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Rapid spontaneous accessibility of nucleosomal DNA
Gu Li1, Marcia Levitus, Carlos Bustamante
1Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208-3500, USA.
Nature Structural & Molecular Biology
|December 8, 2004
Summary
Proteins access DNA within nucleosomes through rapid, spontaneous unwrapping and rewrapping events. This dynamic process allows proteins access to DNA on biologically relevant timescales.
Area of Science:
- Molecular Biology
- Epigenetics
- Biochemistry
Background:
- DNA is packaged into nucleosomes, with the DNA wrapped around histone proteins.
- This packaging sterically occludes DNA, posing challenges for proteins that need to access it.
- The mechanisms by which proteins access DNA within nucleosomes are not fully understood.
Purpose of the Study:
- To investigate the dynamics of nucleosome conformational changes.
- To determine the rates of spontaneous DNA unwrapping and rewrapping from nucleosomes.
- To elucidate how proteins gain access to DNA buried within nucleosomes.
Main Methods:
- Measurement of spontaneous nucleosome conformational changes.
- Quantification of DNA unwrapping and rewrapping rates.
- Analysis of nucleosome dynamics at the single-molecule level.
Main Results:
- Nucleosomal DNA undergoes rapid spontaneous conformational changes.
- DNA remains fully wrapped for approximately 250 ms before unwrapping.
- DNA rewraps within approximately 10-50 ms after unwrapping.
- Spontaneous unwrapping provides rapid protein access to buried DNA.
Conclusions:
- Nucleosome dynamics facilitate protein access to DNA.
- Remodeling factors can be recruited to nucleosomes via these rapid DNA dynamics.
- Nucleosomal DNA rewrapping, not unwrapping, is the primary barrier for RNA polymerase entry.