Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Distinct nucleosome organization around p53 response elements associated with cell cycle arrest and apoptosis

DNA is severely deformed in tetrameric complex with the tumor suppressor protein p53, both in solution and in co-crystal structures. The DNA deformations occur not only at the CWWG motifs in the p53 half sites, but also in the central region of a full site, YYRR. As a result, the DNA fragment is bent in such a way that p53 tetramer is located on the external side of the DNA loop. The overall shape of the p53-bound DNA (bending and sliding) resembles nucleosomal DNA, suggesting that p53 may recognize its cognate site embedded in nucleosome. Recent studies established unambiguously that p53 is a nucleosome-binding protein. In particular, the p53 site in a nucleosome is accessible if it is bent in the direction similar to that found in the p53-DNA co-crystals; the site becomes inaccessible if the orientation is changed by ~180° (see Figure). This implies that the rotational setting of a p53 site in nucleosomes is critical for its accessibility, which may have a direct impact on how p53 recognizes its target binding sites in the chromatin context.


Figure. The p53 site embedded in nucleosome is accessible for direct p53 binding (A) if the center of the site is separated by ~10n+5 bp from the dyad. The p53 site is inaccessible (B) if the center of the site is separated by ~10n bp from the dyad. The YR score profiles (11) exhibit distinct patterns for the accessible (C) and inaccessible sites (D). The (C) and (D) profiles are typical for the CCA- and Apo-sites, respectively.

We illustrate the functional importance of this idea by comparing the p53 sites associated with cell cycle arrest (CCA-sites) and sites associated with apoptosis (Apo-sites), the two extreme cellular outcomes after the p53 activation. To elucidate the rotational setting of p53 sites in nucleosomal DNA, we developed computational approach (Cui & Zhurkin, 2010) based on well-established DNA sequence patterns related to nucleosome positioning. Importantly, we found that the CCA-sites are oriented in such a way that they tend to be ‘open’ and ‘exposed’ on the nucleosomal surface. This result is corroborated by human nucleosomes mapped in high resolution (Gaffney et al., 2012). The nucleosome dyad positions are “out of phase” with the CCA-sites, separated by ~10n+5 bp from the site centers. In other words, the CCA-sites embedded in nucleosomes are accessible for direct p53 recognition, thereby facilitating p53 binding and subsequent gene induction.

By contrast, our computations suggest that most of the Apo-sites have a different rotational setting from the CCA-sites, consistent with the high-resolution nucleosome mapping. That is, the Apo-sites in general are likely to be ‘closed’ in the chromatin context. This would hinder direct p53 binding to DNA, and require additional factors like chromatin remodeling complexes to expose the Apo-sites, which may account for the ‘delayed’ kinetics of apoptotic genes in vivo.


    Cui, F. & Zhurkin, V. B. (2010). Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro. J. Biomol. Struct. Dyn 27, 821-841.

    Gaffney, D. J., McVicker, G., Pai, A. A., Fondufe-Mittendorf, Y. N., Lewellen, N., Michelini, K., Widom, J., Gilad, Y. & Pritchard, J. K. (2012). Controls of nucleosome positioning in the human genome. PLoS Genet. 8, e1003036.

Feng Cui 1
Victor B. Zhurkin 2

1Thomas H. Gosnell School of Life Sciences
Rochester Institute of Technology
Rochester, NY 14623
2Laboratory of Cell Biology
National Cancer Institute, NIH
Bethesda, MD 20892

Phone: (585)475-4115
Fax: (585)475-2398
Phone: (301)496-8913
Fax: (301)402-4724