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Increasing evidence suggests that chromosome folding and genetic expressionare intimately connected. For example, the co-expression of a large number ofgenes can benefit from their spatial co-localization in the cellular space.Furthermore, functional structures can result from the particular folding ofthe chromosome. Such phenomena have in common to result from the binding ofdivalent proteins that can bridge regions sometimes far away on the DNAsequence. The physical system consisting of the chromosome interacting withdivalent proteins can be very complex. As such, most of the mechanismsresponsible for chromosome folding and for the formation of functionalstructures have remained elusive.  Using methods from statistical physics, we investigated models of chromosomearchitecture. A common denominator of our approach has been to represent thechromosome as a polymer with bending rigidity and consider its interaction witha solution of DNA-binding proteins. Structures entailed by the binding of suchproteins were then characterized at the thermodynamical equilibrium.Furthermore, we complemented theoretical results with Brownian dynamicssimulations, allowing to reproduce more of the biological complexity.  The main contributions of this thesis have been: (i) to provide a model forthe existence of transcription factories characterized in vivo withfluorescence microscopy; (ii) to propose a physical basis for a conjecturedregulatory mechanism of the transcription involving the formation of DNAhairpin loops by the H-NS protein as characterized with atomic-force microscopyexperiments; (iii) to propose a physical model of the chromosome thatreproduces contacts measured in chromosome conformation capture (CCC)experiments. Consequences on the regulation of transcription are discussed ineach of these studies.

Models of chromosome architecture and connection with the regulation of genetic expression