Conserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor.

Abstract

We have cloned and sequenced the teleost homoiogs of the human genes encoding platelet-derived growth factor receptor-13 (PDGFRI3) and macrophage colony-stimulating factor I receptor (CSF1R) from the puffer fish Fugu rubripes. The Fugu PDGFRI3 and CSFIR genes each consist of 21 coding exons similar to the human CSFIR gene, but are considerably smaller than their human counterparts because of the smaller introns. Furthermore, the two Fugu genes are linked tandemly in a head-to-tail array similar to their human homologs with 2.2 kb of intergenic sequence. Amino acid sequences of the Fugu and human PDGFRI3 and CSFIR genes show an overall homology of 45% and 39%, respectively, with the kinase domains showing a much higher degree of conservation. Dot-matrix analysis revealed several short stretches of conserved sequences in the 3' untranslated regions of the PDGFRI3 genes and the adjacent promoter regions of the CSFIR genes. These conserved sequences may have a role in the regulation of expression of either or both of these closely linked genes.[The sequence data described in this paper have been submitted to GenBank under accession no. U63926.]The Japanese puffer fish Fugu rubripes has a small genome of 390 Mb which is -8 times smaller than the mammalian genomes (Brenner et al. 1993). Because teleosts have a body plan similar to that of mammals and possess most of their complex physiological functions, it is not surprising that the Fugu genome has a gene repertoire comparable to that of mammals (Brenner et al. 1993).This implies that the gene density in the Fugu genome is higher than in mammalian genomes.The compact genome of Fugu with small introns and a low abundance of repetitive elements (Brenner et

Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human

“…Further studies will be required to con®rm these preliminary results, but this is consistent with several reports of conserved non-coding sequences, between Fugu and human genes, located in promoters, 3' UTR and even introns How et al, 1996;Kimura et al, 1997;Rowitch et al, 1998;Miles et al, 1998;Gellner and Brenner 1999). Some of them have been shown to have functional signi®cance in vivo Kimura et al, 1997;Rowitch et al, 1998).…”

Insights from human/mouse genome comparisons

“…Several additional examples where human/fugu comparisons led to putative gene regulatory elements are available (Abrahams et al 2002;Aparicio et al 1995;Bagheri-Fam et al 2001;Gilligan et al 2002;How et al 1996;Kimura et al 1997;Rowitch et al 1998;Venkatesh et al 1997). These studies highlight that a comparative genomic driven approach can be successful for identifying gene regulatory elements even in distant mammal/fish comparisons.…”

Less Is More: Compact Genomes Pay Dividends

“…Similarly, studies of intergenic distances in Fugu also prove reduction to be the order of the day. How et al (1996) and Schofield et al (1997) have both examined tandemly arrayed genes that span large chromosomal regions in human and found substantial compaction in pufferfish. Aparicio et al (1997) showed that Fugu Hox gene clusters are compact by virtue of a combination of gene loss and reduction in intergenic distances.…”