Nucleosomal arrays are one of the fundamental levels of chromatin organization. They often occur in the gene promoter areas, thus being important for transcription regulation. Investigating the effect of variant histone H2A.Z over the dynamic structure of single nucleosomes and their arrays is important for understanding the transcription within chromatin. Recently we highlighted the influence of histone variants over the functional dynamics of single nucleosome. The present work further analyzes the higher order structures of the nucleosome arrays (dimer, trimer and tetramer) with regular histones as well as with H2A.Z variant. The analysis reveals that the modeled nucleosome dimer with both histone types exhibits a completely relaxed motion with respect to the linker DNA. The dimer also possesses the symmetric dynamics as of the monomeric nucleosome more pronounced in the dimer of variant histones. The trimer expresses larger amplitude of dynamics either by keeping the central nucleosome as a rigid one or the edged nucleosome as a rigid domain in the global modes. The tetramer expresses a symmetric coupled dynamics between the two non-adjacent nucleosomes, consistent with the collective motion of the trimer in the second slowest mode. Like those of the dimer, the dynamics of the trimer and tetramer are considerably enhanced by the presence of variant histone H2A.Z as follows from the larger fluctuations in the respective conformations.

MOTIVATION: The subject of our paper is bioinformatics analysis of the distinguishing features of human promoter DNA sequences, in particular of synergetic combinations of core promoter elements therein. We suppose that specific scenarios of transcription initiation are essentially related to various particular implementations of the interaction of basal transcription machinery with promoter DNA, depending on the presence and mutual positioning of core promoter elements. RESULTS: In addition to the combinations of core promoter elements previously experimentally confirmed [TATA box and Initiator (Inr), Downstream Promoter Element (DPE) and Inr, and TFIIB recognition element (BRE) and TATA box] we propose other alternate synergetic combinations: BRE and Inr, BRE and DPE, and TATA and DPE with respective models. The suggestion is based on a high statistical significance of the alternate combinations in promoters, comparable with the significance of the known combinations. We also present arguments that the BRE element is statistically more important than previously thought, and suggest possible mechanisms of action of the core elements in the promoters with multiple transcription start sites. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary information is available at http://bmi.osu.edu/~ilya/synergy/Gershenzon_SuppMat-R.pdf.