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PMID: 3221864 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Structures of spontaneous deletions in Caenorhabditis elegans.

Molecular and cellular biology ·Vol. 8 ·No. 9 ·1988-09-00 ·Pages 3748-54

Pulak RA, Anderson P

Abstract

We have investigated the structural features of spontaneous deletions in Caenorhabditis elegans. We cloned and sequenced the junctions of 16 spontaneous deletions affecting the unc-54 myosin heavy-chain gene and compared their sequences with those of the wild type. We analyzed these sequences in an attempt to identify structural features of the gene that are consistently involved in the spontaneous deletion process. Most deletions (15 of 16) removed a single contiguous region of DNA, with no nucleotides inserted or rearranged at the deletion junctions; one deletion was more complex. unc-54 deletions were small, averaging 600 base pairs in length, and were randomly distributed throughout the gene. Unlike deletions that occur in Escherichia coli, spontaneous unc-54 deletions did not contain statistically significant direct or inverted repeats at or near their termini. Except for their small average size, we have not identified any distinguishing features of their sequence or structure. We discuss these results with regard to the mechanisms for spontaneous deletion in eucaryotic and procaryotic cells.

MeSH Terms
Alleles Animals Base Sequence Caenorhabditis/genetics Chromosome Deletion Cloning, Molecular DNA/genetics Genes Molecular Sequence Data Myosin Subfragments Myosins/genetics Peptide Fragments/genetics
Chemicals
Myosin Subfragments Peptide Fragments DNA Myosins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Pulak R A
Department of Genetics, University of Wisconsin, Madison 53706.
Anderson P
References (60)
60 references, click to expand
  1. Association of crossover points with topoisomerase I cleavage sites: a model for nonhomologous recombination.
    Science. 1985 Nov 22;230(4728):954-8 PMID: 2997924
  2. Mutation in LDL receptor: Alu-Alu recombination deletes exons encoding transmembrane and cytoplasmic domains.
    Science. 1985 Jan 11;227(4683):140-6 PMID: 3155573
  3. A pattern of partially homologous recombination in mouse L cells.
    Proc Natl Acad Sci U S A. 1984 Jan;81(1):206-10 PMID: 6320165
  4. Bacteriophage T4 DNA topoisomerase mediates illegitimate recombination in vitro.
    Proc Natl Acad Sci U S A. 1986 Feb;83(4):922-6 PMID: 3006033
  5. The Stability of Broken Ends of Chromosomes in Zea Mays.
    Genetics. 1941 Mar;26(2):234-82 PMID: 17247004
  6. Lambda replacement vectors carrying polylinker sequences.
    J Mol Biol. 1983 Nov 15;170(4):827-42 PMID: 6315951
  7. The gene structures of spontaneous mutations affecting a Caenorhabditis elegans myosin heavy chain gene.
    Genetics. 1985 Jan;109(1):67-79 PMID: 2981757
  8. Role of short regions of homology in intermolecular illegitimate recombination events.
    Proc Natl Acad Sci U S A. 1983 May;80(9):2452-6 PMID: 6302684
  9. Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli.
    J Mol Biol. 1978 Dec 25;126(4):847-57 PMID: 370408
  10. Relative rates of homologous and nonhomologous recombination in transfected DNA.
    Proc Natl Acad Sci U S A. 1985 May;82(10):3355-9 PMID: 2987922
  11. Recombination at the human alpha-globin gene cluster: sequence features and topological constraints.
    Cell. 1987 May 8;49(3):369-78 PMID: 3032452
  12. Extraordinary recombinational events in Escherichia coli. Their independence of the rec+ function.
    Genetics. 1967 Apr;55(4):699-707 PMID: 5341209
  13. Yeast recombination: the association between double-strand gap repair and crossing-over.
    Proc Natl Acad Sci U S A. 1983 Jul;80(14):4417-21 PMID: 6308623
  14. The genetics of Caenorhabditis elegans.
    Genetics. 1974 May;77(1):71-94 PMID: 4366476
  15. On the production of deletions in the chromosome of Escherichia coli.
    J Mol Biol. 1970 Oct 14;53(1):49-67 PMID: 4922221
  16. Differences in intracellular DNA ligation after microinjection and transfection.
    Mol Cell Biol. 1984 Feb;4(2):240-6 PMID: 6321956
  17. In vitro packaging of lambda and cosmid DNA.
    Methods Enzymol. 1979;68:299-309 PMID: 161604
  18. Modification of DNA ends can decrease end joining relative to homologous recombination in mammalian cells.
    Proc Natl Acad Sci U S A. 1987 Jul;84(14):4959-63 PMID: 3037530
  19. A Chinese G gamma + (A gamma delta beta)zero thalassemia deletion: comparison to other deletions in the human beta-globin gene cluster and sequence analysis of the breakpoints.
    Nucleic Acids Res. 1985 Sep 25;13(18):6559-75 PMID: 2997715
  20. DNA sequence studies of simian virus 40 chromosomal excision and integration in rat cells.
    J Mol Biol. 1984 Mar 25;174(1):55-84 PMID: 6325709
  21. Mechanisms of nonhomologous recombination in mammalian cells.
