title: Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine.
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.
authors.affiliation: Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America.
authors.forename: Ping
authors.initials: P
authors.lastname: Yu
authors.affiliation: Institute of Bioinformatics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America.
authors.forename: Lexiang
authors.initials: L
authors.lastname: Ji
authors.affiliation: Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America.|GRU-UGA Medical Partnership, University of Georgia Health Sciences Campus, Prince Avenue, Athens, GA, 30602, United States of America.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Lee
authors.affiliation: Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA.
authors.forename: Miao
authors.initials: M
authors.lastname: Yu
authors.affiliation: Department of Chemistry, University of Chicago, 5735 S Ellis Ave, Chicago, IL, 60637 USA.
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.affiliation: Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America.
authors.forename: Suresh
authors.initials: S
authors.lastname: Ambati
authors.affiliation: Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America.
authors.forename: Elizabeth C
authors.initials: EC
authors.lastname: McKinney
authors.affiliation: Abeome Corporation, Athens, GA, 111 Riverbend Road, 30602, United States of America.
authors.forename: Crystal
authors.initials: C
authors.lastname: Jackson
authors.affiliation: Department of Foods and Nutrition, University of Georgia, 305 Sanford Dr, Athens, GA, 30602, United States of America.
authors.forename: Clifton A
authors.initials: CA
authors.lastname: Baile
authors.affiliation: Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.affiliation: Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, United States of America.
authors.forename: Richard B
authors.initials: RB
authors.lastname: Meagher
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D017667:Adipocytes / Q000166:cytology / Q000378:metabolism; D000818:Animals; D001483:Base Sequence; D015415:Biomarkers / Q000378:metabolism; D002453:Cell Cycle; D002467:Cell Nucleus / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism; D004247:DNA / Q000378:metabolism; D005434:Flow Cytometry; D005455:Fluorescent Antibody Technique; D020869:Gene Expression Profiling; D050152:Intra-Abdominal Fat / Q000166:cytology* / Q000378:metabolism*; D047495:PPAR gamma / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D034421:Sus scrofa
chemical_list: D015415:Biomarkers; D002843:Chromatin; D047495:PPAR gamma; D012333:RNA, Messenger; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D004247:DNA