NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes

Sci Rep. 2016 Jul 26;6:30255. doi: 10.1038/srep30255.

Abstract

Mutations in mouse and human Nfe2, Fli1 and Runx1 cause thrombocytopenia. We applied genome-wide chromatin dynamics and ChIP-seq to determine these transcription factors' (TFs) activities in terminal megakaryocyte (MK) maturation. Enhancers with H3K4me2-marked nucleosome pairs were most enriched for NF-E2, FLI and RUNX sequence motifs, suggesting that this TF triad controls much of the late MK program. ChIP-seq revealed NF-E2 occupancy near previously implicated target genes, whose expression is compromised in Nfe2-null cells, and many other genes that become active late in MK differentiation. FLI and RUNX were also the motifs most enriched near NF-E2 binding sites and ChIP-seq implicated FLI1 and RUNX1 in activation of late MK, including NF-E2-dependent, genes. Histones showed limited activation in regions of single TF binding, while enhancers that bind NF-E2 and either RUNX1, FLI1 or both TFs gave the highest signals for TF occupancy and H3K4me2; these enhancers associated best with genes activated late in MK maturation. Thus, three essential TFs co-occupy late-acting cis-elements and show evidence for additive activity at genes responsible for platelet assembly and release. These findings provide a rich dataset of TF and chromatin dynamics in primary MK and explain why individual TF losses cause thrombopocytopenia.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / genetics
  • Core Binding Factor Alpha 2 Subunit / genetics*
  • Enhancer Elements, Genetic
  • Gene Expression Regulation, Developmental / genetics
  • Histones / genetics
  • Humans
  • Megakaryocytes / metabolism*
  • Mice
  • NF-E2 Transcription Factor, p45 Subunit / genetics*
  • Promoter Regions, Genetic
  • Protein Binding / genetics
  • Proto-Oncogene Protein c-fli-1 / genetics*
  • Transcriptional Activation / genetics*

Substances

  • Chromatin
  • Core Binding Factor Alpha 2 Subunit
  • Fli1 protein, mouse
  • Histones
  • NF-E2 Transcription Factor, p45 Subunit
  • Nfe2 protein, mouse
  • Proto-Oncogene Protein c-fli-1
  • Runx1 protein, mouse