Elsevier

Genomics

Volume 83, Issue 4, April 2004, Pages 717-726
Genomics

Genomic sequence and organization of the family of CNR/Pcdhα genes in rat

https://doi.org/10.1016/j.ygeno.2003.09.022Get rights and content

Abstract

CNR/Pcdhα family proteins are known as synaptic cadherins and Reelin receptors. Here we report the complete genomic sequence and organization of the rat CNR. The rat CNR cluster encodes 15 variable and 3 constant exons. The genomic organizations of the rat, mouse, and human CNR/Pcdhα are orthologous. The percentage identity of the coding regions between the rat and the mouse is 93.6% on average at the nucleic acid level, and between rat and human it is 82.8%. The rat CNRs (v1–v13) also contain an RGD motif in the extracellular cadherin 1 domains and cysteine repeats that are characteristic of the transmembrane and cytoplasmic domains of CNR proteins. The number of variable exons in the rat CNR cluster is identical to that of the human. The rat CNR cluster has one more variable exon than is found in laboratory mouse strains, because in the mouse a variable exon located between v7 and v8 is divided by the insertion of a retrotransposon. This exon is not disrupted in the rat, in which it is transcribed. By in silico analysis, CNR/Pcdhα was also mapped to rat chromosome 18, but the orientation was opposite for the mouse CNR/Pcdhα gene cluster. The relative expression profiles of the rat CNRs (v1–v13) show that all the CNRs are transcribed, but there are variations in the expression ratios among the CNRs.

Section snippets

BAC clones

Rat (Long Evans) BAC clones were isolated using two specific probes made by Incyte Genomics. Three clones, 229/F1, 186/M24, and 208/B15, were isolated with a 700-bp SpeI/PvuII mouse constant region probe. Three other clones, 227/J23, 118/K06, and 237/N17, were isolated with a 800-bp BglII/NotI plasmid B1 probe, which was composed of the mouse CNR1 EC1 region inserted into pBluescript II. We assembled the BAC clones using the terminal sequences as PCR primers.

Sequencing and assembly

Three BAC clones covering the 240-kb

Genomic organization of the rat CNR gene clusters on the 18c chromosomal region

Three overlapping BAC clones, 227/J23, 237/N17, and 229/F1, containing sequences that were homologous to the mouse CNR genes (from v1 to c3) were selected for DNA sequencing (Fig. 1). Analysis of the rat genomic DNA sequences revealed 15 CNR genes that were very similar to the mouse CNR genes. The 13 variable exons of the rat CNRs were organized in a tandem array, as with the mouse and human gene clusters. The constant region was divided into 3 small exons that were located downstream of the

Discussion

Here we report the complete DNA sequence, genomic organization, and expression profiles of the rat CNR genes. A detailed comparative sequence analysis of mouse and human CNR/Pcdhα has already been reported [17], [20]. Although many studies have compared genomic sequences in human and mouse, relatively few have compared rat and mouse or rat and human genomic sequences, especially for cluster genes spanning over 200 kb.

We found that the rat CNR genes have an organization similar to those of the

Acknowledgements

We thank members of the Yagi labs (Graduate School of Frontier Biosciences, Osaka University, and NIPS, Japan) for useful comments and help. This work was supported in part by a grant from CREST, Japan Science and Technology Corp., the Ministry of Education and Science of Japan, and the Uehara Memorial Foundation.

References (23)

  • M. Bunsey et al.

    Conservation of hippocampal memory function in rats and humans

    Nature

    (1996)
  • Cited by (0)

    Sequence data from this article have been deposited with the GenBank Data Library under Accession Nos. AB113484AB113485AB113486AB113487AB113488AB113489AB113490AB113491AB113492AB113493AB113494AB113495AB113496AB113497AB113498 to AB113499.

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