Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes

Persistent Link:
http://hdl.handle.net/10150/618693
Title:
Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes
Author:
Day, Samantha E.; Coletta, Richard L.; Kim, Joon Young; Campbell, Latoya E.; Benjamin, Tonya R.; Roust, Lori R.; De Filippis, Elena A.; Dinu, Valentin; Shaibi, Gabriel Q.; Mandarino, Lawrence J.; Coletta, Dawn K.
Affiliation:
Univ Arizona, Div Endocrinol Diabet & Metab, Dept Med, UA Coll Med; Univ Arizona, Coll Med, Dept Basic Med Sci
Issue Date:
2016-07-18
Publisher:
BioMed Central
Citation:
Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes 2016, 8 (1) Clinical Epigenetics
Journal:
Clinical Epigenetics
Rights:
© 2016 The Author(s). Open Access.This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/),
Collection Information:
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
Abstract:
Background: Obesity is a metabolic disease caused by environmental and genetic factors. However, the epigenetic mechanisms of obesity are incompletely understood. The aim of our study was to investigate the role of skeletal muscle DNA methylation in combination with transcriptomic changes in obesity. Results: Muscle biopsies were obtained basally from lean (n = 12; BMI = 23.4 +/- 0.7 kg/m(2)) and obese (n = 10; BMI = 32.9 +/- 0.7 kg/m(2)) participants in combination with euglycemic-hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing (RRBS) next-generation methylation and microarray analyses on DNA and RNA isolated from vastus lateralis muscle biopsies. There were 13,130 differentially methylated cytosines (DMC; uncorrected P < 0.05) that were altered in the promoter and untranslated (5' and 3'UTR) regions in the obese versus lean analysis. Microarray analysis revealed 99 probes that were significantly (corrected P < 0.05) altered. Of these, 12 genes (encompassing 22 methylation sites) demonstrated a negative relationship between gene expression and DNA methylation. Specifically, sorbin and SH3 domain containing 3 (SORBS3) which codes for the adapter protein vinexin was significantly decreased in gene expression (fold change -1.9) and had nine DMCs that were significantly increased in methylation in obesity (methylation differences ranged from 5.0 to 24.4 %). Moreover, differentially methylated region (DMR) analysis identified a region in the 5' UTR (Chr. 8: 22,423,530-22,423,569) of SORBS3 that was increased in methylation by 11.2 % in the obese group. The negative relationship observed between DNA methylation and gene expression for SORBS3 was validated by a site-specific sequencing approach, pyrosequencing, and qRT-PCR. Additionally, we performed transcription factor binding analysis and identified a number of transcription factors whose binding to the differentially methylated sites or region may contribute to obesity. Conclusions: These results demonstrate that obesity alters the epigenome through DNA methylation and highlights novel transcriptomic changes in SORBS3 in skeletal muscle.
Note:
Open Access Journal
ISSN:
1868-7075; 1868-7083
PubMed ID:
27437034
DOI:
10.1186/s13148-016-0246-x
Keywords:
Methylation; Next-generation sequencing; Skeletal muscle; Obesity
Version:
Final published version
Sponsors:
National Institutes of Health [R01DK094013]
Additional Links:
http://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-016-0246-x

Full metadata record

DC FieldValue Language
dc.contributor.authorDay, Samantha E.en
dc.contributor.authorColetta, Richard L.en
dc.contributor.authorKim, Joon Youngen
dc.contributor.authorCampbell, Latoya E.en
dc.contributor.authorBenjamin, Tonya R.en
dc.contributor.authorRoust, Lori R.en
dc.contributor.authorDe Filippis, Elena A.en
dc.contributor.authorDinu, Valentinen
dc.contributor.authorShaibi, Gabriel Q.en
dc.contributor.authorMandarino, Lawrence J.en
dc.contributor.authorColetta, Dawn K.en
dc.date.accessioned2016-08-24T01:17:34Z-
dc.date.available2016-08-24T01:17:34Z-
dc.date.issued2016-07-18-
dc.identifier.citationNext-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes 2016, 8 (1) Clinical Epigeneticsen
dc.identifier.issn1868-7075-
dc.identifier.issn1868-7083-
dc.identifier.pmid27437034-
dc.identifier.doi10.1186/s13148-016-0246-x-
dc.identifier.urihttp://hdl.handle.net/10150/618693-
dc.description.abstractBackground: Obesity is a metabolic disease caused by environmental and genetic factors. However, the epigenetic mechanisms of obesity are incompletely understood. The aim of our study was to investigate the role of skeletal muscle DNA methylation in combination with transcriptomic changes in obesity. Results: Muscle biopsies were obtained basally from lean (n = 12; BMI = 23.4 +/- 0.7 kg/m(2)) and obese (n = 10; BMI = 32.9 +/- 0.7 kg/m(2)) participants in combination with euglycemic-hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing (RRBS) next-generation methylation and microarray analyses on DNA and RNA isolated from vastus lateralis muscle biopsies. There were 13,130 differentially methylated cytosines (DMC; uncorrected P < 0.05) that were altered in the promoter and untranslated (5' and 3'UTR) regions in the obese versus lean analysis. Microarray analysis revealed 99 probes that were significantly (corrected P < 0.05) altered. Of these, 12 genes (encompassing 22 methylation sites) demonstrated a negative relationship between gene expression and DNA methylation. Specifically, sorbin and SH3 domain containing 3 (SORBS3) which codes for the adapter protein vinexin was significantly decreased in gene expression (fold change -1.9) and had nine DMCs that were significantly increased in methylation in obesity (methylation differences ranged from 5.0 to 24.4 %). Moreover, differentially methylated region (DMR) analysis identified a region in the 5' UTR (Chr. 8: 22,423,530-22,423,569) of SORBS3 that was increased in methylation by 11.2 % in the obese group. The negative relationship observed between DNA methylation and gene expression for SORBS3 was validated by a site-specific sequencing approach, pyrosequencing, and qRT-PCR. Additionally, we performed transcription factor binding analysis and identified a number of transcription factors whose binding to the differentially methylated sites or region may contribute to obesity. Conclusions: These results demonstrate that obesity alters the epigenome through DNA methylation and highlights novel transcriptomic changes in SORBS3 in skeletal muscle.en
dc.description.sponsorshipNational Institutes of Health [R01DK094013]en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-016-0246-xen
dc.rights© 2016 The Author(s). Open Access.This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/),en
dc.subjectMethylationen
dc.subjectNext-generation sequencingen
dc.subjectSkeletal muscleen
dc.subjectObesityen
dc.titleNext-generation sequencing methylation profiling of subjects with obesity identifies novel gene changesen
dc.typeArticleen
dc.contributor.departmentUniv Arizona, Div Endocrinol Diabet & Metab, Dept Med, UA Coll Meden
dc.contributor.departmentUniv Arizona, Coll Med, Dept Basic Med Scien
dc.identifier.journalClinical Epigeneticsen
dc.description.noteOpen Access Journalen
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen

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