Isochore structures in the mouse genome

Genomics. 2004 Mar;83(3):384-94. doi: 10.1016/j.ygeno.2003.09.011.


The distribution of the G+C content in the mouse genome has been studied using a windowless technique. We have found that: (i). Abrupt variations of the G+C content from a GC-rich region to a GC-poor region, and vice versa, occur frequently at some sites along the sequence of the mouse genome. (ii). Long domains with relatively homogeneous G+C content (isochores) exist, which usually have sharp boundaries. Consequently, 28 isochores longer than 1 Mb have been identified in the mouse genome. A homogeneity index was used to quantify the variations of the G+C content within isochores. The precise boundaries, sizes, and G+C contents of these isochores have been determined. The windowless technique for the G+C content computation was also used to analyze the DNA sequence containing the mouse MHC region, which has a GC-poor isochore. This isochore is located at the central part of the sequence with boundaries at 468459 and 812716 bp, where the sequence is extended from the centromeric end to the telomeric end. In addition, the analysis of a segment of the rat genome shows that the rat genome also has clear isochore structures.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Centrifugation, Density Gradient
  • Chromosomes, Mammalian
  • GC Rich Sequence
  • Genome*
  • Isochores / genetics*
  • Major Histocompatibility Complex / genetics
  • Mice / genetics*
  • Rats
  • Sequence Analysis, DNA / statistics & numerical data


  • Isochores