Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes

• Published in: PloS one Vol. 6; no. 6; p. e19778
• Main Authors: Lo, Kinyui Alice, Bauchmann, Mary K, Baumann, Amy P, Donahue, Christopher J, Thiede, Mark A, Hayes, Lisa S, des Etages, Shelley Ann G, Fraenkel, Ernest
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02-06-2011; Public Library of Science (PLoS)
• Subjects: 3T3-L1 Cells; Acetates; Acetylation; Adipocytes; Adipocytes - cytology; Adipocytes - metabolism; Androgens; Animals; Base Sequence; Binding sites; Binding Sites - genetics; Bioengineering; Bioinformatics; Biology; CCAAT-Enhancer-Binding Protein-alpha - genetics; CCAAT-Enhancer-Binding Protein-alpha - metabolism; Cell cycle; Cell Differentiation - genetics; Cells, Cultured; Chromatin; Cloning; CREB-Binding Protein - genetics; CREB-Binding Protein - metabolism; Deoxyribonucleic acid; Diabetes; Diabetes mellitus; DNA; DNA binding proteins; DNA sequencing; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; E1A-Associated p300 Protein - genetics; E1A-Associated p300 Protein - metabolism; E2F protein; E2F4 Transcription Factor - genetics; E2F4 Transcription Factor - metabolism; Epidemics; Epigenetic inheritance; Event-related potentials; Gene expression; Gene Expression Profiling; Gene mapping; Gene regulation; Gene sequencing; Genes; Genome, Human - genetics; Genomes; Genomics; Health aspects; Heat shock proteins; Heat Shock Transcription Factors; Histones - metabolism; Homeostasis; Humans; Immunoprecipitation; Insulin; Insulin resistance; Lysine - metabolism; Medicine; Mesenchyme; Mesoderm - cytology; Mesoderm - metabolism; Metabolic disorders; Metabolism; Mice; MicroRNAs; Next-generation sequencing; Nucleotide sequence; Obesity; Proteins; R&D; Research & development; Signaling; SIRT1 protein; Sirtuin 1 - genetics; Sirtuin 1 - metabolism; Stem cell transplantation; Stem cells; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; United States > US; Massachusetts; Connecticut
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0019778

The growing epidemic of obesity and metabolic diseases calls for a better understanding of adipocyte biology. The regulation of transcription in adipocytes is particularly important, as it is a target for several therapeutic approaches. Transcriptional outcomes are influenced by both histone modifications and transcription factor binding. Although the epigenetic states and binding sites of several important transcription factors have been profiled in the mouse 3T3-L1 cell line, such data are lacking in human adipocytes. In this study, we identified H3K56 acetylation sites in human adipocytes derived from mesenchymal stem cells. H3K56 is acetylated by CBP and p300, and deacetylated by SIRT1, all are proteins with important roles in diabetes and insulin signaling. We found that while almost half of the genome shows signs of H3K56 acetylation, the highest level of H3K56 acetylation is associated with transcription factors and proteins in the adipokine signaling and Type II Diabetes pathways. In order to discover the transcription factors that recruit acetyltransferases and deacetylases to sites of H3K56 acetylation, we analyzed DNA sequences near H3K56 acetylated regions and found that the E2F recognition sequence was enriched. Using chromatin immunoprecipitation followed by high-throughput sequencing, we confirmed that genes bound by E2F4, as well as those by HSF-1 and C/EBPα, have higher than expected levels of H3K56 acetylation, and that the transcription factor binding sites and acetylation sites are often adjacent but rarely overlap. We also discovered a significant difference between bound targets of C/EBPα in 3T3-L1 and human adipocytes, highlighting the need to construct species-specific epigenetic and transcription factor binding site maps. This is the first genome-wide profile of H3K56 acetylation, E2F4, C/EBPα and HSF-1 binding in human adipocytes, and will serve as an important resource for better understanding adipocyte transcriptional regulation.