No 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...

No abstract

Nucleotide sequences of DNA regions containing eukaryotic ribosomal promoters were analysed using strategies designed to reveal sequence-directed structural features. DNA curvature, duplex stability and pattern of twist angle variation were studied by computer modelling. Although ribosomal promoters are known to lack sequence homology (unless very closely related species are considered), investigation of these structural characteristics uncovered striking homologies in all the taxonomic groups examined so far. This wide conservation of DNA structures, while DNA sequence is not conserved, suggests that the determined structures are fundamental for ribosomal promoter function. Moreover, this result agrees well with the recent observations showing that RNA polymerase I transcription factors have not evolved as intensively as previously suspected.