A thermodynamic model for agglomeration of DNA-looping proteins

Details A thermodynamic model for agglomeration of DNA-looping proteins A thermodynamic model for agglomeration of DNA-looping proteins

2008-01-09

arxiv.org/abs/0801.1480v2

J. Stat. Mech. (2008) P11005

Biology

Quantitative Biology

Subcellular Processes

12 pages, 5 figures, to app. in JSTAT

Scientific paper

10.1088/1742-5468/2008/11/P11005

In this paper, we propose a thermodynamic mechanism for the formation of transcriptional foci via the joint agglomeration of DNA-looping proteins and protein-binding domains on DNA: The competition between the gain in protein-DNA binding free energy and the entropy loss due to DNA looping is argued to result in an effective attraction between loops. A mean-field approximation can be described analytically via a mapping to a restricted random-graph ensemble having local degree constraints and global constraints on the number of connected components. It shows the emergence of protein clusters containing a finite fraction of all looping proteins. If the entropy loss due to a single DNA loop is high enough, this transition is found to be of first order.

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