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Diabetologia

pp 1–13 | Cite as

Genome-wide profiling of histone H3K27 acetylation featured fatty acid signalling in pancreatic beta cells in diet-induced obesity in mice

  • Takao Nammo
  • Haruhide Udagawa
  • Nobuaki Funahashi
  • Miho Kawaguchi
  • Takashi Uebanso
  • Masaki Hiramoto
  • Wataru Nishimura
  • Kazuki Yasuda
Article

Abstract

Aims/hypothesis

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.

Methods

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.

Results

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.

Conclusions/interpretation

These results suggest novel roles for DNA-binding proteins and fatty acid signalling in obesity-induced epigenomic regulation of beta cell function.

Data availability

The next-generation sequencing data in the present study were deposited at ArrayExpress.

RNA-Seq:

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.

ChIP-Seq:

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.

Keywords

Epigenetics Fatty acid oxidation Glucose intolerance High-fat diet Histone acetylation Insulin secretion Next-generation sequencing Obesity Pancreatic islets Transcriptome Type 2 diabetes 

Abbreviations

ChIP

Chromatin immunoprecipitation

ChIP-Seq

Chromatin immunoprecipitation coupled with high-throughput sequencing

DAVID

The Database for Annotation, Visualization and Integrated Discovery

DIO

Diet-induced obesity

FOXA1

Forkhead box A1

GABPA

GA repeat binding protein α

GEO

Gene Expression Omnibus

GSIS

Glucose-stimulated insulin secretion

GWAS

Genome-wide association study (studies)

H3K27ac

Histone H3 lysine 27 acetylation

HFD

High-fat diet

HNF1

HNF1 homeobox A

HOMER

Hypergeometric Optimization of Motif EnRichment

IPGTT

Intraperitoneal glucose tolerance test

KEGG

Kyoto Encyclopedia of Genes and Genomes

MAFK

v-maf musculoaponeurotic fibrosarcoma oncogene family protein K

MEF2A

Myocyte enhancer factor 2A

NRF1

Nuclear respiratory factor 1

qPCR

Quantitative PCR

RFXDC2

Regulatory factor X, 7

RNA-Seq

High-throughput RNA sequencing

SICER

Spatial clustering for identification of ChIP-enriched regions

TSS

Transcription start site

Notes

Acknowledgements

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.

Contribution statement

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.

Funding

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.

Supplementary material

125_2018_4735_MOESM1_ESM.pdf (1007 kb)
ESM (PDF 0.98 mb)
125_2018_4735_MOESM2_ESM.xlsx (5.6 mb)
ESM Additional tables (XLSX 5749 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Metabolic Disorder, Diabetes Research Center, Research Institute, National Center for Global Health and MedicineTokyoJapan
  2. 2.Department of Preventive Environment and Nutrition, Institute of Biomedical SciencesTokushima University Graduate SchoolTokushimaJapan
  3. 3.Department of BiochemistryTokyo Medical UniversityTokyoJapan
  4. 4.Department of Molecular BiologyInternational University of Health and Welfare School of MedicineNaritaJapan
  5. 5.Division of Anatomy, Bio-imaging and Neuro-cell ScienceJichi Medical UniversityShimotsukeJapan

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