title: DNA methylation analysis of phenotype specific stratified Indian population.
abstract: BACKGROUND
  DNA 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.
  
  
  METHODS
  Following 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.
  
  
  RESULTS
  Differentially 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).
  
  
  CONCLUSIONS
  Differential DNA methylation signatures in three distinct prakriti phenotypes demonstrate the epigenetic basis of Indian traditional human classification which may have relevance to personalized medicine.
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. harishnbrotti@yahoo.co.in.
authors.forename: Harish
authors.initials: H
authors.lastname: Rotti
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. sandeep.mallya@manipal.edu.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Mallya
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. spbhat81@gmail.com.
authors.forename: Shama Prasada
authors.initials: SP
authors.lastname: Kabekkodu
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. sanjiban.c@gmail.com.
authors.forename: Sanjiban
authors.initials: S
authors.lastname: Chakrabarty
authors.affiliation: Department of Biotechnology, Sinhgad College of Engineering, Pune, Maharashtra, India. bhalesameer@yahoo.co.in.
authors.forename: Sameer
authors.initials: S
authors.lastname: Bhale
authors.affiliation: Centre for Clinical Research, Foundation for Revitalization of Local Health Traditions, Bangalore, Karnataka, India. rcbharadwaj@gmail.com.
authors.forename: Ramachandra
authors.initials: R
authors.lastname: Bharadwaj
authors.affiliation: Department of Rognidana/Shalyatantra, Shri Dharmasthala Manjunatheshwara College of Ayurveda, Udupi, Karnataka, India. aparna329@yahoo.com.
authors.forename: Balakrishna K
authors.initials: BK
authors.lastname: Bhat
authors.affiliation: Department of Biotechnology, Sinhgad College of Engineering, Pune, Maharashtra, India. amrish1511@rediffmail.com.
authors.forename: Amrish P
authors.initials: AP
authors.lastname: Dedge
authors.affiliation: Department of Biotechnology, Sinhgad College of Engineering, Pune, Maharashtra, India. vikramayu@rediffmail.com.
authors.forename: Vikram Ram
authors.initials: VR
authors.lastname: Dhumal
authors.affiliation: Centre for Clinical Research, Foundation for Revitalization of Local Health Traditions, Bangalore, Karnataka, India. vaidya.ganga@frlht.org.
authors.forename: G G
authors.initials: GG
authors.lastname: Gangadharan
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. gopinathpm@yahoo.com.
authors.forename: Puthiya M
authors.initials: PM
authors.lastname: Gopinath
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India. pgovinth@ccmb.res.in.
authors.forename: Periyasamy
authors.initials: P
authors.lastname: Govindaraj
authors.affiliation: Department of Biotechnology, Sinhgad College of Engineering, Pune, Maharashtra, India. joshikalpana@gmail.com.
authors.forename: Kalpana S
authors.initials: KS
authors.lastname: Joshi
authors.affiliation: Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka, India. Paturu@mrdg.iisc.ernet.in.
authors.forename: Paturu
authors.initials: P
authors.lastname: Kondaiah
authors.affiliation: Department of Statistics, Manipal University, Manipal, Karnataka, India. sree.nair@manipal.edu.
authors.forename: Sreekumaran
authors.initials: S
authors.lastname: Nair
authors.affiliation: Centre for Clinical Research, Foundation for Revitalization of Local Health Traditions, Bangalore, Karnataka, India. venu.gopal@frlht.org.
authors.forename: S N Venugopalan
authors.initials: SN
authors.lastname: Nair
authors.affiliation: Department of Rognidana/Shalyatantra, Shri Dharmasthala Manjunatheshwara College of Ayurveda, Udupi, Karnataka, India. nayakjk2004@yahoo.co.in.
authors.forename: Jayakrishna
authors.initials: J
authors.lastname: Nayak
authors.affiliation: Department of Rognidana/Shalyatantra, Shri Dharmasthala Manjunatheshwara College of Ayurveda, Udupi, Karnataka, India. drbvidyaprasanna@gmail.com.
authors.forename: B V
authors.initials: BV
authors.lastname: Prasanna
authors.affiliation: Department of Biotechnology, Sinhgad College of Engineering, Pune, Maharashtra, India. pooja.shintre@gmail.com.
authors.forename: Pooja
authors.initials: P
authors.lastname: Shintre
authors.affiliation: Department of Biotechnology, Sinhgad College of Engineering, Pune, Maharashtra, India. mayura.sule@gmail.com.
authors.forename: Mayura
authors.initials: M
authors.lastname: Sule
authors.affiliation: CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India. thangs@ccmb.res.in.
authors.forename: Kumarasamy
authors.initials: K
authors.lastname: Thangaraj
authors.affiliation: Interdisciplinary School of Health Sciences, University of Pune, Pune, India. bpatwardhan@gmail.com.
authors.forename: Bhushan
authors.initials: B
authors.lastname: Patwardhan
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. msvaliathan@gmail.com.
authors.forename: Marthanda Varma Sankaran
authors.initials: MV
authors.lastname: Valiathan
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India. ksatyamoorthy@manipal.edu.
authors.forename: Kapaettu
authors.initials: K
authors.lastname: Satyamoorthy
mesh_terms: D000328:Adult; D002851:Chromatography, High Pressure Liquid; D018899:CpG Islands; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D023281:Genomics; D006801:Humans; D047468:Immunoprecipitation; D007194:India; D008297:Male; D008515:Medicine, Ayurvedic; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D057285:Precision Medicine; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D055815:Young Adult
chemical_list: D004247:DNA