Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Nucleosome Positioning Sequences

Using in vitro selection methods we have isolated the DNA sequences that form the most stable nucleosomes among those occurring in the mouse genome. The selected DNA has distinct sequence features that can be attributed to their nucleosome positioning ability. Among the sequences were those with TATAAACGCC repeats; tracts of 3-4 adenines spaced every 10 bp, and CA- and CAG-runs. We then performed selection in reverse, isolating the DNA sequences that are most reluctant to nucleosome formation starting from a synthetic library. Here, the most interesting sequences contained TGGA and TGA runs. We discuss the selected sequences in terms of their positioning abilities and their possible roles in living systems.

    References and Footnotes
  1. H. Widlund, H. Cao, S. Simonson, E. Magnusson, T. Simonson, J. D. Kahn, D. M. Crothers, P. E. Nielsen, M. Kubista. Identification and Characterization of genomic nucleosome positioning sequences. J. Mol. Biol., 267, 807-817 (1997).
  2. A.-C. Th?str?m, P. Lowary, H. Widlund, M. Kubista & J. Widom. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol. 288, 213-229 (1999).
  3. H. R. Widlund, P. N. Kuduvalli, M. Bengtsson, H. Cao, T. D. Tullius & M. Kubista. Nucleosome structural features and intrinsic properties of the (TATAAACGCC)-repeat sequence. J. Biol. Chem. 274, 31847-31852 (1999).
  4. H. Cao, H. Widlund, T. Simonsson & M. Kubista. TGGA-repeats impair nucleosome formation. J. Mol. Biol. 281, 253-260 (1998).
  5. H Widlund, J Vitolo, C. Thiriet, J Hayes. DNA sequence-dependent contributions of core histone tails to nucleosome stability: differential effects of acetylation and proteolytic tail removal. Biochemistry 39, 3835-3841 (2000).

H. Widlund, C. Hui, T. Simonsson and M. Kubista

Department of Molecular Biotechnology. Chalmers University of Technology, G?teborg, SE-412 96, Sweden. Mikael.Kubista@molbiotech.chalmers.se