Kinetic proofreading of chromatin remodeling: from gene activation to gene repression and back

Raghvendra P Singh; Guillaume Brysbaert; Marc F Lensink; Fabrizio Cleri; Ralf Blossey; Raghvendra P Singh; Guillaume Brysbaert; Marc F Lensink; Fabrizio Cleri; Ralf Blossey

doi:10.3934/biophy.2015.4.398

AIMS Biophysics

2015, Volume 2, Issue 4: 398-411. doi: 10.3934/biophy.2015.4.398

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Kinetic proofreading of chromatin remodeling: from gene activation to gene repression and back

1.
University of Lille, CNRS UMR 8576 Unit´e de Glycobiologie Structurale et Fonctionnelle(UGSF) and FRABio FR3688, 59000 Lille, France
2.
University of Lille, CNRS UMR8520, Institut d'Electronique, de Micro electronique et de Nanotechnologie (IEMN), 59000 Lille, France

Received: 06 August 2015 Accepted: 21 August 2015 Published: 31 August 2015

ATP-dependent chromatin remodeling is the active displacement of nucleosomes along or off DNA induced by chromatin remodeling complexes. This key process of gene regulation in eukaryote organisms has recently been argued to be controlled by a kinetic proofreading mechanism. In this paper we present a discussion of the current understanding of this process. We review the case of gene repression via heterochromatin formation by remodelers from the ISWI family and then discuss the activation of the IFN-β gene, where the displacement of the nucleosome is initiated by histone tail acetylations by the enzyme GCN5 which are required for the recruitment of SWI-SNF remodelers. We quantify the speci city of the acetylation step in the remodeling process by peptide docking simulations.
- chromatin,
- histone code,
- remodeler,
- bromodomain,
- nucleosome,
- histone
Citation: Raghvendra P Singh, Guillaume Brysbaert, Marc F Lensink, Fabrizio Cleri, Ralf Blossey. Kinetic proofreading of chromatin remodeling: from gene activation to gene repression and back[J]. AIMS Biophysics, 2015, 2(4): 398-411. doi: 10.3934/biophy.2015.4.398

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Abstract

ATP-dependent chromatin remodeling is the active displacement of nucleosomes along or off DNA induced by chromatin remodeling complexes. This key process of gene regulation in eukaryote organisms has recently been argued to be controlled by a kinetic proofreading mechanism. In this paper we present a discussion of the current understanding of this process. We review the case of gene repression via heterochromatin formation by remodelers from the ISWI family and then discuss the activation of the IFN-β gene, where the displacement of the nucleosome is initiated by histone tail acetylations by the enzyme GCN5 which are required for the recruitment of SWI-SNF remodelers. We quantify the speci city of the acetylation step in the remodeling process by peptide docking simulations.

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