Analysis of 148 kb of genomic DNA around the wnt1 locus of Fugu rubripes - PubMed (original) (raw)

Comparative Study

Analysis of 148 kb of genomic DNA around the wnt1 locus of Fugu rubripes

K Gellner et al. Genome Res. 1999 Mar.

Abstract

The analysis of the sequence of approximately 150 kb of a genomic region corresponding to the wnt1 gene of the Japanese pufferfish Fugu rubripes confirms the compact structure of the genome. Fifteen genes were found in this region, and 26.6% of the analyzed sequence is coding sequence. With an average intergenic distance of <5 kb, this gene density is comparable to that of Caenorhabditis elegans. The compactness of this region corresponds to the reduction of the overall size of the genome, consistent with the conclusion that the gene number in Fugu and human genomes is approximately the same. Eight of the genes have been mapped in the human genome and all of them are found in the chromosomal band 12q13, indicating a high degree of synteny in both species, Fugu and human. Comparative sequence analysis allows us to identify potential regulatory elements for wnt1 and ARF3, which are common to fish and mammals.

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Figures

Figure 1

Figure 1

Schematic representation of the genomic organization of the Fugu wnt1 locus and adjacent genes. Cosmids from the Elgar Fugu library that were fully sequenced are shown as dumbbells. Also cosmids 28L23, 34D20, and 133H20 cover this region and were sample sequenced (data not shown). Arrows indicate the direction of transcription of the identified genes. Gene names are shown below.

Figure 2

Figure 2

Predicted exon–intron structure of the four new vertebrate genes of group 3. Exons are indicated by solid boxes or solid arrows (last exon). Shaded boxes indicate regions with significant homology to entries of the dbEST library. Letters above solid boxes show whether exons have been predicted by XGRAIL (g), FGENES (f), by both (gf), or by neither (−) of these two gene prediction programs.

Figure 3

Figure 3

Highly conserved noncoding vertebrate sequences. Stars indicate identical nucleotides. (A) A stretch of ∼240 bp at the 3′ end of wnt1 is 68% homologous between mouse and Fugu. Homeodomain binding sites HBS1 and HBS2 (Iler et al. 1995) are labeled. (B) Extremely high conservation of the 5′ wnt1 noncoding region of Fugu and zebrafish (Danio rerio). The core sequence of 187 bp shows 85% identity in both species. Base pairs are counted from the translation start sites. (C) Region of homology 5′ of human and Fugu ARF3.

References

    1. Adamson MC, Dennis C, Delaney S, Christiansen J, Monkley S, Kozak CA, Wainwright B. Isolation and genetic mapping of two novel members of the murine Wnt gene family, Wnt11 and Wnt12, and the mapping of Wnt5a and Wnt7a. Genomics. 1994;24:9–13. - PubMed
    1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Angrist M. Less is more: Compact genomes pay dividends. Genome Res. 1998;8:683–685. - PubMed
    1. Aparicio S, Morrison A, Gould A, Gilthorpe J, Chaudhuri C, Rigby P, Krumlauf R, Brenner S. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc Natl Acad Sci. 1995;92:1684–1688. - PMC - PubMed
    1. Aparicio S, Hawker K, Cottage A, Mikawa Y, Zuo L, Venkatesh B, Chen E, Krumlauf R, Brenner S. Organization of the Fugu rubripes HOX clusters: Evidence for continuing evolution of vertebrate Hox complexes. Nat Genet. 1997;16:79–83. - PubMed

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