A novel method to predict regulatory regions based on histone mark landscapes in macrophages

Immunobiology. 2013 Nov;218(11):1416-27. doi: 10.1016/j.imbio.2013.07.006. Epub 2013 Jul 26.


Macrophages as phagocytes and professional antigen presenting cells play critical roles in both innate and adaptive immunity. Main transcription factors acting during their differentiation and function are known, but the behavior and co-operation of these factors still remained unexplored. We introduce a new approach to map nucleosome-free regions using exclusively active enhancer and core promoter marking histone modification ChIP-seq data. We could detect approximately 56,000 potential active enhancers/promoters showing different lengths and histone modification shapes. Beside the highly enriched PU.1 and C/EBP sites, we could also detect binding sites for RUNX and AP-1, as well as for the MiT (MITF-TFE) family and MEF2 proteins. The PU.1 and C/EBP transcription factors are known for transforming cells into macrophages. The other transcription factors found in this study can play a role in macrophages as well, since it is known that the MiT family proteins are responsible for phagocytic activity and the MEF2 proteins specify monocytic differentiation over the granulocyte direction. Our results imply that this method can provide novel information about transcription factor organization at enhancers and core promoters as well as about the histone modifications surrounding regulatory regions in any immune or other cell types.

Keywords: BWA; Burrows–Wheeler Alignment Tool; CRE; ChIP; DMEM; Dulbecco's modified Eagle's medium; ENCODE; Enhancer; FAIRE; HLH; HOMER; HTH; Histone modification; IGV; Macrophage; NFR; NOR; Nucleosome-free region; PU.1; Promoter; SRA; TSS; bZIP; basic leucine zipper; cAMP response element; chromatin immunoprecipitation; encyclopedia of DNA elements; formaldehyde-assisted isolation of regulatory elements; helix–loop–helix; helix–turn–helix; hypergeometric optimization of motif EnRichment; integrative genomics viewer; nucleosome occupied region; nucleosome-free region; sequence read archive; transcription start site.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Bone Marrow Cells / cytology*
  • Bone Marrow Cells / immunology
  • Cell Differentiation / immunology
  • Chromosome Mapping
  • Core Binding Factor alpha Subunits / genetics
  • Core Binding Factor alpha Subunits / metabolism
  • DNA-Binding Proteins / analysis
  • Histones / genetics*
  • Histones / metabolism
  • MEF2 Transcription Factors / genetics
  • MEF2 Transcription Factors / metabolism
  • Macrophages / cytology*
  • Macrophages / immunology
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Microphthalmia-Associated Transcription Factor / genetics
  • Microphthalmia-Associated Transcription Factor / metabolism
  • Nucleosomes / genetics
  • Promoter Regions, Genetic / genetics
  • Protein Binding / genetics
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Sequence Analysis, DNA
  • Transcription Factor AP-1 / genetics
  • Transcription Factor AP-1 / metabolism
  • Transcriptional Activation


  • Core Binding Factor alpha Subunits
  • DNA-Binding Proteins
  • Histones
  • MEF2 Transcription Factors
  • Microphthalmia-Associated Transcription Factor
  • Nucleosomes
  • Transcription Factor AP-1