Chromosomes 21 and 22: Gene Density


Isochores are long DNA segments that are fairly homogeneous in base composition. The GC‐richest and GC‐poorest isochores of the genomes from warm‐blooded vertebrates are characterized by the highest and the lowest gene concentrations respectively. Chromosomes 21 and 22 can be used to show some properties of both the GC‐richest and GC‐poorest isochores of the human genome.

Keywords: isochores; GC level; chromosome bands; Gene density; SINEs

Figure 1.

GC level profiles of chromosomes 21 and 22. GC level of 300 kb nonoverlapping segments (average of the GC level from the corresponding 20 kb subwindows) from the long arm of chromosomes 21 and 22. The standard deviation is indicated for each of the 300 kb DNA segments. A and B indicate the chromosomal regions (3 Mb in size) shown in Figure in more detail. The shaded area represents the intermediate compositional regions, namely the DNA regions, composed by L2 and H1 isochores, separating the GC‐richer H2/H3 and the GC‐poorer L1 isochores. Two evident band borders are indicated by arrows (see Figure for details).

Figure 2.

Compositional features of bands from chromosomes 21 and 22. (Bottom to top) Bands, ideograms showing the H3+, H3, L1 and L1+ bands. GC%, average GC level of each chromosomal band (horizontal blue lines), and GC levels observed at band borders (red and blue arrows indicate the GC level on the R and G band side respectively; vertical red lines indicate the GC difference over 300 kb regions around band borders). All G bands (L1+ or L1 bands) show lower GC levels than the adjacent R bands (H3+ or H3 bands), and all the R bands (H3+ or H3 bands) show higher GC levels than the adjacent G bands (L1+ or L1 bands). Note that the sizes of the two chromosomes were scaled according to the cytogenetic ideograms of Francke . (Modified from Saccone et al.)

Figure 3.

Gene density at the chromosomal band level. (a) Distribution of genes in chromosomes 21 and 22 showing the very different gene density between the L1+ and the H3+ bands. (b) Plot showing the correlation between the average GC level of each band (from chromosomes 21 and 22) and the relative gene density. Three points, indicated by arrows, represent three outliers (two L1 and one H3+ bands) not taken into consideration when drawing the regression line. Inclusion of these points does not significantly change the lower slope and changes the higher slope only slightly. (Modified from Saccone et al..)

Figure 4.

GC level‐related properties in two compositionally different genomic regions. (a) and (b) show, at higher resolution, the DNA regions indicated in Figure . Upper panels: Average GC‐level profiles of the 20 kb nonoverlapping windows that form each DNA region. The yellow areas indicate the intermediate compositional regions. The horizontal broken line is the average GC level of the GC‐richest H3 isochores. Bottom panels: At different levels of resolution, gene and repeated sequence contents are shown for each chromosomal region (from the UCSC Human Genome Browser Each gene is indicated by vertical (exons) and horizontal (introns) lines. BP: base position, indicating nucleotides from the short arm telomere. Genes Kn.: indicate the known protein‐coding genes; Pr.: indicate the Fgenesh++ prediction based on Softberry's gene‐finding software (see UCSC Human Genome Browser; SINEs and LINEs: location of these repeats in the sequence.



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Saccone, Salvatore, and Bernardi, Giorgio(Sep 2005) Chromosomes 21 and 22: Gene Density. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005013]