Facilitated diffusion of a DNA binding protein on chromatin

Facilitated diffusion accounts for the rapid rate of association of many bacterial DNA binding proteins with specific DNA sequences in vitro. In this mechanism the proteins bind at random to non‐specific sites on the DAN and diffuse (by ‘sliding’ or ‘hopping’) along the DNA chain until they arrive a...

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Bibliographic Details
Published in:The EMBO journal 1986-12, Vol.5 (12), p.3313-3319
Main Authors: Hannon, R., Richards, E.G., Gould, H.J.
Format: Article
Language:English
Subjects:
Animals
Biological and medical sciences
Chickens
chromatin
Chromatin - metabolism
Chromatin. Chromosome
Diffusion
DNA-binding protein
DNA-Binding Proteins - metabolism
DNA-Directed RNA Polymerases - antagonists & inhibitors
Erythrocytes - metabolism
Escherichia coli
Escherichia coli - enzymology
Fundamental and applied biological sciences. Psychology
Histones - metabolism
Kinetics
Models, Structural
Molecular and cellular biology
Molecular genetics
Nucleosomes - metabolism
Nucleosomes - ultrastructure
Promoter Regions, Genetic
RNA polymerase
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Summary:Facilitated diffusion accounts for the rapid rate of association of many bacterial DNA binding proteins with specific DNA sequences in vitro. In this mechanism the proteins bind at random to non‐specific sites on the DAN and diffuse (by ‘sliding’ or ‘hopping’) along the DNA chain until they arrive at their specific functional sites. We have investigated whether such a mechanism can operate in chromatin by using a bacterial DNA binding protein, Escherichia coli RNA polymerase, that depends on linear diffusion to locate initiation sites on DNA. We have measured the competition between chromatin and its free DNA for the formation of initiation complexes. Only the short linker segments exposed by the removal of histone H1 are available for interaction with the polymerase, but the sparsely distributed promoter sites on the linker DNA of such a polynucleosome chain are located at the same rate as those on DNA. We conclude that the polymerase is free to migrate between the separate linker DNA segments of a polynucleosome chain to reach a promoter site. This chain thus permits the ‘hopping’ of proteins between neighboring linker segments in their search for a target site on the accessible DNA.
ISSN:0261-4189
1460-2075
DOI:10.1002/j.1460-2075.1986.tb04645.x