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Nucleic Acids Research Advance Access originally published online on August 10, 2006
Nucleic Acids Research 2006 34(14):3887-3896; doi:10.1093/nar/gkl529
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Nucleic Acids Research, 2006, Vol. 34, No. 14 3887-3896
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Gene function correlates with potential for G4 DNA formation in the human genome

Johanna Eddy1 and Nancy Maizels1,2,3,*

1 Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine 1959 NE Pacific Street, Seattle, WA 98195-7650, USA 2 Department of Immunology, University of Washington School of Medicine 1959 NE Pacific Street, Seattle, WA 98195-7650, USA 3 Department of Biochemistry, University of Washington School of Medicine 1959 NE Pacific Street, Seattle, WA 98195-7650, USA

*To whom correspondence should be addressed. Tel: +1 206 221 6876; Fax: +1 206 221 6781; Email: maizels{at}u.washington.edu

Received June 13, 2006. Revised July 9, 2006. Accepted July 10, 2006.

G-rich genomic regions can form G4 DNA upon transcription or replication. We have quantified the potential for G4 DNA formation (G4P) of the 16 654 genes in the human RefSeq database, and then correlated gene function with G4P. We have found that very low and very high G4P correlates with specific functional classes of genes. Notably, tumor suppressor genes have very low G4P and proto-oncogenes have very high G4P. G4P of these genes is evenly distributed between exons and introns, and it does not reflect enrichment for CpG islands or local chromosomal environment. These results show that genomic structure undergoes selection based on gene function. Selection based on G4P could promote genomic stability (or instability) of specific classes of genes; or reflect mechanisms for global regulation of gene expression.


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