Oct4 interacts with subnucleosomal particles generated by Brg1 at enhancers

Mammalian SWI/SNF complexes (mSWI/SNF) are ATP-dependent chromatin remodelling factors that possess tumour suppressor properties. Brg1 (Smarca4), the catalytic subunit of mSWI/SNF, is essential for chromatin opening at enhancers, but the detailed mechanism of this activity remains unclear. Using mou...

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Published inbioRxiv
Main Authors Nocente, Marina C, Mesihovic, Anida, Drouineau, Emilie, Albawardi, Waad, Dulary, Cecile, Ribierre, Florence, Picaud, Helene, Alibert, Olivier, Jean-Christophe Aude, Gilbert, Nick, Ochsenbein, Francoise, Chantalat, Sophie, Gerard, Matthieu
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 16.09.2022
Subjects
BRG1 protein
Chromatin remodeling
Deoxyribonucleic acid
DNA
Enhancers
Genomics
Histones
Molecular weight
Nuclease
Nucleosomes
Oct-4 protein
Phenotypes
Sucrose
Transcription factors
Tumor suppressor genes
Tumors
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Summary:Mammalian SWI/SNF complexes (mSWI/SNF) are ATP-dependent chromatin remodelling factors that possess tumour suppressor properties. Brg1 (Smarca4), the catalytic subunit of mSWI/SNF, is essential for chromatin opening at enhancers, but the detailed mechanism of this activity remains unclear. Using mouse embryonic stem (ES) cells, we show that Brg1 generates subnucleosomal particles which protect genomic DNA fragments of 50-80 bp in length from micrococcal nuclease (MNase) digestion. These particles, which contain all four histones H3, H4, H2A, and H2B, sediment in sucrose gradients with an apparent molecular weight markedly inferior to that of canonical nucleosomes. Genome-wide analysis of the positioning of these particles provides strong evidence that they arise from the splitting of Brg1-targeted nucleosomes into hemisomes. In vivo, these hemisome-like particles are bound by Oct4 (Pou5f1), a transcription factor essential for the maintenance of the ES cell phenotype. Oct4 has a mode of interaction with these particles that is distinct from its binding to accessible, histone-free DNA. Whereas Oct4 binds the latter substrate at the level of its consensus DNA motif, its interaction with the subnucleosome persists even when Oct4 motifs are removed from the particle, suggesting that Oct4 binding is stabilized by contacts with histones. Our data establish that one critical activity of Brg1 at enhancers involves splitting selected nucleosomes into subnucleosomes, which are major genomic binding targets for transcription factors. Competing Interest Statement The authors have declared no competing interest. Footnotes * order of authors
DOI:10.1101/2022.09.15.507958