Chromosomes 21 and 22: Gene Density

Abstract

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 http://genome.ucsc.edu/). 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 http://genome.ucsc.edu/); SINEs and LINEs: location of these repeats in the sequence.

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References

Bernardi G, Olofsson B, Filipski J, et al. (1985) The mosaic genome of warm‐blooded vertebrates. Science 228: 953–958.

Federico C, Andreozzi L, Saccone S and Bernardi G (2000) Gene density in the Giemsa bands of human chromosomes. Chromosome Research 8: 737–746.

Francke U (1994) Digitized and differentially shaded human chromosome ideograms for genomic applications. Cytogenetics and Cell Genetics 6: 206–219.

Fukagawa T, Sugaya K, Matsumoto K, et al. (1995) A boundary of long‐range G+C% mosaic domains in the human MHC locus: pseudoautosomal boundary‐like sequence exists near the boundary. Genomics 25: 184–191.

Saccone S, Federico C and Bernardi G (2002) Localization of the gene‐richest and the gene‐poorest isochores in the interphase nuclei of mammals and birds. Gene 300: 169–178.

Saccone S, Federico C, Solovei I, et al. (1999) Identification of the gene‐richest bands in human prometaphase chromosomes. Chromosome Research 7: 379–386.

Saccone S, Pavlicek A, Federico C, Paces J and Bernardi G (2001) Genes, isochores and bands in human chromosomes 21 and 22. Chromosome Research 9: 533–539.

Smit AF (1996) The origin of interspersed repeats in the human genome. Current Opinions in Genetics and Development 6: 743–748.

Soriano P, Meunier‐Rotival M and Bernardi G (1983) The distribution of interspersed repeats is non‐uniform and conserved in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America 80: 1816–1820.

Zoubak S, Clay O and Bernardi G (1996) The gene distribution of the human genome. Gene 174: 95–102.

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