Molecular Biology Reports

, Volume 39, Issue 6, pp 6781–6789 | Cite as

Genome-wide identification of palmitate-regulated immediate early genes and target genes in pancreatic beta-cells reveals a central role of NF-κB

  • Hyung Jin Choi
  • Seungwoo Hwang
  • Se-Hee Lee
  • You Ri Lee
  • Jiyon Shin
  • Kyong Soo Park
  • Young Min Cho


Free fatty acid-induced pancreatic β-cell dysfunction plays a key role in the pathogenesis of type 2 diabetes. We conducted gene expression microarray analysis to comprehensively investigate the transcription machinery of palmitate-regulated genes in pancreatic β-cells in vitro. In particular, mouse pancreatic βTC3 cells were treated with palmitate in the presence or absence of cycloheximide (CHX), which blocks protein synthesis and thereby allows us to distinguish immediate early genes (IEGs) from their target genes. The microarray experiments identified 34 palmitate-regulated IEGs and 74 palmitate-regulated target genes. In silico promoter analysis revealed that transcription factor binding sites for NF-κB were over-represented, regulating approximately one-third of the palmitate-regulated target genes. In cells treated with CHX, nfkb1 showed an up-regulation by palmitate, suggesting that NF-κB could be an IEG. Functional enrichment analysis of 27 palmitate-regulated genes with NF-κB binding sites showed an over-representation of genes involved in immune response, inflammatory response, defense response, taxis, regulation of cell proliferation, and regulation of cell death pathways. Electrophoretic mobility shift assay showed that palmitate stimulates NF-κB activity both in the presence and absence of CHX. In conclusion, by identifying IEGs and target genes, the present study depicted a comprehensive view of transcription machinery underlying palmitate-induced inflammation and cell proliferation/death in pancreatic β-cells and our data demonstrated the central role of NF-κB.


Fatty acids, Nonesterified Genes, Immediate-early NF-kappa B Oligonucleotide array sequence analysis Palmitates Insulin-secreting cells 



Free fatty acid




Immediate early gene


Transcription factor


Transcription factor binding site


Differentially expressed genes


Matrix metalloproteinase



This work was supported by Grants from the National Research Foundation (M10753020005-07N5302-00500), the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program and Seoul National University Hospital intramural research fund (0620083589), South Korea. We thank Dominique Glauser for helpful discussion on the confounding effects of cycloheximide.

Supplementary material

11033_2012_1503_MOESM1_ESM.doc (318 kb)
Supplementary material 1 (DOC 318 kb)


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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Hyung Jin Choi
    • 1
  • Seungwoo Hwang
    • 2
  • Se-Hee Lee
    • 1
  • You Ri Lee
    • 1
  • Jiyon Shin
    • 1
  • Kyong Soo Park
    • 1
  • Young Min Cho
    • 1
  1. 1.Department of Internal MedicineSeoul National University College of MedicineSeoulKorea
  2. 2.Korean Bioinformation Center, Korea Research Institute of Bioscience and BiotechnologyDaejeonKorea

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