Skip to main content
SpringerLink
Log in

Generation of Aberrant Transcripts of and Free DNA Ends in Zebrafish no tail Gene

  • Published:
Marine Biotechnology Aims and scope Submit manuscript

Abstract

The zebrafish no tail gene (ntl) is indispensable for the formation of the notochord and the tail structure. In a wild-type zebrafish population, we occasionally observed adult zebrafish with a narrow or no tailfin. This led us to examine the hypothesis that the activity of ntl was somehow genetically unstable. Here we present two findings regarding the gene. First, approximately 3% of ntl transcripts were aberrant; most of them carried deletions at various positions. Second, free, DNA double-stranded ends (DSEs) were formed at an AT dinucleotide repeat in ntl. DSEs were also generated in another zebrafish gene, noggin2 (nog2). DSEs in ntl and nog2 had common characteristics, which suggested that the AT repeats in these genes elicited DSEs by blocking progression of the replication.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4

Similar content being viewed by others

References

  • J.C. Connelly D.R.F. Leach (1996) ArticleTitleThe sbcC and sbcD genes of Escherichia coli encode a nuclease involved in palindrome inviability and genetic recombination Genes Cells 1 285–291 Occurrence Handle10.1046/j.1365-2443.1996.23024.x Occurrence Handle9133662

    Article  PubMed  Google Scholar 

  • K.A. Eckert T.A. Kunkel (1991) PCR: A Practical Approach Oxford University Press New York, N.Y. 225–244

    Google Scholar 

  • Y. Fujimura T. Horiuchi (1995) ArticleTitleRecombinational rescue of the stalled DNA replication fork: a model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate J Bacterial 177 783–791

    Google Scholar 

  • M. Fürthauer B. Thisse C. Thisse (1999) ArticleTitleThree different noggin genes antagonize the activity of bone morphogenetic proteins in the zebrafish embryo Dev Biol 214 181–196 Occurrence Handle10.1006/dbio.1999.9401 Occurrence Handle10491267

    Article  PubMed  Google Scholar 

  • M.E. Halpern R.K. Ho C. Walker C.B. Kimmel (1993) ArticleTitleInduction of muscle pioneers and floor plate is distinguished by the zebrafish no tail mutation Cell 75 99–111 Occurrence Handle10.1016/0092-8674(93)90682-G Occurrence Handle8402905

    Article  PubMed  Google Scholar 

  • D.B. Haniford D.E. Pulleyblank (1985) ArticleTitleTransition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo Nucleic Acids Res 13 4343–4363 Occurrence Handle4011446

    PubMed  Google Scholar 

  • K. Haworth W. Putt B. Cattanach M. Breen M. Binns F. Lingaas Y.H. Edwards (2001) ArticleTitleCanine homolog of the T-box transcription factor T; failure of the protein to bind to its DNA target leads to a short-tail phenotype Mamm Genome 12 212–218 Occurrence Handle10.1007/s003350010253 Occurrence Handle11252170

    Article  PubMed  Google Scholar 

  • B.G. Herrmann A. Kispert (1993) ArticleTitleThe Brachyury gene encodes a novel DNA binding protein EMBO J 12 3211–3220 Occurrence Handle8344258

    PubMed  Google Scholar 

  • B.G. Herrmann A. Kispert (1994) ArticleTitleImmunohistochemical analysis of the Brachyury protein in wild-type and mutant mouse embryos Dev Biol 161 179–193 Occurrence Handle10.1006/dbio.1994.1019 Occurrence Handle8293872

    Article  PubMed  Google Scholar 

  • B.G. Herrmann S. Labeit A. Poustka T.R. King H. Lehrach (1990) ArticleTitleCloning of the T gene required in mesoderm formation in the mouse Nature 343 617–622 Occurrence Handle10.1038/343617a0 Occurrence Handle2154694

    Article  PubMed  Google Scholar 

  • O. Hyrien (2000) ArticleTitleMechanisms and consequences of replication fork arrest Biochimie 82 5–17 Occurrence Handle10.1016/S0300-9084(00)00344-8 Occurrence Handle10717381

    Article  PubMed  Google Scholar 

  • H. Jacobs K. Rajewsky Y. Fukita L. Bross (2001) ArticleTitleIndirect and direct evidence for DNA double-strand breaks in hypermutating immunoglobulin genes Philos Trans R Soc Land B Biol Sci 356 119–125 Occurrence Handle10.1098/rstb.2000.0756

    Article  Google Scholar 

  • A.M. Krichevsky E. Metzer H. Rosen (1999) ArticleTitleTranslational control of specific genes during differentiation of HL-60 cells J Biol Chem 274 14295–14305 Occurrence Handle10.1074/jbc.274.20.14295 Occurrence Handle10318851

    Article  PubMed  Google Scholar 

  • T. Kudoh M. Tsang N.A. Hukriede X. Chen M. Dedekian C.J. Clarke A. Kiang S. Schultz J.A. Epstein R. Toyama I.B. Dawid (2001) ArticleTitleA gene expression screen in zebrafish embryogenesis Genome Res 11 1979–1987 Occurrence Handle10.1101/gr.209601 Occurrence Handle11731487

    Article  PubMed  Google Scholar 

  • J.R. Lupski P. Stankiewicz (2002) ArticleTitleGenome architecture, rearrangements and genomic disorders Trends Genet 18 74–82 Occurrence Handle10.1016/S0168-9525(02)02592-1 Occurrence Handle11818139

    Article  PubMed  Google Scholar 

  • A. MacMurray H.S. Shin (1988) ArticleTitleThe antimorphic nature of the Tc allele at the mouse T locus Genetics 120 545–550 Occurrence Handle3197959

