The transcriptional activity is not evenly distributed inside the cell, but it is concentrated in focal points around so-called transcription factories. The formation of transcription factories and DNA looping are considered to be of fundamental importance for the large-scale spatial organization of the transcriptional activity. 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 description can be solved analytically via a mapping to a restricted random-graph ensemble. 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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