DNA methylation analysis of phenotype specific stratified Indian population

Harish Rotti, Sandeep Mallya, Prasada S. Kabekkodu, Sanjiban Chakrabarty, Sameer Bhale, Ramachandra Bharadwaj, Balakrishna K. Bhat, Amrish P. Dedge, Ram V. Dhumal, G. G. Gangadharan, Puthiya M. Gopinath, Periyasamy Govindaraj, Kalpana S. Joshi, Paturu Kondaiah, Sreekumaran Nair, S. N.Sreekumaran Nair, Jayakrishna Nayak, B. V. Prasanna, Pooja Shintre, Mayura Sule & 4 others Kumarasamy Thangaraj, Bhushan Patwardhan, Varma M. Valiathan, Kapaettu Satyamoorthy

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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). Conclusion: 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.

Original languageEnglish
Article number151
JournalJournal of Translational Medicine
Volume13
Issue number1
DOIs
Publication statusPublished - 08-05-2015

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DNA Methylation
CpG Islands
Phenotype
Precision Medicine
Methylation
5' Untranslated Regions
DNA
DNA Sequence Analysis
Population
Medicine
Genes
Untranslated Regions
Body Regions
Microarray Analysis
Microarrays
Oligonucleotide Array Sequence Analysis
Immunoprecipitation
Metabolism
Epigenomics
Body Mass Index

All Science Journal Classification (ASJC) codes

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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Rotti, Harish ; Mallya, Sandeep ; Kabekkodu, Prasada S. ; Chakrabarty, Sanjiban ; Bhale, Sameer ; Bharadwaj, Ramachandra ; Bhat, Balakrishna K. ; Dedge, Amrish P. ; Dhumal, Ram V. ; Gangadharan, G. G. ; Gopinath, Puthiya M. ; Govindaraj, Periyasamy ; Joshi, Kalpana S. ; Kondaiah, Paturu ; Nair, Sreekumaran ; Nair, S. N.Sreekumaran ; Nayak, Jayakrishna ; Prasanna, B. V. ; Shintre, Pooja ; Sule, Mayura ; Thangaraj, Kumarasamy ; Patwardhan, Bhushan ; Valiathan, Varma M. ; Satyamoorthy, Kapaettu. / DNA methylation analysis of phenotype specific stratified Indian population. In: Journal of Translational Medicine. 2015 ; Vol. 13, No. 1.
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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). Conclusion: 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.",
author = "Harish Rotti and Sandeep Mallya and Kabekkodu, {Prasada S.} and Sanjiban Chakrabarty and Sameer Bhale and Ramachandra Bharadwaj and Bhat, {Balakrishna K.} and Dedge, {Amrish P.} and Dhumal, {Ram V.} and Gangadharan, {G. G.} and Gopinath, {Puthiya M.} and Periyasamy Govindaraj and Joshi, {Kalpana S.} and Paturu Kondaiah and Sreekumaran Nair and Nair, {S. N.Sreekumaran} and Jayakrishna Nayak and Prasanna, {B. V.} and Pooja Shintre and Mayura Sule and Kumarasamy Thangaraj and Bhushan Patwardhan and Valiathan, {Varma M.} and Kapaettu Satyamoorthy",
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Rotti, H, Mallya, S, Kabekkodu, PS, Chakrabarty, S, Bhale, S, Bharadwaj, R, Bhat, BK, Dedge, AP, Dhumal, RV, Gangadharan, GG, Gopinath, PM, Govindaraj, P, Joshi, KS, Kondaiah, P, Nair, S, Nair, SNS, Nayak, J, Prasanna, BV, Shintre, P, Sule, M, Thangaraj, K, Patwardhan, B, Valiathan, VM & Satyamoorthy, K 2015, 'DNA methylation analysis of phenotype specific stratified Indian population', Journal of Translational Medicine, vol. 13, no. 1, 151. https://doi.org/10.1186/s12967-015-0506-0

DNA methylation analysis of phenotype specific stratified Indian population. / Rotti, Harish; Mallya, Sandeep; Kabekkodu, Prasada S.; Chakrabarty, Sanjiban; Bhale, Sameer; Bharadwaj, Ramachandra; Bhat, Balakrishna K.; Dedge, Amrish P.; Dhumal, Ram V.; Gangadharan, G. G.; Gopinath, Puthiya M.; Govindaraj, Periyasamy; Joshi, Kalpana S.; Kondaiah, Paturu; Nair, Sreekumaran; Nair, S. N.Sreekumaran; Nayak, Jayakrishna; Prasanna, B. V.; Shintre, Pooja; Sule, Mayura; Thangaraj, Kumarasamy; Patwardhan, Bhushan; Valiathan, Varma M.; Satyamoorthy, Kapaettu.

In: Journal of Translational Medicine, Vol. 13, No. 1, 151, 08.05.2015.

Research output: Contribution to journalArticle

TY - JOUR

T1 - DNA methylation analysis of phenotype specific stratified Indian population

AU - Rotti, Harish

AU - Mallya, Sandeep

AU - Kabekkodu, Prasada S.

AU - Chakrabarty, Sanjiban

AU - Bhale, Sameer

AU - Bharadwaj, Ramachandra

AU - Bhat, Balakrishna K.

AU - Dedge, Amrish P.

AU - Dhumal, Ram V.

AU - Gangadharan, G. G.

AU - Gopinath, Puthiya M.

AU - Govindaraj, Periyasamy

AU - Joshi, Kalpana S.

AU - Kondaiah, Paturu

AU - Nair, Sreekumaran

AU - Nair, S. N.Sreekumaran

AU - Nayak, Jayakrishna

AU - Prasanna, B. V.

AU - Shintre, Pooja

AU - Sule, Mayura

AU - Thangaraj, Kumarasamy

AU - Patwardhan, Bhushan

AU - Valiathan, Varma M.

AU - Satyamoorthy, Kapaettu

PY - 2015/5/8

Y1 - 2015/5/8

N2 - 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). Conclusion: 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.

AB - 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). Conclusion: 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.

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U2 - 10.1186/s12967-015-0506-0

DO - 10.1186/s12967-015-0506-0

M3 - Article

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JO - Journal of Translational Medicine

JF - Journal of Translational Medicine

SN - 1479-5876

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