Isochores

Abstract

Chromosomes of warm‐blooded vertebrates are mosaics of isochores, megabase deoxyribonucleic acid (DNA) stretches that are fairly homogeneous in base composition. In the human genome, isochores can be assigned to five families that cover a very broad range of guanine+cytosine (30–60% GC; this range is narrower in cold‐blooded vertebrates). The isochore structure of the genome led to new insights into a number of important genome features such as (1) the distribution of genes, (2) the structure of chromatin, and (3) the localisation of insertions/deletions and of the integration of proviral sequences. Moreover it also led to (1) the discovery of a set of correlations (collectively called the genomic code) linking coding sequences and extended flanking noncoding sequences, as well as other genome features, (2) the visualisation of the isochore patterns of the genomes as genome phenotypes, that may be conserved or change in evolution, like the classical phenotypes, and (3) the development of the neoselectionist theory of evolution, which explains the two modes, conservative and shifting, of genome evolution.

Key Concepts:

  • Isochores are the structural, functional and evolutionary units of the genomes of vertebrates and other eukaryotes.

  • Structurally, isochores correspond to the highest resolution bands of chromosomes.

  • Functionally, isochores from different families are characterised by different frequencies of short oligonucleotides, not only in the extended inter‐ and intragenic noncoding sequences, but also in short regulatory sequences upstream and downstream of coding sequences. Moreover, different categories of genes have a different distribution in isochore families.

  • Evolutionarily, the isochore patterns change in different classes of vertebrates, from the relatively simple (low‐heterogeneity) patterns of cold‐blooded vertebrates to the complex (high‐heterogeneity) of warm‐blooded vertebrates.

Keywords: genome structure; genome evolution; isochores; isochore families; genomic code; genome phenotype

Figure 1.

Overview of the isochores of human chromosome 21. The top frame shows the compositional profile at a 100 kb resolution. Broken horizontal guidelines indicate GC levels. In the bottom frame the horizontal red stretches represent isochores. (From data of Costantini et al., .)

Figure 2.

The histogram shows the isochores as pooled in bins of 1% GC. Colours represent isochore families. The Gaussian profile shows the distribution of isochore families, namely the genome phenotype. Reproduced from Costantini et al. with permission of Cold Spring Harbor Laboratory Press.

Figure 3.

A scheme of the major properties (DNA amounts, gene density and chromatin structure) of the isochore families belonging in the two genome spaces: the genome core and the genome desert. Gene densities show two different slopes, a shallow one for GC‐poor isochores and a steep one between GC‐poor and GC‐rich isochores. They cross each other between H1 and H2 isochores, so defining the two genome spaces.

Figure 4.

The two modes of compositional evolution of the vertebrate genome. In the shifting mode, the modestly GC‐rich isochores of the genomes from cold‐blooded vertebrates show a GC increase to become the GC‐rich isochores of the warm‐blooded vertebrates. The further evolution of the latter from the ancestral sequence is characterised by a conservative mode. The GC‐poor regions of the genomes of cold‐blooded vertebrates do not undergo major changes.

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Bernardi, Giorgio(Nov 2012) Isochores. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005003.pub2]