Book of Abstracts: Albany 2005
Superhelical Path of Nucleosomal DNA is Controlled by Base-pair Slide
We report the unexpected effect of base-pair Slide on the superhelical path of nucleosomal DNA. Typically, analyses of DNA structure in the nucleosome core particle focus on the angular parameters (Roll and Tilt) at individual dimeric steps (1). As anticipated by energetic arguments (2), nucleosomal DNA bends anisotropically -- changes in Roll are greater than those in Tilt (1). The most pronounced DNA deformations fall into two categories: relatively sharp kinks localized at single dimeric steps and ?smooth? bends spread over several steps (1). Both modes of bending are accompanied by base-pair Shift and Slide -- in-plane, shear deformations heretofore thought simply to facilitate tight packing of DNA against protein (1).
We now find that the Slide deformations actually control the superhelical trajectory of nucleosomal DNA. Our analysis of the best resolved nucleosome core particle structure, NCP147 (3), shows that the 26 Å superhelical pitch of the DNA can be reduced to 3 Å if the Slide is set to zero at all base-pair steps but other parameters remain unchanged (Figs. 1A, B). On the other hand, comparable changes in Shift have almost no effect on the DNA folding pathway. The zig-zag distortion of the DNA axis is presented in more detail in Figures 1C, D. The sharp bending of CA:TG dimers into the minor groove at sites of large negative Roll is accompanied by positive Slide; such changes in Slide are well known to relieve purine-purine clashes (4) and have also been shown (5) to reduce the sugar-phosphate backbone stress caused by large negative Roll. By contrast, the major groove kinks of nucleosomal DNA are characterized by negative Slide. Thus, steps with alternating positive and negative Slide (separated by 5-6 bp) produce the left-handed DNA superhelix (5) visible in Figure 1A.
Our analysis shows that the base-pair Slide accounts for ∼90% of the superhelical pitch of NCP147, while the impact of base-pair Rise is negligible. This observation shows how ?real? nucleosomal DNA differs from the idealized ribbon used conventionally to represent superhelical DNA (6). Because the ribbon model ignores the shearing of base-pair planes, the superhelical pitch is defined entirely by the projection of the base-pair Rise on the superhelical axis. The change in ?global? Twist of DNA is proportional to the pitch of the superhelix. Here we see that DNA wraps around the histone core via Roll and Slide without significant changes in ?global? Twist (compared to free DNA). This very different mechanism of supercoiling undoubtedly influences the topological properties of DNA in chromatin.
Our assessment of the energetic cost of the deformations (7) imposed on DNA in the nucleosome shows that the deformations in Slide make a contribution to the total elastic energy which is comparable to, if not greater than, that due to the deformations in Roll. Thus, our results suggest that the ability of a sequence to accommodate the Slide deformations is one of the key factors of nucleosome positioning. The most pronounced Slide deformations in NCP147 occur at YR dimeric steps (CA:TG and TA:TA). In this regard, it is important that YR dimers also appear to be the most flexible in terms of Slide variation in other protein-bound DNA structures (7). Thus, we suggest that proper positioning of YR dimeric steps is one of the factors determining nucleosome positioning. But, if earlier it was assumed that the YR location is critical for diminishing the DNA bending energy, now we show that base-pair Sliding is no less important.
Figure 1: Effect of base-pair sliding on the DNA superhelical path in the nucleosome core particle: (A) NCP147 structure (2); (B) model structure with Slide = 0 at all base-pair steps. The DNA trajectories are represented by the lines connecting the centers of consecutive base pairs. Superhelical locations are indicated by numbers. The most severe Slide deformations are located at the sites where the minor-groove edges of the DNA base pairs face the histones (denoted in blue in A). (C), (D) Detailed views of the minor-groove kink with large positive Slide at the TG:CA dimer step (#38) at superhelical location -3.5. The DNA orientation in (C) is the same as in (A), and DNA is rotated by 90° in (D). The kinked step is shown in blue, the rest of DNA is in gray.
References and Footnotes
Michael Y. Tolstorukov1
1Laboratory of Experimental and Computational Biology