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

  title={Local protein–DNA interactions may determine nucleosome positions on yeast plasmids},
  author={Fritz Thoma and Robert T. Simpson},
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… 
Mapping of nucleosome positions.
  • F. Thoma
  • Biology
    Methods in enzymology
  • 1996
Distal chromatin structure influences local nucleosome positions and gene expression
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.
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
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.
Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast
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.
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.


Quantitative analysis of the digestion of yeast chromatin by staphylococcal nuclease.
The yeast genome seems to have variable spacing of the nucleaseresistant cores, to produce the average repeat size of about 160 base pairs, and the presence of more than one species of monomer and dimer at certain times of digestion suggests a possible heterogeneity in the subunit structure.
SV40 viral minichromosome: preferential exposure of the origin of replication as probed by restriction endonucleases.
Findings suggest that the arrangement of nucleosomes in the compact SV40 minichromosomes is nonrandom at least with regard to sequences near the origin of DNA replication.
Structure of the nucleosome core particle at 7 Å resolution
The crystal structure of the nucleosome core particle has been solved to 7 Å resolution and the central turn of superhelix and H3 · H4 tetramer have dyad symmetry, but the H2A · H2B dimers show departures due to interparticle associations.