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Comment
. 2014 Dec 9;111(49):17344-5.
doi: 10.1073/pnas.1418978111. Epub 2014 Dec 2.

Increased subtlety of transcription factor binding increases complexity of genome regulation

Peter H von Hippel  1
Affiliations
Comment

Increased subtlety of transcription factor binding increases complexity of genome regulation

Peter H von Hippel. Proc Natl Acad Sci U S A. .
No abstract available

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Conflict of interest statement

The author declares no conflict of interest.

Figures

Fig. 1.
Fig. 1.
TF binding interactions with specific and nonspecific DNA. (A) Schematic representations of binding interactions of TF (here represented by Escherichia coli lac R) with various DNA binding sites. Arrows indicate DNA base-pair sequence-specific contacts, “+” charge signs indicate basic amino acid residue contacts with DNA phosphates, and recessed symbols indicate interactions that are not “formed” in the complexes shown. Specific TF–DNA binding involves both base-pair–specific and charge–charge contacts, whereas nonspecific binding involves no base-pair–specific contacts and (here, for lac R) additional charge–charge interactions. Intermediate (nonconsensus) binding forms (1) would fall between these extreme forms and likely involve both base-specific and charge–charge interactions. The lower schematic shows a model of the nonspecifically bound form “sliding” on the DNA in a 1D random walk, accompanied by the displacement of condensed monovalent cations from the DNA (12, 18). Reprinted with permission from ref. 12. (B) Known structures for the free, nonspecifically bound, and specifically bound lac R–DNA complexes (19). Reprinted with permission from ref. 19. (C) The “window of specificity” concept in which specific TF target site occupancy is plotted against log [TF] (for details, see text). The top x axis indicates the estimated number of TF molecules present in an idealized E. coli cell (1 μm3 estimated volume) at the TF concentrations shown. These numbers should also apply roughly to a eukaryotic cell nucleus of about this size. Reprinted from ref. 14.
See this image and copyright information in PMC

Comment on

References

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