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Nucleosome organization on Kluyveromyces lactis centromeric DNAs
Sonia Mattei1, Beatrice Sampaolese, Pasquale De Santis
1Department of Genetic and Molecular Biology, Università di Roma La Sapienza, Piazzale A. Horo 5-00185, Rome, Italy.
Biophysical Chemistry
|June 7, 2002
Summary
Budding yeast centromeres preferentially assemble specialized nucleosomes. This study reveals canonical nucleosomes on centromeric DNA are more stable than bulk DNA nucleosomes, explaining this preference.
Area of Science:
- Molecular Biology
- Genetics
- Biophysics
Background:
- Budding yeast centromeres exhibit preferential assembly of specialized nucleosomes.
- This preference may stem from differential nucleosome stability (specialized vs. canonical) or canonical nucleosome instability relative to bulk nucleosomes.
Purpose of the Study:
- To evaluate the thermodynamic stability of canonical nucleosomes on Kluyveromyces lactis centromeric DNAs.
- To investigate the role of sequence-dependent DNA elasticity in nucleosome stability and positioning.
Main Methods:
- Competitive reconstitution assay to determine thermodynamic stability.
- Theoretical modeling based on sequence-dependent DNA elasticity.
- DNA 'footprinting' to analyze nucleosome positioning.
Main Results:
- All five known K. lactis centromeric DNAs can organize canonical nucleosomes with higher thermodynamic stability than bulk DNA nucleosomes.
- Centromeric canonical nucleosomes exhibit multiple, rotationally phased positioning along the nucleosome dyad axis.
- A strong agreement was found between theoretical predictions and experimental results.
Conclusions:
- Canonical nucleosomes on centromeric DNA are thermodynamically more stable than bulk nucleosomes.
- Sequence-dependent DNA elasticity is a key factor in the thermodynamic stability and positioning of centromeric nucleosomes.
- Multiple nucleosome positioning sites are crucial for understanding the transition to specialized nucleosomes upon interaction with centromere protein complexes.