November 14, 2005 12:57 WSPC/INSTRUCTION FILE heermann Modelling of Polycomb-dependent chromosomal interactions involved in Drosophila gene silencing Silke Ritter, Jens Odenheimer and Dieter W. Heermann Institut f¨ ur Theoretische Physik, Universit¨at Heidelberg, Philosophenweg 19, D-69120 Heidelberg, Germany j.odenheimer@tphys.uni-heidelberg.de heermann@tphys.uni-heidelberg.de Frederic Bantignies, Charlotte Grimaud and Giacomo Cavalli CNRS Institute of Human Genetics, 141, rue de la Cardonille F-34396 Montpellier, France Frederic.BANTIGNIES@igh.cnrs.fr Giacomo.Cavalli@igh.cnrs.fr Received Day Month Year Revised Day Month Year The conditions of the chromosomes inside the nucleus in the Rabl configuration have been modelled as self-avoiding polymer chains under restraining conditions. To ensure that the chromosomes remain stretched out and lined up, we fixed their end points to two opposing walls. The numbers of segments N, the distances d 1 and d 2 between the fixpoints, and the wall-to-wall distance z (as measured in segment lengths) determine an approximate value for the Kuhn segment length k l . We have simulated the movement of the chromosomes using molecular dynamics to obtain the expected distance distribution between the genetic loci in the absence of further attractive or repulsive forces. A com- parison to biological experiments on Drosophila Melanogaster yields information on the parameters for our model. With the correct parameters it is possible to draw conclusions on the strength and range of the attraction that leads to pairing. Keywords : biomolecules, structure and physical properties, gene expression, molecular dynamics, self-avoiding random walks, constraint geormetry PACS Nos.: 87.15.Aa, 87.16.Sr, 87.14.Gg 1. Introduction The process of gene silencing is a crucial building block for the picture geneticists developed during the last decade about the functioning of genes within all kinds of organisms. Gene silencing is a highly complex area of research, and several mecha- nisms have been identified that inhibit gene expression within the nucleus. The simplest molecular model to explain gene silencing postulates that specific repressors regulate the onset of transcription, by binding directly to specific DNA sequences and counteracting the action of activators and of the transcriptional ma- chinery. A second possibility is that repressors, bound at specific sequences called 1