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Vol. 11, Issue 3, 389-404, March 2001

LETTER
Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters

Qiang Wu,1 Theresa Zhang,2 Jan-Fang Cheng,3 Youngwook Kim,1 Jane Grimwood,4 Jeremy Schmutz,4 Mark Dickson,4 James P. Noonan,4 Michael Q. Zhang,2 Richard M. Myers,4 and Tom Maniatis1,5

1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA; 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; 3 Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 4 Department of Genetics and The Stanford Human Genome Center, Stanford University School of Medicine, Stanford, California 94305, USA

The genomic organization of the human protocadherin alpha , beta , and gamma  gene clusters (designated Pcdhalpha [gene symbol PCDHA], Pcdhbeta [PCDHB], and Pcdhgamma [PCDHG]) is remarkably similar to that of immunoglobulin and T-cell receptor genes. The extracellular and transmembrane domains of each protocadherin protein are encoded by an unusually large "variable" region exon, while the intracellular domains are encoded by three small "constant" region exons located downstream from a tandem array of variable region exons. Here we report the results of a comparative DNA sequence analysis of the orthologous human (750 kb) and mouse (900 kb) protocadherin gene clusters. The organization of Pcdhalpha and Pcdhgamma gene clusters in the two species is virtually identical, whereas the mouse Pcdhbeta gene cluster is larger and contains more genes than the human Pcdhbeta gene cluster. We identified conserved DNA sequences upstream of the variable region exons, and found that these sequences are more conserved between orthologs than between paralogs. Within this region, there is a highly conserved DNA sequence motif located at about the same position upstream of the translation start codon of each variable region exon. In addition, the variable region of each gene cluster contains a rich array of CpG islands, whose location corresponds to the position of each variable region exon. These observations are consistent with the proposal that the expression of each variable region exon is regulated by a distinct promoter, which is highly conserved between orthologous variable region exons in mouse and human.

[The sequence data described in this paper have been submitted to the GenBank/EMBL/DDBJ data library under accession nos. AY013756-AY013813, AY013873-AY013878, AF332005, and AF332006.]

5 Corresponding author.

11:389-404 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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