Binding of NF-κB to nucleosomes: effect of translational positioning, nucleosome remodeling and linker histone H1

PLoS Genet. 2013;9(9):e1003830. doi: 10.1371/journal.pgen.1003830. Epub 2013 Sep 26.

Abstract

NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility shift assay to investigate the binding of NF-κB to nucleosomal templates. We show that NF-κB p50 homodimer is able to bind to its recognition sequence, when it is localized at the edge of the core particle, but not when the recognition sequence is at the interior of the nucleosome. Remodeling of the nucleosome by the chromatin remodeling machine RSC was not sufficient to allow binding of NF-κB to its recognition sequence located in the vicinity of the nucleosome dyad, but RSC-induced histone octamer sliding allowed clearly detectable binding of NF-κB with the slid particle. Importantly, nucleosome dilution-driven removal of H2A-H2B dimer led to complete accessibility of the site located close to the dyad to NF-κB. Finally, we found that NF-κB was able to displace histone H1 and prevent its binding to nucleosome. These data provide important insight on the role of chromatin structure in the regulation of transcription of NF-κB dependent genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • Chromatin / genetics*
  • Chromatin / ultrastructure
  • DNA-Binding Proteins / genetics
  • Dimerization
  • Histones / genetics*
  • Histones / metabolism
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex
  • NF-kappa B / genetics
  • NF-kappa B / metabolism*
  • Nucleosomes / genetics*
  • Nucleosomes / metabolism
  • Protein Binding
  • Protein Biosynthesis*
  • Ultraviolet Rays
  • Xenopus / genetics

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Histones
  • NF-kappa B
  • Nucleosomes
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex

Grant support

The research leading to these results has received funding from: the European Community's Seventh Framework Programme FP7/2007–2013 under Grant agreement numbers 222008 (“Model-in”) and 289611 (“HEM_ID”); the Association pour la Recherche sur le Cancer - ARC (Grant SFI20101201424); the Agence Nationale de la Recherche: ANR-09-BLAN-NT09-485720 ‘CHROREMBER’ and ANR-12-BSV5-0017-03 Blanc SVSE 5 “CHROME” (to DA and SD). SD acknowledges the funding from La Ligue Nationale contre le Cancer (Equipe Labelliseé La Ligue). Funding for open access charge: the Agence Nationale de la Recherche, grant “CHROME.” The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.