Repertoires of the Nucleosome-Positioning Dinucleotides Thomas Bettecken1*, Edward N. Trifonov2,3 1 CAGT – Center for Applied Genotyping, Max Planck Institute of Psychiatry, Munich, Germany, 2 Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa, Israel, 3 Division of Functional Genomics and Proteomics, Faculty of Science, Masaryk University, Brno, Czech Republic Abstract It is generally accepted that the organization of eukaryotic DNA into chromatin is strongly governed by a code inherent in the genomic DNA sequence. This code, as well as other codes, is superposed on the triplets coding for amino acids. The history of the chromatin code started three decades ago with the discovery of the periodic appearance of certain dinucleotides, with AA/TT and RR/YY giving the strongest signals, all with a period of 10.4 bases. Every base-pair stack in the DNA duplex has specific deformation properties, thus favoring DNA bending in a specific direction. The appearance of the corresponding dinucleotide at the distance 10.4 xn bases will facilitate DNA bending in that direction, which corresponds to the minimum energy of DNA folding in the nucleosome. We have analyzed the periodic appearances of all 16 dinucleotides in the genomes of thirteen different eukaryotic organisms. Our data show that a large variety of dinucleotides (if not all) are, apparently, contributing to the nucleosome positioning code. The choice of the periodical dinucleotides differs considerably from one organism to another. Among other 10.4 base periodicities, a strong and very regular 10.4 base signal was observed for CG dinucleotides in the genome of the honey bee A. mellifera. Also, the dinucleotide CG appears as the only periodical component in the human genome. This observation seems especially relevant since CpG methylation is well known to modulate chromatin packing and regularity. Thus, the selection of the dinucleotides contributing to the chromatin code is species specific, and may differ from region to region, depending on the sequence context. Citation: Bettecken T, Trifonov EN (2009) Repertoires of the Nucleosome-Positioning Dinucleotides. PLoS ONE 4(11): e7654. doi:10.1371/journal.pone.0007654 Editor: Cathal Seoighe, National University of Ireland Galway, Ireland Received June 1, 2009; Accepted October 2, 2009; Published November 2, 2009 Copyright: 2009 Bettecken, Trifonov. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The work was mostly funded by the regular budget of the authors. Partial support by the Israel Science Foundation (grant 222/09 to ENT) is appreciated. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: bettecken@mpipsykl.mpg.de Introduction A number of different dinucleotides have been indicated to be involved in the nucleosome positioning sequence pattern [1–5]. However, only for the dinucleotides AA, TT, RR and YY a prominent periodical appearance in natural chromatin DNA sequences could be demonstrated directly by positional autocorre- lation (distance) analysis [1,6–7]. These signal dinucleotides are preferentially appearing at distances which are multiples of the nucleosome DNA structural period, 10.460.2 bases. This value has been estimated by several independent approaches – from beat effect analysis of DNaseI digestion data [8], from superhelicity of the nucleosome DNA [9], from data on digestion by various nucleases (for review see reference [10]), and most recently - from analysis of DNA sequence periodicity, and from known coordinates of phosphates in the crystallized nucleosomes [11]. The 10.4 base periodicity of dinucleotides today is an undebated hallmark of nucleosome positioning. There are certain phase relationships between various dinucleotides, reflecting preferential orientations of the respective base-pair stacks, this way facilitating unidirectional bending of the nucleosome DNA. These phase relationships can be expressed in form of matrices of bendability [12,2,5], where, according to the recent data of Gabdank et al. [5], the highest positional selectivity is displayed by the dinucleotides AT and CG. Participation of CG dinucleotides in the nucleosome positioning has been demonstrated experimentally [13–15] and implicated from computational analysis of the Alu sequence repeats [16]. In this work we applied the distance analysis technique for determining which of the 16 dinucleotides display the 10.4 base periodicity in thirteen diverse eukaryotic organisms for which the complete, or at least nearly complete, genome sequences are available. Results A total of 208 periodicity plots for 13 eukaryotic genomes and all 16 dinucleotides are calculated, revealing that each one of the 16 dinucleotides clearly shows the periodical positioning in at least one of the genomes analyzed. In Fig. 1 the most prominent examples of emerging periodicities are shown, as calculated from the genomes of A. thaliana (AA and GG) and A. mellifera (CG and GC). All histograms display the maxima at positions closely corresponding to multiples of 10.4 bases, all the way to 104 bases and even beyond. This appears especially clear in the case of CG in A. mellifera. Here the maxima are observed at positions that are the closest integers to the 10.4 xn series: 21(20.8), 31(31.2), 41(41.6), 52(52.0), 72(72.8), 83(83.2), 93(93.6), 104(104.0), 114(114.4), 125(124.8). In the other three graphs the fit is almost as good. Because of some reason, probably due to various noise components of the distance histograms, the 1st peaks in Fig. 1 appear rather at positions 11 or 12, up to 1.6 bases off the expected 10.4 base position. Other clear examples of the easily visible periodicities, for the remaining 12 dinucleotides are presented in Fig. 2, where three or PLoS ONE | www.plosone.org 1 November 2009 | Volume 4 | Issue 11 | e7654