Wrapping eukaryotic genomic DNA around histone octamers to form an array of nucleosome core particles influences the functions encoded in the underlying sequence. The proteins that comprise the nucleosome core particle are among the most highly constrained [26
], an observation that underscores their biological significance. Recent improvements in high-throughput genome profiling methods have yielded high-resolution nucleosome occupancy maps for a number of species [27
]. Examination of nucleosome-bound sequences has led to the conclusion that nucleosome positioning is sequence-directed [30
], yet the histone octamer makes no base-specific contacts with DNA [17
]. This scenario leads to the intriguing hypothesis that DNA structure, and not sequence per se
, can direct nucleosome positioning.
Properties of DNA that influence nucleosome positioning can be segregated into two general categories—those that are conducive to nucleosome formation, and those that exclude nucleosomes. A recent study performed a statistical analysis of sequence features that are predictive of nucleosome occupancy, and concluded that G+C content is the most dominant [33
]. While this is an informative conclusion, the DNA structural property of minor groove width also was found to be important and, unsurprisingly, G+C content generally correlates with many other DNA structural features [34
]. Consistent with this finding is extensive evidence that long A-tracts—stretches of consecutive deoxyadenosine nucleotides on one strand of the double helix—strongly influence nucleosome organization [35
]. A-tracts are enriched in eukaryotic genomes, and have unique structural and mechanical properties that likely resist the DNA structural deformation required for nucleosome formation. Systematic mutagenesis and subsequent functional analysis of short A/T-rich sequences found that they can act as core promoter elements [36
]. To explain this finding, the authors proposed complementary and redundant mechanisms of nucleosome exclusion by A/T-rich sequences, and binding site recognition by TFIID.
Other efforts to explain nucleosome positioning focused more on physical properties of DNA. For example, nucleosome occupancy in yeast and fly can be predicted using only DNA flexibility and curvature [37
]. Another group developed the Repositioned Mutation (RM) test, which is an elegant algorithm designed to detect evolutionary selection for nucleosome positioning by comparing patterns at orthologous loci (originally proposed in [38
]). Implementation of the RM test on the yeast genome revealed that the biophysical property of nucleosomal deformation energy is preserved across species so as to maintain chromatin organization in non-coding regions [39
]. Together, these results suggest that physical properties of DNA are crucial for chromatin organization.
Two recent studies that used different methods to carefully analyze nucleotide substitution patterns in the yeast genome are particularly insightful about nucleosome positioning codes and the selective pressures that can act upon them. In the first study, the authors performed a thorough analysis of substitution patterns overlaid on high resolution nucleosome positioning data [40
]••. Knowing that G+C content and A-tracts influence nucleosome positioning (see above), the authors focused on substitution patterns that would affect these signals in regions that positioning data show are important (for example, well-defined nucleosomes or nucleosome-depleted regions). Remarkably, they found regionally linked compensatory substitutions that serve to maintain nucleosome-positioning dynamics. They conclude that local sequence composition is influenced by nucleosome organization. The other study also looked at substitution patterns, but took a different approach in which the authors measured the effects of substitutions on a structurally based model of nucleosomal deformation energy [41
]••. They observed a strong anti-correlation between substitution frequency and the DNA structure-based energetics of nucleosome formation. Together, these studies demonstrate the functional conservation of chromatin organization through natural selection operating on DNA shape-based signals.
Selection for DNA structural features that maintain nucleosomal positioning signals could result in a large fraction of the genome being under structural constraint. This could be considered a kind of low-level and pervasive form of DNA structural selection, whereas DNA structural selection acting on transcription factor binding sites would likely be less pervasive and, possibly, more intense. It is interesting to note that a DNA structure-based code for nucleosome positioning has been found in protein coding regions [42
]•, indicating the compatible superimposition of the genetic code and a nucleosome positioning code. An intriguing possibility is that variations in local DNA shape that are encoded along genomic sequences could have a profound impact on chromatin organization, and therefore the evolution of regulatory systems.