Physics of Life Reviews 8 (2011) 53–55

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Comment

The nature of DNA sequence preferences for nucleosomepositioning. Comment on ‘Cracking the chromatin code: Precise rule

of nucleosome positioning’ by Trifonov

Andrew Travers ∗

MRC Laboratory for Molecular Biology, Hills Road, Cambridge CB21 4HT, United Kingdom

Received 24 January 2011; accepted 26 January 2011

Available online 31 January 2011

Communicated by M. Frank-Kamenetskii

The sequence signals for precise positioning of the histone octamer on a DNA molecule have long been a matter ofdebate. The review by Trifonov [1] describes the development of an individual and controversial perspective on thisissue. It is generally agreed that an important determinant of positioning – as contrasted with affinity – is the propertyof bending anisotropy [2–4] in which a given sequence confers a preferred direction of bending. This loss of degreesof bending freedom implies that anisotropically bendable sequences will, on average, be stiffer than the most flexibleisotropically bendable sequences.

Three general models of anisotropy have been proposed: that the AA and TT dinucleotide be separated on av-erage by half a double-helical turn and be located where the minor groove is parallel to the direction of curvature[2]; that pyrimidine–purine and purine–pyrimidine dinucleotides be preferentially located where the minor groovepoints respectively away and towards the histone octamer [5]; and finally that the curvature of nucleosomal DNA isaccommodated by alternating blocks of A/T and G/C rich sequences pointing respectively towards and away fromthe octamer [4]. While both the Satchwell et al. [4] and Zhurkin [5] models imply that base-step roll is the principaldeformation responsible for inducing curvature the Trifonov model [3] argues that base-step tilt is the dominant defor-mation. The Satchwell et al. [4] and Trifonov [3] models also differ in the relative phases of AA and TT periodicities.Whereas the Trifonov model [3] predicts that the phases of these two periodicities should differ by ∼180◦ in the rawSatchwell et al. data [4] these two phases are approximately the same [6,7].

The Satchwell et al. data [4] unequivocally demonstrate the average preferred orientation of A/T and G/C richsequences with respect to the histone octamer in chicken erythrocyte nucleosomes, a conclusion supported and rein-forced by recent genomic studies on yeast nucleosomal DNA [8–10]. The structural basis for this preference wouldbe that, on average, as demonstrated in the crystal structures of DNA oligomers, both free and protein-bound [11,12],there is a tendency on average for A/T rich sequences to adopt a narrow minor groove than G/C rich sequences. Thesepreferred conformations would then be compatible with the different average groove widths on the inside and outsideof DNA on the nucleosome. Nevertheless, there are also well-documented examples where G/C-rich sequences arepreferentially located at inward-facing minor grooves on nucleosomal DNA. For example, in the DNA from nucleo-somes reconstituted in vitro using ovine β-lactoglobulin DNA the dinucleotide GG/CC exhibits strong periodicities of

DOI of original article: 10.1016/j.plrev.2011.01.004.* Tel.: +44 1223 891921.

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54 A. Travers / Physics of Life Reviews 8 (2011) 53–55

opposite phase associated with strand reversal, i.e. GG/CC and CC/GG [13]. These nucleosomal DNA sequences alsolack a strong AA/TT periodicity. It is important to realize that these different patterns depend to a certain extent onthe base composition as well as the sequence organisation of the nucleosomal DNA sampled. Thus, these argumentsimply that a more general solution for a preferred bending anisotropy encompassing all base compositions is that theaverage preferred roll angle for outward facing dinucleotides in the minor groove is more positive than that of inwardfacing dinucleotides.

The nucleosome positioning sequence motif, GRAAATTTYC, proposed in the review [1] is consistent with thebendability model of Trifonov [3] but inconsistent with those of both Satchwell et al. [4] and Zhurkin [5]. In particular,the rotational orientations proposed in the review on the one hand for this sequence and on the other those predictedby the Zhurkin model [5] and the Satchwell et al. data [4] are opposite. The Satchwell orientation is strongly favouredby direct experimental evidence. Hydroxyl-radical footprinting has demonstrated that the ‘TATA’ sequence with arepeating TATAAACGCC motif selected by Widlund et al. [14] for high affinity binding to the octamer wraps ona nucleosome with either AT or AA/TT steps placed at inward facing minor grooves and CG or CC/GG base-stepsplaced at outward facing minor grooves [15,16]. This is consistent with the bending orientation predicted by Traversand Klug [6] for the repeating sequences [CAAAATTTTG]n and [AAAAATTTTT]n, both closely related to thesequence motif for positioning deduced in the review. The direction of bending of the former sequence in solutionhas been confirmed by NMR spectroscopy [17]. Similarly, in a FIS–DNA complex, where the DNA curvature iscomparable to that in the nucleosome, the central A/T rich region is again located at an inward-facing minor groove[18]. In the crystal structures of the 601 nucleosomal sequence exactly the same pattern is observed with the A/Trich sequences, in this case the TA dinucleotide, occurring at inward-facing minor grooves and G/C rich sequences atoutward-facing minor grooves [19,20]. Additionally the positioning of an A/T rich narrow minor grooves immediatelyadjacent to the octamer surface would strongly favour interactions with successive spaced arginine residues [21].

Is there a structural preference for base-step deformation? A notable feature of the crystal structures of the nucle-osome core particle is that the largest deformations or kinks (in terms of roll angle extremes) occur at inward-facingminor grooves [22,23]. This suggests that opening the major groove can more easily accommodate an increase inthe exterior circumference induced by tight bending than opening the minor groove. The argument for the rotationalorientation adopted by the universal sequence motif presented in the review assumes the opposite, i.e. that greatestdeformation occurs at outward-facing minor grooves. The postulated reversal of the bending direction between freeand octamer-bound DNA for an anisotropically curved DNA [1] is likely to be energetically unfavourable and thusthe formation of stable nucleosomes on such DNA sequences would be principally favoured not by DNA deformationbut by minimisation of the entropic penalty.

The value of the sequence periodicity is also relevant to the discussion. Experimentally determined periodicityvalues for di- or tri-nucleotides range from ∼9.90 to ∼10.4 bp [24]. The preferred value in the review [1] is at thehigh end of range. In crystal structures of the nucleosome core particle the local helical repeat – corresponding tothe sequence periodicity – varies between 10.13 and 10.30 bp depending on the number of base-pairs in the particle[22,23], while the laboratory repeat, corresponding to the intrinsic DNA helical repeat (which is not the same as thesequence repeat), for a 147 bp particle is 10.43 bp. The available data strongly suggest that the actual average localhelical repeat of nucleosomal DNA can vary significantly. Even within the nucleosome variation in the local sequencerepeat is observed with excellent correspondence between sequence organisation and nuclease digestion profiles [6,25].

References

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dimers. FEBS Lett 1983;158:293–7.[6] Travers AA, Klug A. The bending of DNA in nucleosomes and its wider implications. Phil Trans R Soc London B 1987;317:537–61.[7] Wang JPZ, Widom J. Improved alignment of nucleosome DNA sequences using a mixture model. Nucleic Acids Res 2005;22:6743–55.[8] Mavrich TN, et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res

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