Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure

Nucleic Acids Res. 1999 Jan 15;27(2):517-25. doi: 10.1093/nar/27.2.517.

Abstract

The organization of DNA into chromatin is important in the regulation of transcription, by influencing the access of transcription factors to their DNA binding sites. Nuclear factor 1 (NF-1) is a transcription factor which binds to DNA constitutively and which interacts with its cognate DNA site with high affinity. However, this affinity is drastically reduced, approximately 100- to 300-fold, when the binding site is organized into a nucleosome. Here we demonstrate that the introduction of stretches of adenines of length 5 nt (A-tracts) on both sides of the NF-1 binding site has a distinct effect on NF-1 binding to a nucleosomal, but not to a free, NF-1 binding site. The position of the A-tracts, relative to the rotational phase of a synthetic DNA bending sequence, the TG-motif, decides whether the NF-1 affinity increases or decreases. The NF-1 binding affinity is seven times stronger when the flanking A-tracts are positioned out-of-phase with the TG-motif than it is when the A-tracts are positioned in-phase with the TG-motif. We demonstrate that this effect correlates with differences in DNA curvature and apparent histone octamer affinity. We conclude that DNA curvature influences the local histone-DNA contacts and hence the accessibility of the NF-1 site in a nucleosome context.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence*
  • Binding Sites
  • CCAAT-Enhancer-Binding Proteins*
  • DNA / chemistry
  • DNA / metabolism
  • DNA-Binding Proteins / metabolism*
  • Histones / metabolism
  • Molecular Sequence Data
  • NFI Transcription Factors
  • Nuclear Proteins
  • Nucleic Acid Conformation
  • Nucleosomes / metabolism*
  • Protein Binding
  • Transcription Factors / metabolism*
  • Y-Box-Binding Protein 1

Substances

  • CCAAT-Enhancer-Binding Proteins
  • DNA-Binding Proteins
  • Histones
  • NFI Transcription Factors
  • Nuclear Proteins
  • Nucleosomes
  • Transcription Factors
  • Y-Box-Binding Protein 1
  • YBX1 protein, human
  • DNA