.observed.The frequency of t>C transition was high in the population studied and was present in all the four Nucleotide substitution pattern estimation: The breeds of buffalo, however, the two transversions viz.transition/transversion bias (R) was primarily esti-t>A and c>G were respectively present in Banni and mated under the Kimura 2-parameter model.Substitu-Surti breed of buffalo (Table -1).The frequency of tion patterns and the transitions/ transversions rates (r) transitions was 3.5 times higher than the frequency of were then estimated by Tamura-Nei-I and Tamura-Neitransversions as evinced by the transition/transversion II models.bias (R) estimated under Kimura 2 parameter model [8] Further, the transition/transversion bias (R) was which equaled to 3.50.The maximum Log likelihood also estimated by 24 different nucleotide substitution for this computation was -1689.545.Substitution models available in MEGA 5.0.Models with the lowest patterns and the Transitions/Transversions rates (r) AICc scores (Akaike Information Criterion, corrected) estimated by Tamura-Nei-I [9] and Tamura-Nei-II were considered to describe the best substitution model [10] are enlisted in Table-2 which demonstrates pattern.For each model, BIC value (Bayesian the significantly higher values of transitions.The AICc Information Criterion), Maximum Likelihood value score, as calculated using 24 models, for HKY model (lnL), and the number of parameters (including 101 was the lowest (3459.1)among all the 24 models used tree branch lengths) were also presented.The and thus displayed the best Nucleotide Substitution Transition/Transversion bias (R) was calculated by pattern.The transition/transversion bias calculated by R the HKY model was 3.5021 (Table -3) which is nearly equivalent to the values calculated by the Kimura 2 CpG island search: CpG islands were searched in the parameter model.However, the transition bias intron I of OLR1 gene of buffalo to get an idea computed by Jukes Cantor (JC) and related models regarding the probability of CpG methylations which displayed the lowest value of transition/transversion could lead higher mutations, cytosine to thymine, in bias (0.5) and a frequency of 0.25 for each nucleotide.particular due to the deamination of methyl cytosine.

Discussion
times higher than that of transversions in our study entailing the Intron I of OLR1 gene in Buffalo.It is also In our previous studies we have demonstrated the in agreement with a previous study in bovines where phylogenetic analysis and thus analyzed the genetic they evaluated 15,110 SNPs and found that 69.8% of distance between the two Jaffarabadi and Surti buffalo the total SNPs were transitions [6].The lower values of based on intronic region of OLR1 gene [11].However, transition/transversion bias by Jukes cantor and related this study focuses on the nucleotide substitution pattern models is on account of the fact that Jukes cantor model in intronI of OLR1 gene in four breeds of buffalo.In assumes the equality of nucleotide substitution among previous studies in the nuclear DNA of mammals, the sites and equal nucleotide frequencies [14].frequency of transition mutations appeared to be twice The nucleotide substitution rates calculated by 24 higher than transversions which is well evinced by the different nucleotide substitution models show that t>C nucleotide substitution patterns in synonymous and nucleotide substitutions were present at the highest non-coding SNPs in humans [12], and in SNPs in mice frequency.The earlier studies on CpG methylation [13] however, the frequency of transitions was three    have demonstrated that methylations usually occur in nucleotide substitution patterns in four breeds of the CpG rich regions of the genome, usually buffalo, however, larger stretches of DNA, introns and promoters/Introns, and the methylated cytosines after exons, need to be evaluated to derive a generalized deamination get mutated into thymines [15].No conclusion on the nucleotide substitution patterns in putative CpG islands were identified in the Intron I of buffalo genome.OLR1 gene of buffalo (Figure -1) which means that this Authors' contributions region of OLR1 is a CpG rich region and has higher The present study is a review and analysis of master's possibilities of being methylated.
research work of NS and CVJ.NS and CVJ did the Previous study [16] have demonstrated that review and drafted the manuscript.NAC and CDB cytosine of most CpGs are methylated which leads to assisted in data analysis.DNR and CGJ supervised the frequent deaminations of cytosine leading to work and critically analyzed the data.All authors read mismatches.Recently, a study revealed high mutation and approved the final manuscript.rates in low to moderately methylated CpG sites at different scales in human embryonic stem cells [17].

Figure- 1 .
Figure-1.Shows the observed/expected ratio of CpG, the percentage of CpG throughout the length of Intron I of OLR1, and the absence of putative CpG islands in IntronI of OLR1.
Table-4).The nucleotide the Intron I of OLR1 gene in Mehsana and Banni nucleotide substitutions.The CpG island search did not buffalo [8].Out of the total nine SNPs explored in four reveal any putative CpG islands in Intron I of OLR1 breeds of Indian buffalo in Intron I of OLR1 gene, only gene of buffalo (Figure-1).Further, the Observed/ two transversions were observed and the rest were Expected ratio of CpG as calculated by the EBI soft-transitions (Table-1).Four t>C, two a>G and one c>T ware turned out to be greater than 0.60 and the Percent transitions were present out of the seven transitions C + Percent G was observed to be greater than 50.

Table - 2
. Maximum composite likelihood estimate of the pattern of nucleotide substitution using Tamura Nei models Each entry shows the probability of substitution from one base (row) to another base (column).Rates of different transitional substitutions are shown in bold and those of transversionsal substitutions are shown in italics.

Table - 4
. The frequency of four different nucleotides in Intron I of OLR1 gene in Buffalo.