Home LiteratureArticle Details
PMID: 10077531 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

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

Genome research ·Vol. 9 ·No. 3 ·1999-03-00 ·Pages 251-8

Gellner K, Brenner S

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.

MeSH Terms
3' Untranslated Regions/genetics 5' Untranslated Regions/genetics Animals Base Sequence/genetics Chromosome Mapping DNA/analysis DNA-Binding Proteins/genetics Fishes, Poisonous/genetics Humans Molecular Sequence Data Neoplasm Proteins Nucleic Acid Hybridization Sequence Alignment Sequence Analysis, DNA/methods Sequence Homology, Nucleic Acid Zinc Fingers/genetics
Chemicals
3' Untranslated Regions 5' Untranslated Regions DNA-Binding Proteins KMT2D protein, human Neoplasm Proteins DNA
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Gellner K
Molecular Sciences Institute, Berkeley, California 94704 USA. kgellner@pan.zoo.uni.jena.de
Brenner S
References (42)
42 references, click to expand
  1. Isolation of cloned DNA sequences containing ribosomal protein genes from Saccharomyces cerevisiae.
    Cell. 1979 Dec;18(4):1247-59 PMID: 391408
  2. Less is more: compact genomes pay dividends.
    Genome Res. 1998 Jul;8(7):683-5 PMID: 9685314
  3. Chromosome localization of the human oncogene INT1 to 12q13 by in situ hybridization.
    Cytogenet Cell Genet. 1988;47(1-2):86-7 PMID: 3281802
  4. Isolation and characterization of ERBB3, a third member of the ERBB/epidermal growth factor receptor family: evidence for overexpression in a subset of human mammary tumors.
    Proc Natl Acad Sci U S A. 1989 Dec;86(23):9193-7 PMID: 2687875
  5. Genomic structure and restricted neural expression of the zebrafish wnt-1 (int-1) gene.
    EMBO J. 1991 Apr;10(4):799-807 PMID: 2009859
  6. Prediction of human mRNA donor and acceptor sites from the DNA sequence.
    J Mol Biol. 1991 Jul 5;220(1):49-65 PMID: 2067018
  7. Diversification of the Wnt gene family on the ancestral lineage of vertebrates.
    Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):5098-102 PMID: 1534411
  8. A physical map of a 1.3-Mb region on the long arm of chromosome 12, spanning the GLI and LRP loci.
    Genomics. 1992 Sep;14(1):117-20 PMID: 1427818
  9. New protocols for DNA sequencing with dye terminators.
    DNA Seq. 1992;3(1):61-4 PMID: 1457810
  10. Characterization of the human ADP-ribosylation factor 3 promoter. Transcriptional regulation of a TATA-less promoter.
    J Biol Chem. 1993 Apr 25;268(12):8793-800 PMID: 8473323
  11. dbEST--database for "expressed sequence tags".
    Nat Genet. 1993 Aug;4(4):332-3 PMID: 8401577
  12. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome.
    Nature. 1993 Nov 18;366(6452):265-8 PMID: 8232585
  13. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans.
    Nature. 1994 Mar 3;368(6466):32-8 PMID: 7906398
  14. A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1.
    Nature. 1994 Aug 18;370(6490):567-71 PMID: 7914354
  15. Recognizing exons in genomic sequence using GRAIL II.
    Genet Eng (N Y). 1994;16:241-53 PMID: 7765200
  16. Cis-acting regulatory sequences governing Wnt-1 expression in the developing mouse CNS.
    Development. 1994 Aug;120(8):2213-24 PMID: 7925022
  17. The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins.
    Mol Cell Biol. 1994 Dec;14(12):8292-303 PMID: 7969165
  18. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 PMID: 7984417
  19. DWnt-4, a novel Drosophila Wnt gene acts downstream of homeotic complex genes in the visceral mesoderm.
    Development. 1995 Jan;121(1):209-18 PMID: 7867502
  20. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes.
    Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1684-8 PMID: 7878040
  21. 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 Nov 1;24(1):9-13 PMID: 7896292
  22. Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx.
    Cell. 1995 Jun 30;81(7):1031-42 PMID: 7600572
  23. Comparative sequence analysis of the human and pufferfish Huntington's disease genes.
    Nat Genet. 1995 May;10(1):67-76 PMID: 7647794
  24. An update and lessons from whole-genome sequencing projects.
    Curr Opin Genet Dev. 1995 Jun;5(3):349-53 PMID: 7549430
  25. Genomic structure and nucleotide sequence of the p55 gene of the puffer fish Fugu rubripes.
    Genomics. 1995 Jun 10;27(3):442-6 PMID: 7558025
  26. Gene loss and gain in the evolution of the vertebrates.
    Dev Suppl. 1994;:155-61 PMID: 7579516
  27. A single homeodomain binding site restricts spatial expression of Wnt-1 in the developing brain.
    Mech Dev. 1995 Sep;53(1):87-96 PMID: 8555114
  28. The Ikaros gene encodes a family of lymphocyte-restricted zinc finger DNA binding proteins, highly conserved in human and mouse.
    J Immunol. 1996 Jan 15;156(2):585-92 PMID: 8543809
  29. Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease (AD3 locus)
    Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1366-9 PMID: 8643637
  30. Assignment of human ADP ribosylation factor (ARF) genes ARF1 and ARF3 to chromosomes 1q42 and 12q13, respectively.
    Genomics. 1996 Jun 1;34(2):263-5 PMID: 8661066
  31. Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes).
    Trends Genet. 1996 Apr;12(4):145-50 PMID: 8901419
  32. Conserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor.
    Genome Res. 1996 Dec;6(12):1185-91 PMID: 8973913
  33. A novel human Wnt gene, WNT10B, maps to 12q13 and is expressed in human breast carcinomas.
    Oncogene. 1997 Mar 13;14(10):1249-53 PMID: 9121776
  34. Organization of the Fugu rubripes Hox clusters: evidence for continuing evolution of vertebrate Hox complexes.
    Nat Genet. 1997 May;16(1):79-83 PMID: 9140399
  35. Structure and expression pattern of human ALR, a novel gene with strong homology to ALL-1 involved in acute leukemia and to Drosophila trithorax.
    Oncogene. 1997 Jul 31;15(5):549-60 PMID: 9247308
  36. Evolution and orthology of hedgehog genes.
    Trends Genet. 1996 Dec;12(12):496-7 PMID: 9257526
  37. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  38. Molecular cloning and mapping of a human cDNA (PA2G4) that encodes a protein highly homologous to the mouse cell cycle protein p38-2G4.
    Cytogenet Cell Genet. 1997;78(1):31-5 PMID: 9345902
  39. Isolation of two novel WNT genes, WNT14 and WNT15, one of which (WNT15) is closely linked to WNT3 on human chromosome 17q21.
    Genomics. 1997 Dec 15;46(3):450-8 PMID: 9441749
  40. Chromosomal localization of three human genes encoding members of the TGF-beta superfamily of type I serine/threonine kinase receptors.
    Mamm Genome. 1998 Mar;9(3):266-8 PMID: 9501322
  41. Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate.
    Development. 1998 Jul;125(14):2735-46 PMID: 9636087
  42. Chromosomal distribution of ribosomal protein genes in the mouse.
    Cell. 1981 May;24(2):307-12 PMID: 7237550
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
Email
kgellner@pan.zoo.uni.jena.de
Published
1999-03-00
Pages
251-8
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC310722
Subset
IM
Databases
GENBANK
AF056116
External Links
PubMed source PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2