Genome-wide profiling of histone H3K27 acetylation featured fatty acid signalling in pancreatic beta cells in diet-induced obesity in mice
Epigenetic regulation of gene expression has been implicated in the pathogenesis of obesity and type 2 diabetes. However, detailed information, such as key transcription factors in pancreatic beta cells that mediate environmental effects, is not yet available.
To analyse genome-wide cis-regulatory profiles and transcriptome of pancreatic islets derived from a diet-induced obesity (DIO) mouse model, we conducted chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) of histone H3 lysine 27 acetylation (histone H3K27ac) and high-throughput RNA sequencing. Transcription factor-binding motifs enriched in differential H3K27ac regions were examined by de novo motif analysis. For the predicted transcription factors, loss of function experiments were performed by transfecting specific siRNA in INS-1, a rat beta cell line, with and without palmitate treatment. Epigenomic and transcriptional changes of possible target genes were evaluated by ChIP and quantitative RT-PCR.
After long-term feeding with a high-fat diet, C57BL/6J mice were obese and mildly glucose intolerant. Among 39,350 islet cis-regulatory regions, 13,369 and 4610 elements showed increase and decrease in ChIP-Seq signals, respectively, significantly associated with global change in gene expression. Remarkably, increased H3K27ac showed a distinctive genomic localisation, mainly in the proximal-promoter regions, revealing enriched elements for nuclear respiratory factor 1 (NRF1), GA repeat binding protein α (GABPA) and myocyte enhancer factor 2A (MEF2A) by de novo motif analysis, whereas decreased H3K27ac was enriched for v-maf musculoaponeurotic fibrosarcoma oncogene family protein K (MAFK), a known negative regulator of beta cells. By siRNA-mediated knockdown of NRF1, GABPA or MEF2A we found that INS-1 cells exhibited downregulation of fatty acid β-oxidation genes in parallel with decrease in the associated H3K27ac. Furthermore, in line with the epigenome in DIO mice, palmitate treatment caused increase in H3K27ac and induction of β-oxidation genes; these responses were blunted when NRF1, GABPA or MEF2A were suppressed.
These results suggest novel roles for DNA-binding proteins and fatty acid signalling in obesity-induced epigenomic regulation of beta cell function.
The next-generation sequencing data in the present study were deposited at ArrayExpress.
Dataset name: ERR2538129 (Control), ERR2538130 (Diet-induced obesity)
Repository name and number: E-MTAB-6718 - RNA-Seq of pancreatic islets derived from mice fed a long-term high-fat diet against chow-fed controls.
Dataset name: ERR2538131 (Control), ERR2538132 (Diet-induced obesity)
Repository name and number: E-MTAB-6719 - H3K27ac ChIP-Seq of pancreatic islets derived from mice fed a long-term high-fat diet (HFD) against chow-fed controls.
KeywordsEpigenetics Fatty acid oxidation Glucose intolerance High-fat diet Histone acetylation Insulin secretion Next-generation sequencing Obesity Pancreatic islets Transcriptome Type 2 diabetes
Chromatin immunoprecipitation coupled with high-throughput sequencing
The Database for Annotation, Visualization and Integrated Discovery
Forkhead box A1
GA repeat binding protein α
Gene Expression Omnibus
Glucose-stimulated insulin secretion
Genome-wide association study (studies)
Histone H3 lysine 27 acetylation
HNF1 homeobox A
Hypergeometric Optimization of Motif EnRichment
Intraperitoneal glucose tolerance test
Kyoto Encyclopedia of Genes and Genomes
v-maf musculoaponeurotic fibrosarcoma oncogene family protein K
Myocyte enhancer factor 2A
Nuclear respiratory factor 1
Regulatory factor X, 7
High-throughput RNA sequencing
Spatial clustering for identification of ChIP-enriched regions
Transcription start site
We thank C. B. Wollheim (Lund University, Lund, Sweden; University of Geneva, Geneva, Switzerland) and N. Sekine (University of Geneva) for providing INS-1 cells. We appreciate the assistance given by D. Suzuki, K. Nagase, N. Ishibashi (Lab Managers), H. Shiina and T. Shibuya (Administrative Assistants) (Department of Metabolic Disorder, National Center for Global Health and Medicine). We would like to thank Editage (www.editage.jp) for English language editing.
TN and KY conceived this study. TN and HU performed the experiments. TN performed the computational analyses. TN and KY wrote the manuscript. TN, HU, NF, MK, TU, MH, WN and KY analysed the data, interpreted the results and contributed to discussions. The manuscript was critically reviewed, revised and given final approval by all co-authors. TN and KY are the guarantors of this work.
This work was supported by Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research (KAKENHI), a grant from the National Center for Global Health and Medicine, the Japan Diabetes Foundation (to TN) and JSPS KAKENHI and a grant from the National Center for Global Health and Medicine (to KY). The study sponsors were not involved in the design of the study; the collection, analysis, and interpretation of data; writing the report; or the decision to submit the report for publication.
Duality of interest
The authors declare that there is no duality of interest associated with this manuscript.
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