A Novel 'Kink-and-Slide' Mechanism of DNA Folding in Chromatin. Implications for Nucleosome Positioning and p53-DNA Binding

Tuesday, September 18, 2007 - 3:00pm - 4:00pm
EE/CS 3-180
Victor Zhurkin (National Cancer Institute)
Despite 30 years of effort, it is still unclear how DNA sequence contributes to the known positioning of nucleosomes. Currently, there is a wide gap between the experimental characterization of positioned nucleosomes in solution and the interpretation of the known high-resolution X-ray structures of nucleosomal DNA. This gap in understanding stems, in our opinion, from the traditional use of a simplified elastic-rod model, in which only the DNA bending and twisting deformations are considered, and the effects of the shearing displacements of adjacent base pairs are neglected. In collaboration with Wilma Olson [1], we have demonstrated that these displacements play a much more important structural role than ever imagined.

First, the lateral Slide deformations observed at sites of local anisotropic bending of DNA define its superhelical trajectory in chromatin. (Note that the nucleosomal DNA twisting remains close, on average, to that in solution [2]. In other words, the 'real' DNA wrapping around the histone core is inconsistent with the conventional model of superhelical DNA, which links changes in superhelical pitch to DNA twisting.) Second, the computed cost of deforming DNA on the nucleosome is sequence specific: in optimally positioned sequences the most easily deformed base-pair steps (CA:TG and TA) occur at sites of large positive Slide and negative Roll (where the DNA bends, or kinks, into the minor groove). Here, we incorporate all the degrees of freedom of 'real' DNA, thereby going beyond the limits of the conventional model - the latter ignores the lateral Slide displacements of base pairs, and as a result, fails to account for the preferable positioning of the TA steps. Indeed, only after lateral Slide displacements are considered, are we able to account for the sequence-specific positioning of nucleosomes in vitro.

In addition to DNA folding in nucleosomes, the shearing deformations are implicated in the sequence-specific recognition of DNA by transcription factors, such as the tumor suppressor protein p53. The DNA bending, twisting and sliding observed in solution upon p53 binding [3] are entirely consistent with the 'Kink-and-Slide' conformation described above. Therefore, structural organization of a p53 binding site in chromatin can regulate its affinity to p53 - for example, exposure of the DNA site on nucleosomal surface (in appropriate orientation) would facilitate the p53 binding. We illustrate the functional importance of this concept by comparing the chromatin organization of two classes of p53 response elements: the high affinity p53 sites inducing cell cycle arrest, and the low affinity sites associated with apoptosis.

Our results indicate that there is a complex interplay between the structural codes encrypted in eukaryotic genomes - one code for DNA packaging in chromatin, and the other code for DNA recognition by regulatory proteins. Rather than being mutually exclusive (as was assumed earlier), the two codes appear to be consistent with each other. At least in some cases, such as p53, the DNA wrapping in nucleosomes can facilitate binding of the transcription factor to its cognate sequence, provided that the latter is properly exposed in chromatin.

[1] Tolstorukov M.Y., Colasanti A.V., McCandlish D., Olson W.K. and Zhurkin V.B. A Novel 'Roll-and-Slide' Mechanism of DNA Folding in Chromatin. Implications for Nucleosome Positioning. J. Mol. Biol. 2007, 371(3): 725-38.

[2] Richmond T.J. and Davey C.A. The structure of DNA in the nucleosome core. Nature 423, 145-150, 2003

[3] Nagaich A.K., Zhurkin V.B., Durell S.R., Jernigan R.L., Appella E. and Harrington R.E. p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting. Proc. Natl. Acad. Sci. USA 96: 1875-1880, 1999.