Using DNA mechanics to predict in vitro nucleosome positions and formation energies

Abstract

In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While competition with other DNA-binding factors and action of chromatin remodeling enzymes significantly affect nucleosome formation in vivo, nucleosome positions in vitro are determined by steric exclusion and sequence alone. We have developed a biophysical model, DNABEND, for the sequence dependence of DNA bending energies, and validated it against a collection of in vitro free energies of nucleosome formation and a set of in vitro nucleosome positions mapped at high resolution. We have also made a first ab initio prediction of nucleosomal DNA geometries, and checked its accuracy against the nucleosome crystal structure. We have used DNABEND to design both strong and weak histone- binding sequences, and measured the corresponding free energies of nucleosome formation. We find that DNABEND can successfully predict in vitro nucleosome positions and free energies, providing a physical explanation for the intrinsic sequence dependence of histone–DNA interactions.

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

“…Indeed, we find that with a 74 bp window the highest predicted binding preference coincides with the experimentally determined 601 dyad ( Fig. 2B) (30). The fact that in vitro reconstitution does not yield nucleosomes at their thermodynamically most favorable positions has been observed by Flaus and Owen-Hughes (41).…”

“…As shown in Fig. 3A, our model is able to locate dyad position(s) within 2 bp, except for the pGUB nucleosome positioning element, where we detect only one of the two mapped dyad positions (30). Altogether, the above shows that the dyad positions of nucleosomes reconstituted on multiple positioning elements can be mapped at bp accuracy by our model.…”

“…We extended this characterization to other nucleosome positioning elements (Table S1) to detect their respective dyad positions, analogous to a previously published study (30), using N ¼ 74 bp, B ¼ 0.2, and p ¼ 10.0 bp. As shown in Fig.…”

“…Having tested the ability to predict the position of single nucleosome positioning elements, we now test whether the model has predictive power for nucleosome binding affinity, as reported for multiple positioning sequences (13,30,45,47,48). In these affinity experiments, the assembly process was dominated by the histone tetramer (40).…”

“…Two different classes of models can be distinguished. The first class is based on the structural parameters of superhelical DNA organized in the nucleosome, as obtained from crystal structures, to predict the propensity to form a nucleosome with sequences other than those present in crystal structures (27)(28)(29)(30). This approach has been applied mainly in single-histone-octamer positioning models and yielded an accuracy of several tens of base pairs.…”