L Isochore Map: Gene‐poor Isochores

Abstract

The genomes of warm‐blooded vertebrates are composed of isochores of relatively homogeneous G+C content. The L isochores are those with the lowest G+C content and are associated with the lowest density of genes.

Keywords: GC‐poor isochores; human X chromosome; band Xq25; gene distribution; repeat distribution

Figure 1.

Analysis of the sequence of human Xq25 and its flanking regions. The G‐banding pattern is represented at the top. A selection of genes is shown on the cytogenetic map. These genes are linked by dotted lines to the 1‐Mb sequence intervals in which they lie. The upper histogram shows the percentage of each 100‐kb sequence window that is accounted for by LINE or Alu elements. The lower histogram shows the G+C content of 100‐kb windows (scale in Mb). Horizontal lines show the upper limits designated for L1, L2 and H1 isochores. The two gaps between the three sequences are shown as vertical white lines. Below the G+C plot are the gene counts for each 1‐Mb interval. At the base of the figure is the suggested isochore structure of the region taken from the IsoFinder segmentation results. Thin vertical lines indicate predicted boundaries between isochores of the same family.

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References

Bernardi G (2001) Misunderstandings about isochores. Part 1. Gene 276: 3–13.

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

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Further Reading

Bernardi G (2000) Isochores and the evolutionary genomics of vertebrates. Gene 241: 3–17.

Filipski J, Thiery J‐P and Bernardi G (1973) An analysis of the bovine genome by Cs2SO4‐Ag+ density gradient centrifugation. Journal of Molecular Biology 80: 177–197.

Gardiner K (1996) Base composition and gene distribution: critical patterns in mammalian genome organization. Trends in Genetics 12: 519–524.

Haring D and Kypr J (2001) No isochores in the human chromosomes 21 and 22? Biochemical Biophysical Research Communications 280: 567–573.

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

Web Links

The following web addresses can be used to access the human xq25 DNA sequence discussed above and the results of its analysis. National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/

The Ensembl browser for the human genome sequence http://www.ensembl.org/Homo_sapiens/

Results of the IsoFinder segmentation approach applied to finished and draft sequences from the IHGSC http://bioinfo2.ugr.es/isochores/

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How to Cite close
Ross, Mark T(Sep 2005) L Isochore Map: Gene‐poor Isochores. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005014]