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Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.

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Collepardo-Guevara, R 
Portella, G 
Vendruscolo, Michele  ORCID logo
Schlick, T 


Histone tails and their epigenetic modifications play crucial roles in gene expression regulation by altering the architecture of chromatin. However, the structural mechanisms by which histone tails influence the interconversion between active and inactive chromatin remain unknown. Given the technical challenges in obtaining detailed experimental characterizations of the structure of chromatin, multiscale computations offer a promising alternative to model the effect of histone tails on chromatin folding. Here we combine multimicrosecond atomistic molecular dynamics simulations of dinucleosomes and histone tails in explicit solvent and ions, performed with three different state-of-the-art force fields and validated by experimental NMR measurements, with coarse-grained Monte Carlo simulations of 24-nucleosome arrays to describe the conformational landscape of histone tails, their roles in chromatin compaction, and the impact of lysine acetylation, a widespread epigenetic change, on both. We find that while the wild-type tails are highly flexible and disordered, the dramatic increase of secondary-structure order by lysine acetylation unfolds chromatin by decreasing tail availability for crucial fiber-compacting internucleosome interactions. This molecular level description of the effect of histone tails and their charge modifications on chromatin folding explains the sequence sensitivity and underscores the delicate connection between local and global structural and functional effects. Our approach also opens new avenues for multiscale processes of biomolecular complexes.



Acetylation, Chromatin, Epigenesis, Genetic, Histones, Lysine, Magnetic Resonance Spectroscopy, Molecular Dynamics Simulation, Monte Carlo Method, Nucleosomes

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Journal of the American Chemical Society

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American Chemical Society
European Commission (654812)
Engineering and Physical Sciences Research Council (EP/I001352/1)
This work was supported by the European Union Seventh Framework Programme (FP7/2007–2013) [275096 to R.C.-G. and M.O.]; the European Union’s Horizon 2020 research and innovation programme under a Marie Sklodowska-Curie grant [654812 to G.P. and M.V.]; Sara Borrell Fellowships [to G.P. and M.O.]; the Spanish MINECO [BIO2012–32868 to M.O.]; the Spanish National Institute of Bioinformatics (INB) [to M.O.]; the European Research Council (ERC) [Advanced Investigator Grant to M.O.]; the National Science Foundation [MCB0316771 to T. S.]; the National Institutes of Health [R01 GM55164 to T. S.]; Philip Morris USA [to T. S.]; and Philip Morris International [to T.S.]. M.O. is an ICREA-Academia fellow.