    PubMed  Google Scholar 

  • R.M. Mader W.M. Schmidt R. Sedivy B. Rizovski J. Braun M. Kalipciyan M. Exner G.G. Steger M.W. Mueller (2001) ArticleTitleReverse transcriptase template switching during reverse transcriptase–polymerase chain reaction: artificial generation of deletions in ribonucleotide reductase mRNA J Lab Clin Med 137 422–428 Occurrence Handle10.1067/mlc.2001.115452 Occurrence Handle11385363

    Article  PubMed  Google Scholar 

  • M. Nishioka H. Mizuguchi S. Fujiwara S. Komatsubara M. Kitabayashi H. Uemura M. Takagi T. Imanaka (2001) ArticleTitleLong and accurate PCR with a mixture of KOD DNA polymerase and its exonuclease deficient mutant enzyme J Biotechnol 88 141–149 Occurrence Handle10.1016/S0168-1656(01)00275-9 Occurrence Handle11403848

    Article  PubMed  Google Scholar 

  • J. Odenthal P. Haffter E. Vogelsang M. Brand F.J.M. Eeden Particlevan M. Furutani-Seiki M. Granato M. Hammerschmidt C.P. Heisenberg Y.J. Jiang D.A. Kane R.N. Kelsh M.C. Mullins R.M. Warga M.L. Allende E.S. Weinberg C. Nüsslein-Volhard (1996) ArticleTitleMutations affecting the formation of the notochord in the zebrafish, Danio rerio Development 123 103–115 Occurrence Handle9007233

    PubMed  Google Scholar 

  • F.N. Papavasiliou D.G. Schatz (2000) ArticleTitleCell-cycle-regulated DNA double-strand breaks in somatic hypermutation of immunoglobulin genes Nature 408 216–221 Occurrence Handle10.1038/35041599 Occurrence Handle11089977

    Article  PubMed  Google Scholar 

  • M.J. Parsons S.M. Polland L. Saúde B. Feldman P. Coutinho E.M.A. Hirst D.L. Stemple (2002) ArticleTitleZebrafish mutants identify an essential role for laminins in notochord formation Development 129 3137–3146 Occurrence Handle12070089

    PubMed  Google Scholar 

  • M. Schlissel A. Constantinescu T. Morrow M. Baxter A. Peng (1993) ArticleTitleDouble-strand signal sequence breaks in V(D)J recombination are blunt, 5′-phosphorylated, RAG-dependent, and cell cycle regulated Genes Dev 7 2520–2532 Occurrence Handle8276236

    PubMed  Google Scholar 

  • S. Schulte-Merker R.K. Ho E.G. Herrmann C. Nüsslein-Volhard (1992) ArticleTitleThe protein product of the zebrafish homologue of the mouse T gene is expressed in nuclei of the germ ring and the notochord of the early embryo Development 116 1021–1032 Occurrence Handle1295726

    PubMed  Google Scholar 

  • S. Schulte-Merker F.J.M. Eeden Particlevan M.E. Halpern C.B. Kimmel C. Nüsslein-Volhard (1994) ArticleTitleno tail (ntl) is the zebrafish homologue of the mouse T (Brachyury) gene Development 120 1009–1015 Occurrence Handle7600949

    PubMed  Google Scholar 

  • M. Seigneur V. Bidnenko S.D. Ehrlich B. Michel (1998) ArticleTitleRuvAB acts at arrested replication forks Cell 95 419–430 Occurrence Handle10.1016/S0092-8674(00)81772-9 Occurrence Handle9814711

    Article  PubMed  Google Scholar 

  • Singh, G., Lykke-Anderson, J. (2003) “New insights into the formation of active nonsense-mediated decay complexes” Trends Biochem Sci 28: 464–466

    Google Scholar 

  • D.L. Stemple L. Solnica-Krezel F. Zwartkruis S.C.F. Neuhauss A.F. Schier J. Malicki D.Y.R. Stainier S. Abdelilah Z. Rangini E. Mountcastle-Shah W. Driever (1996) ArticleTitleMutations affecting development of the notochord in zebrafish Development 123 117–128 Occurrence Handle9007234

    PubMed  Google Scholar 

  • K.O. Yanagisawa (1990) ArticleTitleDoes the T gene determine the anteroposterior axis of a mouse embryo? Jpn J Genet 65 287–297 Occurrence Handle2248783

    PubMed  Google Scholar 

  • M. Zuker (2003) ArticleTitleMfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res 31 3406–3415 Occurrence Handle10.1093/nar/gkg595 Occurrence Handle12824337

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Dr. H. Siomi for providing facilities throughout the course of this study; F. Unemi, T. Nagami and R. Makimoto for fish maintenance; H. Takeda and M. Seiki-Furutani for the ntl mutants; and the members of H. Siomi lab for technical assistance and advice.

Author information

Author notes

  1. Nobuyoshi Shimoda

    Present address: Laboratory of Developmental Genetics, Department of Biological Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

Authors and Affiliations

  1. Japan Science and Technology Corporation (JST), Institute for Genome Research, University of Tokushima, 3-18-15 Kuramoto, Tokushima, 770-8503, Japan

    Kimi Yamakoshi, Yuji Shishido & Nobuyoshi Shimoda

Authors
  1. Kimi Yamakoshi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuji Shishido
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nobuyoshi Shimoda
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nobuyoshi Shimoda.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yamakoshi, K., Shishido, Y. & Shimoda, N. Generation of Aberrant Transcripts of and Free DNA Ends in Zebrafish no tail Gene. Mar Biotechnol 7, 163–172 (2005). https://doi.org/10.1007/s10126-004-3500-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-004-3500-8

Keywords

Search

Navigation