Dataset Information

Systems pharmacology of adiposity reveals inhibition of EP300 as a common therapeutic mechanism of caloric restriction and resveratrol in obesity

ABSTRACT: Both caloric restriction (CR) and resveratrol (RSV) have beneficial effects on obesity. However, the biochemical pathways that mediate the beneficial effects of CR and RSV can be highly interconnected and have not been fully elucidated. To reveal the common therapeutic mechanism of CR and RSV, we performed comparative transcriptome analysis of adipose tissues from diet-induced obese (DIO) zebrafish and obese human. We identified 9 and 7 genes whose expressions were regulated in common by CR and RSV in DIO zebrafish and obese human, respectively. Although the gene lists were not overlapped except for one gene, the gene ontologies enriched in the gene lists were highly overlapped, including adipocyte differentiation, lipid storage and lipid metabolism. Bioinformatic analysis of cis-regulatory sequence of these genes revealed that their transcriptional regulators were also well overlapped, including EP300, HDAC2, CEBPB, CEBPD, FOXA1 and FOXA2. We also identified 15 and 46 genes dysregulated in adipose tissue of DIO zebrafish and obese human, respectively. The bioinformatics analysis identified EP300, HDAC2, and CEBPB as common transcriptional regulators for these genes. EP300 is a histone and lysyl acetyltransferase that modulate the function of histone and various proteins including CEBPB, CEBPD, FOXA1 and FOXA2. We were able to demonstrate that the adiposity in larval zebrafish were significantly reduced by C646, an inhibitor of EP300 that antagonizes acetyl-CoA. The reduction of adiposity by C646 was not significantly different to those by RSV or co-treatment of C646 and RSV. These results suggest that inhibition of EP300 may be a common therapeutic mechanism between CR and RSV in adipose tissue of obese individuals.

ORGANISM(S): Danio rerio

PROVIDER: GSE70281 | GEO | 2015/11/17

SECONDARY ACCESSION(S): PRJNA288154

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. The second contained 180,000 features with each CG containing 8-mer present three times. The first design was better for identification of binding motifs, while the second was better for quantification. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. This methodology can be used to identify new methylated DNA sequences preferentially bound by TF, which may be functional in vivo. To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. The second contained 180,000 features with each CG containing 8-mer present three times. The first design was better for identification of binding motifs, while the second was better for quantification. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. EMSA confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50X methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. This methodology can be used to identify new methylated DNA sequences preferentially bound by TF, which may be functional in vivo. Protein binding microarray (PBM) experiments were performed for a set of 8 mouse B-ZIP homodimers and one hetrodimer transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded and methylated or unmethylated 44K Agilent microarrays, containing a DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.

Dataset Information

Systems pharmacology of adiposity reveals inhibition of EP300 as a common therapeutic mechanism of caloric restriction and resveratrol in obesity

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure