ELK1 uses different DNA binding modes to regulate functionally distinct classes of target genes

PLoS Genet. 2012;8(5):e1002694. doi: 10.1371/journal.pgen.1002694. Epub 2012 May 10.


Eukaryotic transcription factors are grouped into families and, due to their similar DNA binding domains, often have the potential to bind to the same genomic regions. This can lead to redundancy at the level of DNA binding, and mechanisms are required to generate specific functional outcomes that enable distinct gene expression programmes to be controlled by a particular transcription factor. Here we used ChIP-seq to uncover two distinct binding modes for the ETS transcription factor ELK1. In one mode, other ETS transcription factors can bind regulatory regions in a redundant fashion; in the second, ELK1 binds in a unique fashion to another set of genomic targets. Each binding mode is associated with different binding site features and also distinct regulatory outcomes. Furthermore, the type of binding mode also determines the control of functionally distinct subclasses of genes and hence the phenotypic response elicited. This is demonstrated for the unique binding mode where a novel role for ELK1 in controlling cell migration is revealed. We have therefore uncovered an unexpected link between the type of binding mode employed by a transcription factor, the subsequent gene regulatory mechanisms used, and the functional categories of target genes controlled.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actin Cytoskeleton / genetics
  • Actin Cytoskeleton / metabolism
  • Binding Sites / genetics*
  • Cell Movement / genetics*
  • DNA-Binding Proteins* / genetics
  • DNA-Binding Proteins* / metabolism
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • Genome, Human / genetics
  • Humans
  • Promoter Regions, Genetic
  • Protein Structure, Tertiary / genetics
  • RNA Interference
  • RNA, Small Interfering
  • ets-Domain Protein Elk-1* / genetics
  • ets-Domain Protein Elk-1* / metabolism


  • DNA-Binding Proteins
  • ELK1 protein, human
  • RNA, Small Interfering
  • ets-Domain Protein Elk-1