The distribution of genes in the human genome

Abstract

Previous investigations on the human genome determined: ( i) the base compositions (GC levels) and the relative amounts of its isochore families; ( ii)the compositional correlations (i.e., the correlations between GC levels) between third codon positions of a set of genes and the DNA fractions in which the genes were localized; and ( iii) the compositional correlations between (a) third and first + second codon positions, as well as that between (b) introns and exons from the set of ‘localized genes’ and from all the coding sequences and genes (genomic sequences of exons + introns) available in gene banks. Here, we have shown that the correlations ( iii, a and b) for ‘localized genes’ and genes from the bank are in full agreement, indicating that the former set is representative of the latter. We haven then used the data ( i) and the correlation ( ii) to estimate the distribution of genes in isochore families. We have found that 34% of the genes are located in the GC-poor isochores (which represent 62% of the genome), 38% in the GC-rich isochores (31% of the genome) and 28% in the GC-richest isochores (3 % of the genome). There is, therefore, a compositional gradient of gene concentration in the human genome. The gene density in the GC-richest 3% of the genome is about eight times higher than in the GC-rich 31%, and about 16 times higher than in the GC-poorest 62%.