GC3 of Genes Can Be Used as a Proxy for Isochore Base Composition: A Reply to Elhaik et al. | Zendy

Oliver Clay | Zendy; Giorgio Bernardi | Zendy

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GC3 of Genes Can Be Used as a Proxy for Isochore Base Composition: A Reply to Elhaik et al.

Author(s) -

Oliver Clay,

Giorgio Bernardi

Publication year - 2010

Publication title -

molecular biology and evolution

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 6.637

H-Index - 218

eISSN - 1537-1719

pISSN - 0737-4038

DOI - 10.1093/molbev/msq222

Subject(s) - proxy (statistics) , biology , gene , gc content , genome , human genome , coding (social sciences) , composition (language) , genetics , evolutionary biology , statistics , mathematics , philosophy , linguistics

In an article published in these pages, Elhaik et al. (Elhaik E, Landan G, Graur D. 2009. Can GC content at third-codon positions be used as a proxy for isochore composition? Mol Biol Evol. 26:1829-1833) asked if GC3, the GC level of the third-codon positions in protein-coding genes, can be used as a "proxy" to estimate the GC level of the surrounding isochore. We use available data to directly answer this simple question in the affirmative and show how the use of indirect methods can lead to apparently conflicting conclusions. The answer reasserts that in human and other vertebrates, genes have a strong tendency to reside in compositionally corresponding isochores, which has far-reaching implications for genome structure and evolution.

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