DNA methylation analysis of phenotype specific stratified Indian populationReport as inadecuate

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Journal of Translational Medicine

, 13:151

First Online: 08 May 2015Received: 23 February 2015Accepted: 27 April 2015DOI: 10.1186-s12967-015-0506-0

Cite this article as: Rotti, H., Mallya, S., Kabekkodu, S.P. et al. J Transl Med 2015 13: 151. doi:10.1186-s12967-015-0506-0


BackgroundDNA methylation and its perturbations are an established attribute to a wide spectrum of phenotypic variations and disease conditions. Indian traditional system practices personalized medicine through indigenous concept of distinctly descriptive physiological, psychological and anatomical features known as prakriti. Here we attempted to establish DNA methylation differences in these three prakriti phenotypes.

MethodsFollowing structured and objective measurement of 3416 subjects, whole blood DNA of 147 healthy male individuals belonging to defined prakriti Vata, Pitta and Kapha between the age group of 20-30years were subjected to methylated DNA immunoprecipitation MeDIP and microarray analysis. After data analysis, prakriti specific signatures were validated through bisulfite DNA sequencing.

ResultsDifferentially methylated regions in CpG islands and shores were significantly enriched in promoters-UTRs and gene body regions. Phenotypes characterized by higher metabolism Pitta prakriti in individuals showed distinct promoter 34 and gene body methylation 204, followed by Vata prakriti which correlates to motion showed DNA methylation in 52 promoters and 139 CpG islands and finally individuals with structural attributes Kapha prakriti with 23 and 19 promoters and CpG islands respectively. Bisulfite DNA sequencing of prakriti specific multiple CpG sites in promoters and 5′-UTR such as; LHX1 Vata prakriti, SOX11 Pitta prakriti and CDH22 Kapha prakriti were validated. Kapha prakriti specific CDH22 5′-UTR CpG methylation was also found to be associated with higher body mass index BMI.

ConclusionDifferential DNA methylation signatures in three distinct prakriti phenotypes demonstrate the epigenetic basis of Indian traditional human classification which may have relevance to personalized medicine.

KeywordDNA methylation MeDIP CpG Island Prakriti Ayurveda AbbreviationsBMIBody Mass Index

ANOVAAnalysis of Variance

mPSRsmethylated Prakriti specific regions

TSSTranscription Start Site

5′UTR5′Un-translated Region

GOGene Ontology

SNPsSingle Nucleotide Polymorphisms

5-mC5′-methyl cytosine

FDRFalse Discovery Rate

KEGGKyoto Encyclopedia of Genes and Genomes

DAVIDDatabase for Annotation Visualization and Integrated Discovery

ESMEEpigenetic Sequencing methylation analysis

Electronic supplementary materialThe online version of this article doi:10.1186-s12967-015-0506-0 contains supplementary material, which is available to authorized users.

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Author: Harish Rotti - Sandeep Mallya - Shama Prasada Kabekkodu - Sanjiban Chakrabarty - Sameer Bhale - Ramachandra Bharadwaj - Bal

Source: https://link.springer.com/

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