  The bacterial genome is organized in a structure called the nucleoid by a
variety of associated proteins. These proteins can form complexes on DNA that
play a central role in various biological processes, including chromosome
segregation. A prominent example is the large ParB-DNA complex, which forms an
essential component of the segregation machinery in many bacteria. ChIP-Seq
experiments show that ParB proteins localize around centromere-like parS sites
on the DNA to which ParB binds specifically, and spreads from there over large
sections of the chromosome. Recent theoretical and experimental studies suggest
that DNA-bound ParB proteins can interact with each other to condense into a
coherent 3D complex on the DNA. However, the structural organization of this
protein-DNA complex remains unclear, and a predictive quantitative theory for
the distribution of ParB proteins on DNA is lacking. Here, we propose the
Looping and Clustering (LC) model, which employs a statistical physics approach
to describe protein-DNA complexes. The LC model accounts for the extrusion of
DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the
structure of the protein-DNA complex is determined by a competition between
attractive protein interactions and the configurational and loop entropy of
this protein-DNA cluster. Indeed, we show that the protein interaction strength
determines the "tightness" of the loopy protein-DNA complex. With this approach
we consider the genomic organization of such a protein-DNA cluster around a
single high-affinity binding site. Thus, our model provides a theoretical
framework to quantitatively compute the binding profiles of ParB-like proteins
around a cognate (parS) binding site.
