Global Egr1-miRNAs binding analysis in PMA-induced K562 cells using ChIP-Seq

J Biomed Biotechnol. 2010:2010:867517. doi: 10.1155/2010/867517. Epub 2010 Aug 3.

Abstract

Although much is known about microRNAs' regulation in gene expression and their contributions in cell fate, to date, globally lineage-(cell-) specific identification of the binding events between a transcription factor and its targeting microRNA genes is still waiting for elucidation. In this paper, we performed a ChIP-Seq experiment to find the targeting microRNA genes of a transcription factor, Egr1, in human erythroleukemia cell line K562. We found Egr1 binding sites near the promoters of 124 distinct microRNA genes, accounting for about 42% of the miRNAs which have high-confidence predicted promoters (294). We also found EGR1 bind to another 63 pre-miRNAs. We chose 12 of the 187 microRNAs with Egr1 binding sites to perform ChIP-PCR assays and the positive binding signal from ChIP-PCR confirmed the ChIP-Seq results. Our experiments provide the first global binding profile between Egr1 and its targeting microRNA genes in PMA-treated K562 cells, which may facilitate the understanding of pathways controlling microRNA biology in this specific cell line.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Chromatin Immunoprecipitation / methods*
  • Computational Biology
  • Early Growth Response Protein 1 / genetics*
  • Gene Expression Regulation, Neoplastic
  • Humans
  • K562 Cells
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • Sequence Analysis, DNA / methods*

Substances

  • EGR1 protein, human
  • Early Growth Response Protein 1
  • MicroRNAs