Identification of the gene-richest bands in human chromosomes

The human genome is a mosaic of isochores, long DNA segments which are compositionally homogeneous and which can be partitioned into five families, L1, L2, H1, H2 and H3, characterized by increasing GC levels and by increasing gene concentrations. Previous investigations showed that in situ hybridization with a DNA fraction derived from the GC-richest and gene-richest isochores of the H3 family produced the highest concentration of signals on 25 R(everse) bands that include the 22 most thermal-denaturation-resistant T(elomeric) bands, a subset of R bands. Using an improved protocol for in situ hybridization and cloned H3 isochore DNA, we have now shown (i) that the number of bands which are characterized by strong hybridization signals, and which are here called T or H3(+), is 28; (ii) that 31 additional R bands, here called T' or H3* bands, also contain H3 isochores, although at a lower concentration than H3(+) bands; and (iii) that the remaining R bands (about 140 out of 200, at a resolution of 400 bands), here called R '' or H3(-) bands, do not contain any detectable H3 isochores. H3(+) and H3* bands contain all the gene-richest isochores of the human genome. The existence of three distinct sets of R bands is further supported (i) by the different compositional features of genes located in them; (ii) by the very low gene density of chromosomes 13 and 18, in which all R bands are H3(-) bands; (iii) by the compositional map of a H3* band, Xq28; (iv) by the overwhelming presence of GC-rich and GC-poor long (>50 kb) DNA sequences in H3(+)/H3* and in H3(-)/G bands, respectively; and (v) by the large degree of coincidence of H3(+) and H3* bands with CpG island-positive bands. These observations have implications for our understanding of the causes of chromosome banding and provide a classification of chromosomal bands that is related to GC level (and to gene concentration).