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Clin Epigenetics. 2018 Nov 26;10(1):148. doi: 10.1186/s13148-018-0582-0.

Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes.

Author information

1
Translational Research Institute for Metabolism and Diabetes, Florida Hospital, 301 E. Princeton Street, Orlando, FL, 32804, USA. adeline.divoux@flhosp.org.
2
Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA. adeline.divoux@flhosp.org.
3
Diabetes and Obesity Research Center, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.
4
Present address: Department of Medicine, Johns Hopkins All Children's Hospital, Johns Hopkins University School of Medicine, St. Petersburg, FL, 33701, USA.
5
Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt 98, Debrecen, 4032, Hungary.
6
Department of Computer Science, University of Central Florida, 4000 Central Florida Blvd, Orlando, 32816, USA.
7
Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Boulevard, Orlando, FL, USA.
8
Translational Research Institute for Metabolism and Diabetes, Florida Hospital, 301 E. Princeton Street, Orlando, FL, 32804, USA.

Abstract

BACKGROUND:

Increased lower body fat is associated with reduced cardiometabolic risk. The molecular basis for depot-specific differences in gluteofemoral (GF) compared with abdominal (A) subcutaneous adipocyte function is poorly understood. In the current report, we used a combination of Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq), RNA-seq, and chromatin immunoprecipitation (ChIP)-qPCR analyses that provide evidence that depot-specific gene expression patterns are associated with differential epigenetic chromatin signatures.

METHODS:

Preadipocytes cultured from A and GF adipose tissue obtained from premenopausal apple-shaped women were used to perform transcriptome analysis by RNA-seq and assess accessible chromatin regions by ATAC-seq. We measured mRNA expression and performed ChIP-qPCR experiments for histone modifications of active (H3K4me3) and repressed chromatin (H3K27me3) regions respectively on the promoter regions of differentially expressed genes.

RESULTS:

RNA-seq experiments revealed an A-fat and GF-fat selective gene expression signature, with 126 genes upregulated in abdominal preadipocytes and 90 genes upregulated in GF cells. ATAC-seq identified almost 10-times more A-specific chromatin-accessible regions. Using a combined analysis of ATAC-seq and global gene expression data, we identified 74 of the 126 abdominal-specific genes (59%) with A-specific accessible chromatin sites within 200 kb of the transcription start site (TSS), including HOXA3, HOXA5, IL8, IL1b, and IL6. Interestingly, only 14 of the 90 GF-specific genes (15%) had GF-specific accessible chromatin sites within 200 kb of the corresponding TSS, including HOXC13 and HOTAIR, whereas 25 of them (28%) had abdominal-specific accessible chromatin sites. ChIP-qPCR experiments confirmed that the active H3K4me3 chromatin mark was significantly enriched at the promoter regions of HOXA5 and HOXA3 genes in abdominal preadipocytes, while H3K27me3 was less abundant relative to chromatin from GF. This is consistent with their A-fat specific gene expression pattern. Conversely, analysis of the promoter regions of the GF specific HOTAIR and HOXC13 genes exhibited high H3K4me3 and low H3K27me3 levels in GF chromatin compared to A chromatin.

CONCLUSIONS:

Global transcriptome and open chromatin analyses of depot-specific preadipocytes identified their gene expression signature and differential open chromatin profile. Interestingly, A-fat-specific open chromatin regions can be observed in the proximity of GF-fat genes, but not vice versa.

TRIAL REGISTRATION:

Clinicaltrials.gov, NCT01745471 . Registered 5 December 2012.

KEYWORDS:

Abdominal fat; Chromatin openness; Fat distribution; Gene expression; Gluteofemoral fat; Histone marks; Preadipocytes

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