Nucleosome positioning by genomic excluding-energy barriers

Abstract

Recent genome-wide nucleosome mappings along with bioinformatics studies have confirmed that the DNA sequence plays a more important role in the collective organization of nucleosomes in vivo than previously thought. Yet in living cells, this organization also results from the action of various external factors like DNAbinding proteins and chromatin remodelers. To decipher the code for intrinsic chromatin organization, there is thus a need for in vitro experiments to bridge the gap between computational models of nucleosome sequence preferences and in vivo nucleosome occupancy data. Here we combine atomic force microscopy in liquid and theoretical modeling to demonstrate that a major sequence signaling in vivo are high-energy barriers that locally inhibit nucleosome formation rather than favorable positioning motifs. We show that these genomic excluding-energy barriers condition the collective assembly of neighboring nucleosomes consistently with equilibrium statistical ordering principles. The analysis of two gene promoter regions in Saccharomyces cerevisiae and the human genome indicates that these genomic barriers direct the intrinsic nucleosome occupancy of regulatory sites, thereby contributing to gene expression regulation.nucleosome statistical ordering | chromatin-mediated gene regulation | physical modeling | atomic force microscopy T he recent flowering of tiled micro-arrays (1, 2) and chipsequencing (3) approaches has provided an unprecedented opportunity to elucidate the extent to which the DNA sequence participates in the positioning of nucleosomes observed in vivo along eukaryotic chromosomes (4, 5). Among the results indicating that nucleosome formation is facilitated by the DNA sequence, it is known that some genomic sequences presenting a ≈10 bp periodicity of some di-or trinucleotides (e.g., AA/TT) show higher affinity for nucleosomes (6-9). The periodic positioning of these motifs over a few helical pitches would contribute to a global spontaneous curvature of DNA that would favor its wrapping on the histone surface (10, 11). However, the statistical significance of this 10-bp periodicity nucleosomal positioning signal remains a subject of great debate (4,5,12,13). According to previous reports (12, 13), in Saccharomyces cerevisiae (1, 2), no more than 20% of the in vivo nucleosome positioning, above what is expected by chance, is determined by intrinsic signals in the genomic DNA. An alternative antipositioning signaling picture has recently emerged from bioinformatic studies (13-16) that bring to light the fact that the sequence is actually highly predictive of the nucleosome-free regions (NFRs) observed in vivo at gene promoters and terminations (1, 2). Excluding-energy barriers coded in the sequence would locally impair nucleosome formation and nonlocally influence the overall nucleosomal chromatin organization according to equilibrium statistical ordering principles (14, 17). Furthermore, by conditioning an activatory or inhibitory nucleosomal chromatin environment, these genomic energy b...

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

“…Furthermore, a strongly positioned histone octamer may position other histone octamers, in a process known as statistical positioning (50). Both these (Table S1) effects are taken into account by applying Percus' equation (34)(35)(36)(37) to the energy landscape for nucleosome positioning (Materials and Methods). The Percus equation introduces a fourth parameter, the chemical potential, defining the average DNA affinity of the histone octamers, which depends on their relative concentrations.…”

“…Physically this effect can be modeled as a fluid of 1D rods with a finite size, distributed in a free energy landscape (34)(35)(36)(37). The nucleosomes are in contact with a thermal bath, which allows the nucleosomes to move freely over the DNA to find their energetically most favorable positions.…”

“…We can use the free energy landscape obtained from Eq. 4 to calculate the thermodynamic equilibrium density of histone octamer positions, nðiÞ, using Percus's equation (34)(35)(36)(37) where μ is the chemical potential of the interaction between histones and DNA and σ the footprint of a histone octamer.…”

Fitness landscape for nucleosome positioning

“…Our Wrapping DNA around histones necessitates specific elastic deformations of its double strand. We evaluate the energy cost of these deformations using the model of references (20,28). The local energy cost depends on sequence content, because different nucleotide triplets have different a priori deformations in the unbound state.…”

“…We call this phenotype the histone binding affinity of the segment. Our analysis uses the thermodynamic model and algorithm of references (20,28) (for details, see Methods). This model successfully predicts the nucleosome positioning observed under in vitro conditions, that is, without the competitive binding of transcription factors (20).…”