Computational study of remodeling in a nucleosomal array

Chromatin remodelers: a concise introduction for biophysicists

Chromatin remodelers are molecular motors that act on nucleosomes: they move them along DNA or (dis-)assemble them. Despite the fact that they perform essential regulatory functions in cells-their deregulation can contribute to the development of cancers and lead to cell death-chromatin remodelers have only received meager attention in the biophysics community so far. In this short text, we attempt to present the key features of this interesting class of enzymes obtained with different experimental and theoretical methods, thereby providing a concise introduction for biophysicists to further stimulate interest in their properties.

ISWI catalyzes nucleosome sliding in condensed nucleosome arrays

How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. Here we investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner, qualitatively agree with our data. We speculate that monkey-bar mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.

ISWI catalyzes nucleosome sliding in condensed nucleosome arrays

How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. We investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner qualitatively agree with our data. We speculate that 'monkey-bar' mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.

Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments

Chromatin remodelers are multidomain enzymatic motor complexes that displace nucleosomes along DNA and hence "remodel chromatin structure," i.e., they dynamically reorganize nucleosome positions in both gene activation and gene repression. Recently, experimental insights from structural biology methods and remodeling assays have substantially advanced the understanding of these key chromatin components. Here we confront the kinetic proofreading scenario of chromatin remodeling, which proposes a mechanical link between histone residue modifications and the ATP-dependent action of remodelers, with recent experiments. We show that recent high-throughput data on nucleosome libraries assayed with remodelers from the Imitation Switch family are in accord with our earlier predictions of the kinetic proofreading scenario. We make suggestions for experimentally verifiable predictions of the kinetic proofreading scenarios for remodelers from other families.

Why Do Nucleosomes Unwrap Asymmetrically?

Nucleosomes, DNA spools with a protein core, engage about three-quarters of eukaryotic DNA and play a critical role in chromosomal processes, ranging from gene regulation, recombination, and replication to chromosome condensation. For more than a decade, micromanipulation experiments where nucleosomes are put under tension, as well as the theoretical interpretations of these experiments, have deepened our understanding of the stability and dynamics of nucleosomes. Here we give a theoretical explanation for a surprising new experimental finding: nucleosomes wrapped onto the 601 positioning sequence (the sequence used in most laboratories) respond highly asymmetrically to external forces by always unwrapping from the same end. Using a computational nucleosome model, we show that this asymmetry can be explained by differences in the DNA mechanics of two very short stretches on the wrapped DNA portion. Our finding suggests that the physical properties of nucleosomes, here the response to forces, can be tuned locally by the choice of the underlying base-pair sequence. This leads to a new view of nucleosomes: a physically highly varied set of DNA-protein complexes whose properties can be tuned on evolutionary time scales to their specific function in the genomic context.