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Originally published as Genetics Published Articles Ahead of Print on September 1, 2006.
Genetics, Vol. 174, 1029-1040, October 2006, Copyright © 2006
doi:10.1534/genetics.105.054445
Isochores Exhibit Evidence of Genes Interacting With the Large-Scale Genomic Environment
William H. Press*,1 and
Harlan Robins
,
* Los Alamos National Laboratory, Los Alamos, New Mexico 87545, Institute for Advanced Study, Princeton, New Jersey 08540 and Fred Hutchison Cancer Research Center, Seattle, Washington 98109
1 Corresponding author: CCS-6 Group, MS F-600, P.O. Box 1663, Los Alamos National Laboratory, Los Alamos, NM 87545.
E-mail: wpress{at}lanl.gov
The genomes of mammals and birds can be partitioned into megabase-long regions, termed isochores, with consistently high, or low, average C + G content. Isochores with high CG contain a mixture of CG-rich and AT-rich genes, while high-AT isochores contain predominantly AT-rich genes. The two gene populations in the high-CG isochores are functionally distinguishable by statistical analysis of their gene ontology categories. However, the aggregate of the two populations in CG isochores is not statistically distinct from AT-rich genes in AT isochores. Genes tend to be located at local extrema of composition within the isochores, indicating that the CG-enriching mechanism acted differently when near to genes. On the other hand, maximum-likelihood reconstruction of molecular phylogenetic trees shows that branch lengths (evolutionary distances) for third codon positions in CG-rich genes are not substantially larger than those for AT-rich genes. In the context of neutral mutation theory this argues against any strong positive selection. Disparate features of isochores might be explained by a model in which about half of all genes functionally require AT richness, while, in warm-blooded organisms, about half the genome (in large coherent blocks) acquired a strong bias for mutations to CG. Using mutations in CG-rich genes as convenient indicators, we show that 
20% of amino acids in proteins are broadly substitutable, without regard to chemical similarity.
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