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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
Published on: September 10, 2013
Oligonucleotide sequence motifs as nucleosome positioning signals
Clayton K Collings1, Alfonso G Fernandez, Chad G Pitschka
1Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.
Plos One
|June 10, 2010
Summary
Specific DNA sequence patterns, particularly eight consensus sequences, drive nucleosome positioning. While DNA sequence influences nucleosome placement in vivo, its role is less dominant than in vitro.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Nucleosomes are fundamental units of DNA packaging in eukaryotes.
- Nucleosome positioning is crucial for regulating DNA accessibility and gene expression.
- Understanding sequence determinants of nucleosome positioning is key to deciphering genome regulation.
Purpose of the Study:
- To identify sequence patterns governing nucleosome positioning.
- To compare sequence contributions to nucleosome positioning in vitro and in vivo.
- To elucidate the role of specific tetranucleotides in nucleosome formation.
Main Methods:
- Analysis of tetranucleotide periodicities in yeast nucleosomal DNA libraries (in vitro reconstitution).
- Identification of consensus sequences and their contribution to periodicities.
- Comparison of in vitro findings with genome-wide in vivo data from yeast and C. elegans.
- Application of experimental and bioinformatic approaches.
Main Results:
- Eight consensus sequences account for most tetranucleotide and dinucleotide periodicities in vitro.
- These tetranucleotides are critical for preferred nucleosome formation in vitro.
- Similar tetranucleotide profiles exist in vivo, indicating DNA sequence influence.
- Tetranucleotide periodicities are significantly stronger in vitro than in vivo.
Conclusions:
- A defined subset of tetranucleotides dictates preferred nucleosome occupancy.
- These tetranucleotides are the primary source of dinucleotide periodicities in positioned nucleosomes.
- DNA sequence is a significant, but not solely dominant, factor in in vivo nucleosome positioning.
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