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Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants

Nelson, David Ra; Zeldin, Darryl Cb; Hoffman, Susan MGc; Maltais, Lois Jd; Wain, Hester Me; Nebert, Daniel Wf

Pharmacogenetics and Genomics: January 2004 - Volume 14 - Issue 1 - p 1-18
Special Paper

Objectives Completion of both the mouse and human genome sequences in the private and public sectors has prompted comparison between the two species at multiple levels. This review summarizes the cytochrome P450 (CYP) gene superfamily. For the first time, we have the ability to compare complete sets of CYP genes from two mammals. Use of the mouse as a model mammal, and as a surrogate for human biology, assumes reasonable similarity between the two. It is therefore of interest to catalog the genetic similarities and differences, and to clarify the limits of extrapolation from mouse to human.

Methods Data-mining methods have been used to find all the mouse and human CYP sequences; this includes 102 putatively functional genes and 88 pseudogenes in the mouse, and 57 putatively functional genes and 58 pseudogenes in the human. Comparison is made between all these genes, especially the seven main CYP gene clusters.

Results and conclusions The seven CYP clusters are greatly expanded in the mouse with 72 functional genes versus only 27 in the human, while many pseudogenes are present; presumably this phenomenon will be seen in many other gene superfamily clusters. Complete identification of all pseudogene sequences is likely to be clinically important, because some of these highly similar exons can interfere with PCR-based genotyping assays. A naming procedure for each of four categories of CYP pseudogenes is proposed, and we encourage various gene nomenclature committees to consider seriously the adoption and application of this pseudogene nomenclature system.

aDepartment of Molecular Sciences, University of Tennessee, Memphis TN 38163, USA and The UT Center of Excellence in Genomics and Bioinformatics, bDivision of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA, cDepartment of Zoology, Miami University, Oxford, OH 45056, USA, dMouse GenomicNomenclature Committee (MGNC), The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609, USA, eHUGO Gene Nomenclature Committee, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK and fDepartment of Environmental Health and Center for Environmental Genetics, University of Cincinnati Medical Center, P.O. Box 670056, Cincinnati OH 45267–0056, USA.

This work was supported in part by NIH Grant P30 ES06096 (D.W.N.) and the NIEHS Division of Intramural Research (D.C.Z.).

Correspondence to Dr David R. Nelson, Department of Molecular Sciences, University of Tennessee, Memphis TN 38163, USA. Tel: +1 901–448–8303; fax: +1 901–448–7360; email dnelson@utmem.edu

Received 19 October 2003 Accepted 7 November 2003

© 2004 Lippincott Williams & Wilkins, Inc.