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Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence
H R Widlund1, P N Kuduvalli, M Bengtsson
1Department of Biochemistry, Lundberg Institute, Chalmers University of Technology, SE 413 90 Göteborg, Sweden. Hans_Widlund@dfci.harvard.edu
The Journal of Biological Chemistry
|November 5, 1999
Summary
Specific DNA sequences with a 10-base pair repeat (TATAAACGCC) show high affinity for nucleosome formation. These sequences exhibit significant flexibility, influencing how nucleosomes position along the genome.
Area of Science:
- Molecular Biology
- Genomics
- Structural Biology
Background:
- Nucleosomes are key structural units of chromatin, essential for genome integrity and transcriptional regulation.
- DNA sequence properties, including flexibility and bending, influence nucleosome formation and positioning.
- Previous work identified genomic nucleosome-positioning sequences with high in vitro nucleosome formation ability.
Purpose of the Study:
- To investigate the intrinsic physical properties of a high-affinity nucleosome-positioning sequence (TATAAACGCC repeat).
- To determine the structural details of the nucleosome formed by this specific DNA sequence.
- To explore the role of DNA flexibility in nucleosome positioning.
Main Methods:
- Analysis of intrinsic physical properties of the DNA sequence.
- Footprinting techniques to analyze nucleosome structure.
- Cyclization kinetics to determine the helical repeat of free DNA.
Main Results:
- The TATAAACGCC sequence exhibits a high affinity for nucleosome formation.
- The DNA sequence has an overall helical repeat of 10.5 base pairs/turn and is highly flexible (25-fold higher J-factor than random DNA).
- Structural analysis reveals specific minor groove orientations (inward at AA steps, outward at CC steps) within the nucleosome.
Conclusions:
- DNA sequence intrinsic properties, particularly flexibility, are critical determinants of nucleosome formation and positioning.
- The identified TATAAACGCC sequence possesses unique physical characteristics that promote high nucleosome affinity.
- Twist flexibility of DNA is a significant factor in the precise translational positioning of nucleosomes, especially around the dyad.