Structure-based Analysis of DNA Sequence Patterns Guiding Nucleosome Positioningin vitro

Abstract

Recent studies of genome-wide nucleosomal organization suggest that the DNA sequence is one of the major determinants of nucleosome positioning. Although the search for underlying patterns encoded in nucleosomal DNA has been going on for about 30 years, our knowledge of these patterns still remains limited. Based on our evaluations of DNA deformation energy, we developed new scoring functions to predict nucleosome positioning. There are three principal differences between our approach and earlier studies: (i) we assume that the length of nucleosomal DNA varies from 146 to 147 bp; (ii) we consider the anisotropic flexibility of pyrimidine-purine (YR) dimeric steps in the context of their neighbors (e.g., YYRR versus RYRY); (iii) we postulate that alternating AT-rich and GC-rich motifs reflect sequence-dependent interactions between histone arginines and DNA in the minor groove. Using these functions, we analyzed 20 nucleosome positions mapped in vitro at single nucleotide resolution (including clones 601, 603, 605, the pGUB plasmid, chicken β-globin and three 5S rDNA genes). We predicted 15 of the 20 positions with 1-bp precision, and two positions with 2-bp precision. The predicted position of the '601' nucleosome (i.e., the optimum of the computed score) deviates from the experimentally determined unique position by no more than 1 bp -an accuracy exceeding that of earlier predictions.Our analysis reveals a clear heterogeneity of the nucleosomal sequences which can be divided into two groups based on the positioning 'rules' they follow. The sequences of one group are enriched by highly deformable YR/YYRR motifs at the minor-groove bending sites SHL ±3.5 and ±5.5, which is similar to the α-satellite sequence used in most crystallized nucleosomes. Apparently, the positioning of these nucleosomes is determined by the interactions between histones H2A/H2B and the terminal parts of nucleosomal DNA. In the other group (that includes the '601' clone) the same YR/YYRR motifs occur predominantly at the sites SHL ±1.5. The interaction between the H3/H4 tetramer and the central part of the nucleosomal DNA is likely to be responsible for the positioning of nucleosomes of this group, and the DNA trajectory in these nucleosomes may differ in detail from the published structures.Thus, from the stereochemical perspective, the in vitro nucleosomes studied here follow either an X-ray-like pattern (with strong deformations in the terminal parts of nucleosomal DNA), or an alternative pattern (with the deformations occurring predominantly in the central part of the nucleosomal DNA). The results presented here may be useful for genome-wide classification of nucleosomes, linking together structural and thermodynamic characteristics of nucleosomes with the underlying DNA sequence patterns guiding their positions.

High resolution positioning of intron ends on the nucleosomes

“…New perspectives for the chromatin studies have been recently opened by introduction of a single-base resolution nucleosome mapping technique, based on the chromatin sequence code (Gabdank et al, 2009(Gabdank et al, , 2010aTrifonov, 2010a,b), and on deformational properties of DNA base pair stacks (Cui and Zhurkin, 2010;Tolstorukov et al, 2008;Trifonov, 2010a;Wang et al, 2010). In the high resolution maps the nucleosomes appear as series of several peaks indicating locations of local dyads in the nucleosome DNA.…”

Nucleosome Positioning and Its Role in Gene Regulation in Yeast

“…It establishes that nucleosome occupancies can be explained by systematic diferences in mono-and dinucleotide content between nucleosomal and linker DNA sequences [28] nuMap Implements the YR and W/S schemes to predict nucleosome positioning at high resolution. This methodology is based on the sequence-dependent anisotropic bending [29,30] NPRD Compiles the available experimental data on locations and characteristics of nucleosome formation sites (NFSs). The object of the database is a single NFS described in an individual entry [31] AWNFR An algorithm based on down-sampling operation and footprint in wavelet [32] ICM Allows users to assess nucleosome stability and fold sequences of DNA into putative chromatin templates.…”

Training-free atomistic prediction of nucleosome occupancy

“…In fact, the guiding-dinucleotide model, which accounts for both periodicity and positional dependence, currently predicts single nucleosome positions most accurately (13). Other powerful knowledge-based approaches for predicting nucleosome organization (14) and single-nucleosome positioning (15) were developed using global and position-dependent preferences for k-mer sequences (14,15). Interestingly, it has been reported (16) that much simpler measures, such as percentage of bases that were G or C (the GC content), could also be used to produce surprisingly accurate predictions of nucleosome occupancy.…”

“…Although sequence based methods (11)(12)(13)(14)(15) are predictive and cost-effective, they cannot directly account for any structural information, which is especially relevant if one is to distinguish identical sequence motifs with distinct epigenetic marks. Furthermore, current structure-based methods (17)(18)(19)(20) either rely on statistical data from prior experiments (17,18) and lack the information needed to capture epigenetic changes (e.g., methylation) or use fragments (19,20) so that the physical system is not modeled as a whole.…”

“…For example, nucleotides adjacent to the motifs may need to be taken into account. One may use a more detailed model by considering longer motifs (12,14,15), however longer motifs require more statistical data that is often not available. Sequence-based methods can, however, collect statistical information on any observed data including our computed occupancy profiles for normal and methylated DNA.…”