An isochore map of the human genome based on the Z curve method

Abstract

The distribution of the G+ C content in the human genome has been studied by using a windowless technique derived from the Z curve method. The most important findings presented in this paper are twofold. First, abrupt variations of the G+ C content along human chromosome sequences are the main variation patterns of G+ C content. It is found that at some sites, the G+ C content undergoes abrupt changes from a G+ C-rich region to a G+ C-poor region alternatively and vice versa. Second, it is shown that long domains with relatively homogeneous G+ C content along each chromosome do exist. These domains are thought to be isochores, which usually have sharp boundaries. Consequently, 56 isochores longer than 3 Mb have been identified in chromosomes 1–22, X and Y. Boundaries, size and G+ C content of each isochore identified are listed in detail. As an example to demonstrate the power of the method, the boundary between the Classes III and II isochores of the MHC sequence has been determined and found to be at 2,477,936, which is in good agreement with the experimental evidence. A homogeneity index is introduced to measure the homogeneity of G+ C content in isochores. We emphasize that the homogeneity of G+ C content is relative. The isochores in which the G+ C content keeps absolutely constant do not exist. Isochore structures appear to be a basic organization of the human genome. Due to the relevance to many important biological functions, the clarification of isochore structures will provide much insight into the understanding of the human genome.