Local protein–DNA interactions may determine nucleosome positions on yeast plasmids

@article{Thoma1985LocalPI,
  title={Local protein–DNA interactions may determine nucleosome positions on yeast plasmids},
  author={Fritz Thoma and Robert T. Simpson},
  journal={Nature},
  year={1985},
  volume={315},
  pages={250-252}
}
The structure of the nucleosome core particle, the basic structural subunit of chromatin, is well known1. Although nucleosomes often appear to be positioned randomly with respect to DNA sequences, in some cases they seem to occupy precisely defined positions on the DNA2–8. The yeast plasmid TRP1ARS1 contains three precisely positioned, stable nucleosomes, I, II and III, which are flanked by nuclease-sensitive regions.5 Our aim in the present study was to determine whether the positions of these… 
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87 Citations
Background Citations
15
Methods Citations
5
Results Citations
1

87 Citations

Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin.
  • F. Thoma
  • Biology
    Journal of molecular biology
  • 1986
Mapping of nucleosome positions.
  • F. Thoma
  • Biology
    Methods in enzymology
  • 1996
Distal chromatin structure influences local nucleosome positions and gene expression
TLDR
This study shows that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called ‘antinucleosomal elements’ like poly(dA:dT) tracts being key determinants of nucleosomes positions.
TGGA repeats impair nucleosome formation.
TLDR
These sequences are identified by selecting those that refrain from nucleosome formation from a large pool of synthetic DNA fragments with a central region of 146 random base-pairs fitted with adapters for PCR amplification used for in vitro salt-induced reconstitution of nucleosomes under thermodynamic equilibrium conditions.
Nucleosome Positioning on Yeast Plasmids Is Determined Only by the Internal Signal of DNA Sequence Occupied by the Nucleosome
TLDR
It was found that nucleosomes' positioning on the NPTII gene and their mutual disposition, namely the spacing between neighboring nucleosome (linker length) are determined by the location of positioning signals only.
Structural analysis of a reconstituted DNA containing three histone octamers and histone H5.
Nucleosome Positioning by a Yeast Repressor Complex
Sequence periodicities in chicken nucleosome core DNA.
Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast
TLDR
High resolution tiling arrays are used to examine the contributions of two general regulatory factors, Abf1 and Rap1, to nucleosome occupancy in Saccharomyces cerevisiae to indicate that DNA-binding transcription factors affect chromatin structure, and probably dynamics, throughout the genome to a much greater extent than previously appreciated.
The translational placement of nucleosome cores in vitro determines the access of the transacting factor suGF1 to DNA.
TLDR
It is proposed that a direct protein-protein steric clash between suGF1 and the histone octamer is the most likely determinant in modulating the binding of suGF2 to its nucleosomally wrapped binding site, and suggests that in vivo suGF 1, like TBP, NF1 and heat shock factor, may require a complementary nucleosome disrupting activity.
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References

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TLDR
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TLDR
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TLDR
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A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome
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