Gene Distribution in Human Chromosomes


The distribution of genes in the human genome is strikingly nonuniform. Gene density is very high in GC (G, guanine; C, cytosine)‐rich isochores and very low in GC‐poor isochores (isochores are long deoxyribonucleic acid (DNA) regions characterized by a fairly homogeneous GC level). Since GC‐rich and GC‐poor isochores can be localized on human chromosomes, this ‘chromosomal compositional mapping’ provides information on the distribution of genes on chromosomes. The completion of the human genome sequence and the mapping of isochores on chromosomes have recently confirmed these results.

Keywords: isochores; chromosomal bands; telomeric bands; gene density; in situ hybridization

Figure 1.

The GC‐richest and GC‐poorest human chromosomal bands. (a) The GC‐richest bands. From left to right of each chromosome group: T, Chromomycin A3+/DAPI and H3+ bands (from Saccone and Bernardi, ). (b) The GC‐poorest bands. The left and right member of each chromosome pair shows the Giemsa banding and the L1 isochore hybridization, respectively (from Federico et al., ). Biotinylated H3 and L1 isochores were detected with avidin‐FITC and chromosomes were stained with propidium iodide. The H3 and the L1 isochores identify the gene‐richest and the gene‐poorest chromosomal regions, respectively. Note the different localization of the two isochore families, near the telomeres for H3 and more internal for L1 isochores.

Figure 2.

H3+ bands at low and high chromosome resolution. Human chromosomes 19 and 22, at different levels of resolution, hybridized with the biotin‐labelled DNA from the H3 isochore family. The hybridized regions were visualized by fluorescein and chromosomes were stained with propidium iodide. Both panels present chromosomes with a band resolution ranging from approximately 300 to approximately 850. The bands in chromosome 22 pointed by the red lines indicate the ribosomal DNA region (modified from Saccone et al., ).

Figure 3.

H3+ and L1+ bands on human chromosome 11. Ideogram of human chromosome 11 at 400 (left) and 850 (right) band resolution showing the bands containing the gene‐richest H3 and the gene‐poorest L1 isochores. At 850 band resolution, the different degrees of darkness of G bands are also shown: note the correspondence among the L1+ bands and the darkest G bands (rightmost scheme). The R bands not containing H3 isochores are called H3 bands, and the G bands not containing L1 isochores are called L1 bands (modified from Saccone et al., ; Federico et al., ).



Ambros PF and Sumner AT (1987) Metaphase bands of human chromosomes, and distinctive properties of telomeric regions. Cytogenetics and Cell Genetics 44: 223–228.

Bernardi G (2004 reprinted in 2005) Structural and Evolutionary Genomics. Natural Selection in Genome Evolution. Amsterdam: Elsevier.

Bernardi G, Olofsson B, Filipski J et al. (1985) The mosaic genome of warm‐blooded vertebrates. Science 228: 953–957.

Costantini M, Clay O, Auletta F and Bernardi G (2006) An isochore map of human chromosomes. Genome Research 16: 536–541.

Dutrillaux B (1973) Nouveau système de marquage chromosomique: les bandes T. Chromosoma 41: 395–402.

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

Federico C, Saccone S and Bernardi G (1998) The gene‐richest bands of human chromosomes replicate at the onset of the S‐phase. Cytogenetics and Cell Genetics 80: 83–88.

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

International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931–945.

Mouchiroud D, D'Onofrio G, Aïssani B et al. (1991) The distribution of genes in the human genome. Gene 100: 181–187.

Saccone S and Bernardi G (2001) Human chromosomal banding by in situ hybridization of isochores. Methods in Cell Science 23: 7–15.

Saccone S, De Sario A, Della Valle G and Bernardi G (1992) The highest gene concentrations in the human genome are in T‐bands of metaphase chromosomes. Proceedings of the National Academy of Sciences of the United States of America 89: 4913–4917.

Saccone S, Federico C, Solovei I, Croquette MF and Della Valle G (1999) Identification of the gene‐richest bands in human prometaphase chromosomes. Chromosome Research 7: 379–386.

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

Further Reading

Bernardi G (2007) The neo‐selectionist theory of genome evolution. Proceedings of the National Academy of Sciences of the United States of America 104: 8385–8390.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Bernardi, Giorgio, and Saccone, Salvatore(Jul 2008) Gene Distribution in Human Chromosomes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005790.pub2]