Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states

Blood. 2012 Jun 14;119(24):e161-71. doi: 10.1182/blood-2012-01-402453. Epub 2012 May 1.

Abstract

Cellular differentiation is orchestrated by lineage-specific transcription factors and associated with cell type-specific epigenetic signatures. In the present study, we used stage-specific, epigenetic "fingerprints" to deduce key transcriptional regulators of the human monocytic differentiation process. We globally mapped the distribution of epigenetic enhancer marks (histone H3 lysine 4 monomethylation, histone H3 lysine 27 acetylation, and the histone variant H2AZ), describe general properties of marked regions, and show that cell type-specific epigenetic "fingerprints" are correlated with specific, de novo-derived motif signatures at all of the differentiation stages studied (ie, hematopoietic stem cells, monocytes, and macrophages). We validated the novel, de novo-derived, macrophage-specific enhancer signature, which included ETS, CEBP, bZIP, EGR, E-Box and NF-κB motifs, by ChIP sequencing for a subset of motif corresponding transcription factors (PU.1, C/EBPβ, and EGR2), confirming their association with differentiation-associated epigenetic changes. We describe herein the dynamic enhancer landscape of human macrophage differentiation, highlight the power of genome-wide epigenetic profiling studies to reveal novel functional insights, and provide a unique resource for macrophage biologists.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Base Sequence
  • CCAAT-Enhancer-Binding Protein-beta / metabolism
  • Cell Differentiation / genetics*
  • Disease / genetics
  • Early Growth Response Protein 2 / metabolism
  • Enhancer Elements, Genetic / genetics*
  • Epigenesis, Genetic*
  • Genetic Variation
  • Histones / metabolism
  • Humans
  • Macrophages / cytology
  • Macrophages / metabolism
  • Methylation
  • Models, Biological
  • Molecular Sequence Data
  • Monocytes / cytology*
  • Monocytes / metabolism*
  • Nucleotide Motifs / genetics
  • Organ Specificity / genetics
  • Protein Binding
  • Proto-Oncogene Proteins / metabolism
  • Trans-Activators / metabolism
  • Transcription Factors / metabolism*

Substances

  • CCAAT-Enhancer-Binding Protein-beta
  • EGR2 protein, human
  • Early Growth Response Protein 2
  • Histones
  • Proto-Oncogene Proteins
  • Trans-Activators
  • Transcription Factors
  • proto-oncogene protein Spi-1