%0 Journal Article
%T Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome
%+ Laboratoire Charles Coulomb (L2C)
%+ Dynamique des interactions membranaires normales et pathologiques (DIMNP)
%+ Lewis-Sigler Institute for Integrative Genomics
%+ Department of Physics and Arnold Sommerfeld Center for Theoretical Physics
%A Walter, Jean-Charles
%A Walliser, Nils-Ole
%A David, Gabriel
%A Dorignac, Jerome
%A Geniet, Frederic
%A Palmeri, John
%A Parmeggiani, Andrea
%A Wingreen, Ned S.
%A Broedersz, Chase P.
%Z 14 pages, 7 figures
%< avec comité de lecture
%Z L2C:17-075
%@ 1367-2630
%J New Journal of Physics
%I Institute of Physics: Open Access Journals
%V 20
%P 035002
%8 2018-03-26
%D 2018
%Z 1707.01373
%R 10.1088/1367-2630/aaad39
%Z Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph]
%Z Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft]
%Z Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC]Journal articles
%X 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.
%G English
%2 https://hal.science/hal-01561696/document
%2 https://hal.science/hal-01561696/file/1707.01373.pdf
%L hal-01561696
%U https://hal.science/hal-01561696
%~ CNRS
%~ UNIV-MONTP1
%~ UNIV-MONTP2
%~ DIMNP
%~ L2C
%~ MIPS
%~ BS
%~ UNIV-MONTPELLIER
%~ LPHI
%~ ANR
%~ UM-2015-2021