The prometaphase bands of human chromosomes: compositional features and gene distribution

Abstract

The human genome is a mosaic of long, compositionally homogeneous DNA segments, the isochores, that can be partitioned into five families. Two GC-poor families (LI and L2) representing 63% of the genome, and three GC-rich families (H1, H2 and H3) representing 24%, 7.5% and 4-5% of the genome, respectively [1]. Gene concentration increases with increasing GC levels, and reaches a 20-fold higher level in H3 compared to L isochores [2].In situhybridization of DNA from different isochore families provides, therefore, information on the chromosomal distribution of genes. Using this approach, three subsets of R(everse) or G(iemsa)-negative bands, H3⁺, H3^*and H3^-, containing large, moderate, and no detectable amounts, respectively, of the gene-richest H3 isochores were identified at a resolution of 400 bands [3]. H3⁺bands largely overlap with the most heat-denaturation-resistant bands [4], the chromomycin-A3-positive, 4,6-diamindino-2-phenylindole (DAPI)-negative bands [5], the bands with the highest CpG island concentrations [6], and the earliest replicating bands [7]. Here we have defined the H3⁺bands at a 850-band resolution, and have thus identified the human genome regions, having an average size of 4 Mb, that are endowed with the highest gene density.