Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions

A multiscale computational study

Rosana Collepardo-Guevara, Guillem Portella, Michele Vendruscolo, Daan Frenkel, Tamar Schlick, Modesto Orozco

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)10205-10215
Number of pages11
JournalJournal of the American Chemical Society
Volume137
Issue number32
DOIs
StatePublished - Aug 19 2015

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Acetylation
Epigenomics
Chromatin
Gene expression regulation
Histones
Molecular dynamics
Compaction
Nuclear magnetic resonance
Availability
Nucleosomes
Fibers
Computer simulation
Ions
Lysine
Gene Expression Regulation
Molecular Dynamics Simulation
Monte Carlo simulation

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions : A multiscale computational study. / Collepardo-Guevara, Rosana; Portella, Guillem; Vendruscolo, Michele; Frenkel, Daan; Schlick, Tamar; Orozco, Modesto.

In: Journal of the American Chemical Society, Vol. 137, No. 32, 19.08.2015, p. 10205-10215.

Research output: Contribution to journalArticle

Collepardo-Guevara, Rosana ; Portella, Guillem ; Vendruscolo, Michele ; Frenkel, Daan ; Schlick, Tamar ; Orozco, Modesto. / Chromatin unfolding by epigenetic modifications explained by dramatic impairment of internucleosome interactions : A multiscale computational study. In: Journal of the American Chemical Society. 2015 ; Vol. 137, No. 32. pp. 10205-10215.
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