Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine

PLoS One. 2016 May 12;11(5):e0154949. doi: 10.1371/journal.pone.0154949. eCollection 2016.

Abstract

The reprogramming of cellular memory in specific cell types, and in visceral adipocytes in particular, appears to be a fundamental aspect of obesity and its related negative health outcomes. We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from visceral adipose tissue (VAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2), to distinguish classes of PPARg2-Positive (PPARg2-Pos) adipocyte nuclei from PPARg2-Negative (PPARg2-Neg) leukocyte and endothelial cell nuclei. PPARg2-Pos nuclei were 10-fold enriched for most adipocyte marker transcripts relative to PPARg2-Neg nuclei. PPARg2-Pos nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed, which regulate the methylation of histones and DNA cytosine (e.g., DNMT1, TET1, TET2, KDM4A, KMT2C, SETDB1, PAXIP1, ARID1A, JMJD6, CARM1, and PRMT5). PPARg2-Pos nuclei were large with decondensed chromatin. TAB-seq demonstrated 5-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in gene bodies of various classes of VAT nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. In short, VAT-derived adipocytes appear to be more actively remodeling their chromatin than non-adipocytes.

MeSH terms

  • 5-Methylcytosine / analogs & derivatives*
  • 5-Methylcytosine / metabolism
  • Adipocytes / cytology
  • Adipocytes / metabolism
  • Animals
  • Base Sequence
  • Biomarkers / metabolism
  • Cell Cycle
  • Cell Nucleus / metabolism*
  • Chromatin / metabolism
  • DNA / metabolism
  • Flow Cytometry
  • Fluorescent Antibody Technique
  • Gene Expression Profiling
  • Intra-Abdominal Fat / cytology*
  • Intra-Abdominal Fat / metabolism*
  • PPAR gamma / metabolism
  • Pluripotent Stem Cells / cytology
  • Pluripotent Stem Cells / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sus scrofa

Substances

  • Biomarkers
  • Chromatin
  • PPAR gamma
  • RNA, Messenger
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • DNA