Binding of NF-κB to Nucleosomes

Effect of Translational Positioning, Nucleosome Remodeling and Linker Histone H1

Imtiaz Nisar Lone, Manu Shubhdarshan Shukla, John Lalith Charles Richard, Zahary Yordanov Peshev, Stefan Dimitrov, Dimitar Angelov

Research output: Contribution to journalArticle

20 Citations (Scopus)

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.

Original languageEnglish
Article numbere1003830
JournalPLoS Genetics
Volume9
Issue number9
DOIs
Publication statusPublished - Sep 2013
Externally publishedYes

Fingerprint

nucleosomes
Nucleosomes
histones
Histones
positioning
chromatin
gene
Chromatin
accessibility
sliding
dilution
laser
Chromatin Assembly and Disassembly
assay
DNA
Electrophoretic Mobility Shift Assay
Hydroxyl Radical
Genes
lasers
Lasers

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Binding of NF-κB to Nucleosomes : Effect of Translational Positioning, Nucleosome Remodeling and Linker Histone H1. / Lone, Imtiaz Nisar; Shukla, Manu Shubhdarshan; Charles Richard, John Lalith; Peshev, Zahary Yordanov; Dimitrov, Stefan; Angelov, Dimitar.

In: PLoS Genetics, Vol. 9, No. 9, e1003830, 09.2013.

Research output: Contribution to journalArticle

Lone, Imtiaz Nisar ; Shukla, Manu Shubhdarshan ; Charles Richard, John Lalith ; Peshev, Zahary Yordanov ; Dimitrov, Stefan ; Angelov, Dimitar. / Binding of NF-κB to Nucleosomes : Effect of Translational Positioning, Nucleosome Remodeling and Linker Histone H1. In: PLoS Genetics. 2013 ; Vol. 9, No. 9.
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