The organization of the genome in the nucleus is related to its function. The functional compartmentalization of the genome is described at the nuclear, chromosomal, subchromosomal, nucleosomal, and DNA sequence level. These descriptions originate from the techniques that were used for analysis. The different levels of compartmentalization are not easily reconciled, because the techniques applied to identify genome compartmentalization generally cannot be performed in combination. We have obtained a large body of information on individual "actors" and "scenes" in the nucleus regarding genome compartmentalization, but we still do not understand how and by what pieces of equipment the "actors" play their game. The next challenge is to understand the combined operation of the various levels of functional genome organization in the nucleus, that is, how do the epigenetic and genetic levels act together. In this paper, I will highlight some of the general features and observations of functional organization of the eukaryotic genome in interphase nuclei and discuss the concepts and views based on observed correlations between genome organization and function. I will reflect on what is to be expected from this field of research when the functional levels of genome compartmentalization are integrated. In this context I will draw attention to what might be needed to improve our understanding.
(c) 2006 Wiley-Liss, Inc.