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Quantitative models for accelerated protein dissociation from nucleosomal DNA.

Chen C, Bundschuh R - Nucleic Acids Res. (2014)

Bottom Line: This reduces the rate of transcription factor binding and is a known mechanism for regulation of gene expression via chromatin structure.There are two possible explanations for such an increase in off-rate short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding or (ii) the nucleosome can change the equilibrium between specific and non-specific binding to the DNA.We explicitly model both scenarios and find that dimeric binding can explain a large increase in off-rate while the non-specific binding model cannot be reconciled with the large, experimentally observed increase.

View Article: PubMed Central - PubMed

Affiliation: Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA Center for RNA Biology, The Ohio State University, Columbus, OH, USA.

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Non-specific binding model of TF dissociation from (A) naked DNA and (B and C) from a nucleosome. (A) In the absence of the nucleosome, the TF can slide along the DNA in two directions (black arrows, k1) or dissociate from the DNA (Purple arrow, kns,off). (B) In the presence of a nucleosome, five possibilities for the next step of a certain state exist: (i) and (ii) the TF can slide along both directions in the unwrapped nucleosome (black arrows, k1); (iii) and (iv) the nucleosome can unwrap and rewrap (orange arrows, kunwrap, krewrap); or (v) the TF can dissociate from the unwrapped nucleosome (purple arrow, kns,off). The figure shows LexA binding to a non-specific site. Among all the binding sites, only one site is the specific target for the TF (red dashed line in (A) and (B)) and the others are non-specific binding sites for the TF. (C) Illustration of the minimum distance (d in bp) between the TF and the unwrapping position of the nucleosome. At this minimum distance when the TF binds to DNA, the nucleosome cannot rewrap anymore and the TF can only slide in one direction.
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Figure 3: Non-specific binding model of TF dissociation from (A) naked DNA and (B and C) from a nucleosome. (A) In the absence of the nucleosome, the TF can slide along the DNA in two directions (black arrows, k1) or dissociate from the DNA (Purple arrow, kns,off). (B) In the presence of a nucleosome, five possibilities for the next step of a certain state exist: (i) and (ii) the TF can slide along both directions in the unwrapped nucleosome (black arrows, k1); (iii) and (iv) the nucleosome can unwrap and rewrap (orange arrows, kunwrap, krewrap); or (v) the TF can dissociate from the unwrapped nucleosome (purple arrow, kns,off). The figure shows LexA binding to a non-specific site. Among all the binding sites, only one site is the specific target for the TF (red dashed line in (A) and (B)) and the others are non-specific binding sites for the TF. (C) Illustration of the minimum distance (d in bp) between the TF and the unwrapping position of the nucleosome. At this minimum distance when the TF binds to DNA, the nucleosome cannot rewrap anymore and the TF can only slide in one direction.

Mentions: Analogously to the dimeric binding model, we first build this model in the case that the TF binds to naked DNA. Here, the TF can slide along the DNA in two directions and can also dissociate from the DNA (Figure 3A). Among all the binding sites, only one site is the specific target for the TF and the others are non-specific binding sites for the TF.


Quantitative models for accelerated protein dissociation from nucleosomal DNA.

Chen C, Bundschuh R - Nucleic Acids Res. (2014)

Non-specific binding model of TF dissociation from (A) naked DNA and (B and C) from a nucleosome. (A) In the absence of the nucleosome, the TF can slide along the DNA in two directions (black arrows, k1) or dissociate from the DNA (Purple arrow, kns,off). (B) In the presence of a nucleosome, five possibilities for the next step of a certain state exist: (i) and (ii) the TF can slide along both directions in the unwrapped nucleosome (black arrows, k1); (iii) and (iv) the nucleosome can unwrap and rewrap (orange arrows, kunwrap, krewrap); or (v) the TF can dissociate from the unwrapped nucleosome (purple arrow, kns,off). The figure shows LexA binding to a non-specific site. Among all the binding sites, only one site is the specific target for the TF (red dashed line in (A) and (B)) and the others are non-specific binding sites for the TF. (C) Illustration of the minimum distance (d in bp) between the TF and the unwrapping position of the nucleosome. At this minimum distance when the TF binds to DNA, the nucleosome cannot rewrap anymore and the TF can only slide in one direction.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4150810&req=5

Figure 3: Non-specific binding model of TF dissociation from (A) naked DNA and (B and C) from a nucleosome. (A) In the absence of the nucleosome, the TF can slide along the DNA in two directions (black arrows, k1) or dissociate from the DNA (Purple arrow, kns,off). (B) In the presence of a nucleosome, five possibilities for the next step of a certain state exist: (i) and (ii) the TF can slide along both directions in the unwrapped nucleosome (black arrows, k1); (iii) and (iv) the nucleosome can unwrap and rewrap (orange arrows, kunwrap, krewrap); or (v) the TF can dissociate from the unwrapped nucleosome (purple arrow, kns,off). The figure shows LexA binding to a non-specific site. Among all the binding sites, only one site is the specific target for the TF (red dashed line in (A) and (B)) and the others are non-specific binding sites for the TF. (C) Illustration of the minimum distance (d in bp) between the TF and the unwrapping position of the nucleosome. At this minimum distance when the TF binds to DNA, the nucleosome cannot rewrap anymore and the TF can only slide in one direction.
Mentions: Analogously to the dimeric binding model, we first build this model in the case that the TF binds to naked DNA. Here, the TF can slide along the DNA in two directions and can also dissociate from the DNA (Figure 3A). Among all the binding sites, only one site is the specific target for the TF and the others are non-specific binding sites for the TF.

Bottom Line: This reduces the rate of transcription factor binding and is a known mechanism for regulation of gene expression via chromatin structure.There are two possible explanations for such an increase in off-rate short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding or (ii) the nucleosome can change the equilibrium between specific and non-specific binding to the DNA.We explicitly model both scenarios and find that dimeric binding can explain a large increase in off-rate while the non-specific binding model cannot be reconciled with the large, experimentally observed increase.

View Article: PubMed Central - PubMed

Affiliation: Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA Center for RNA Biology, The Ohio State University, Columbus, OH, USA.

Show MeSH
Related in: MedlinePlus