    Mol Cell Biol. 1985 Oct;5(10):2599-607 PMID: 3016509
  22. Sequence analysis of mutations that affect the synthesis, assembly and enzymatic activity of the unc-54 myosin heavy chain of Caenorhabditis elegans.
    J Mol Biol. 1985 Jun 25;183(4):543-51 PMID: 4020869
  23. Somatic cells efficiently join unrelated DNA segments end-to-end.
    Mol Cell Biol. 1982 Oct;2(10):1258-69 PMID: 6294502
  24. New M13 vectors for cloning.
    Methods Enzymol. 1983;101:20-78 PMID: 6310323
  25. Unequal crossing-over between two alu-repetitive DNA sequences in the low-density-lipoprotein-receptor gene. A possible mechanism for the defect in a patient with familial hypercholesterolaemia.
    Eur J Biochem. 1987 Apr 1;164(1):77-81 PMID: 3549308
  26. C. elegans unc-105 mutations affect muscle and are suppressed by other mutations that affect muscle.
    Genetics. 1986 Aug;113(4):853-67 PMID: 3744029
  27. Nucleotide sequence preference at rat liver and wheat germ type 1 DNA topoisomerase breakage sites in duplex SV40 DNA.
    Nucleic Acids Res. 1984 Apr 11;12(7):3097-114 PMID: 6326051
  28. Three Tn10-associated excision events: relationship to transposition and role of direct and inverted repeats.
    Cell. 1981 Jan;23(1):215-27 PMID: 6260376
  29. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  30. A deletion involving Alu sequences in the beta-hexosaminidase alpha-chain gene of French Canadians with Tay-Sachs disease.
    J Biol Chem. 1987 Nov 15;262(32):15396-9 PMID: 2824459
  31. Inverted duplication-transposition event in mammalian cells at an illegitimate recombination join.
    Mol Cell Biol. 1986 Jun;6(6):2179-84 PMID: 3023920
  32. The DNA of Caenorhabditis elegans.
    Genetics. 1974 May;77(1):95-104 PMID: 4858229
  33. Screening lambdagt recombinant clones by hybridization to single plaques in situ.
    Science. 1977 Apr 8;196(4286):180-2 PMID: 322279
  34. A 66-base pair insert bridges the deletion responsible for a mouse model of beta-thalassemia.
    J Biol Chem. 1986 Sep 15;261(26):12368-74 PMID: 3017971
  35. Protein structural domains in the Caenorhabditis elegans unc-54 myosin heavy chain gene are not separated by introns.
    Proc Natl Acad Sci U S A. 1983 Jul;80(14):4253-7 PMID: 6576334
  36. Illegitimate recombination at the replication origin of bacteriophage M13.
    Proc Natl Acad Sci U S A. 1986 May;83(10):3386-90 PMID: 3010295
  37. Duplication followed by deletion accounts for the structure of an Indian deletion beta (0)-thalassemia gene.
    Nucleic Acids Res. 1982 Dec 20;10(24):8025-9 PMID: 7162987
  38. Structural intermediates of deletion mutagenesis: a role for palindromic DNA.
    Proc Natl Acad Sci U S A. 1984 Jan;81(2):512-6 PMID: 6582506
  39. Human fetal G gamma- and A gamma-globin genes: complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes.
    Cell. 1980 Oct;21(3):627-38 PMID: 7438203
  40. Concerted deletions and inversions are caused by mitotic recombination between delta sequences in Saccharomyces cerevisiae.
    Mol Cell Biol. 1987 Mar;7(3):1198-207 PMID: 3550432
  41. Transposition of Tc1 in the nematode Caenorhabditis elegans.
    Proc Natl Acad Sci U S A. 1985 Mar;82(6):1756-60 PMID: 2984668
  42. Recombination within the myelin basic protein gene created the dysmyelinating shiverer mouse mutation.
    Proc Natl Acad Sci U S A. 1986 Oct;83(19):7542-6 PMID: 2429310
  43. Cell cycling and DNA replication in a mutant blocked in cell division in the nematode Caenorhabditis elegans.
    Dev Biol. 1978 Mar;63(1):165-78 PMID: 631425
  44. Drosophila topoisomerase II double-strand DNA cleavage: analysis of DNA sequence homology at the cleavage site.
    Nucleic Acids Res. 1985 Feb 25;13(4):1057-72 PMID: 2987816
  45. Unexpected relationships between four large deletions in the human beta-globin gene cluster.
    Cell. 1983 Dec;35(3 Pt 2):701-9 PMID: 6652684
  46. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions.
    Cell. 1982 Jun;29(2):319-28 PMID: 6288254
  47. Spontaneous deletion formation at the aprt locus of hamster cells: the presence of short sequence homologies and dyad symmetries at deletion termini.
    EMBO J. 1986 Jun;5(6):1199-204 PMID: 3015589
  48. Nonhomologous recombination in mammalian cells: role for short sequence homologies in the joining reaction.
    Mol Cell Biol. 1986 Dec;6(12):4295-304 PMID: 3025650
  49. Lac repressor can be fused to beta-galactosidase.
    Nature. 1974 Jun 7;249(457):561-3 PMID: 4599764
  50. Formation of deletion mutations in recombination-deficient mutants of Escherichia coli.
    J Bacteriol. 1967 Oct;94(4):1266-7 PMID: 4860912
  51. Analysis of an inversion within the human beta globin gene cluster.
    Nucleic Acids Res. 1985 Apr 25;13(8):2897-906 PMID: 4000967
  52. Mechanisms of spontaneous mutagenesis: an analysis of the spectrum of spontaneous mutation in the Escherichia coli lacI gene.
    J Mol Biol. 1986 May 20;189(2):273-84 PMID: 3018259
  53. Recombination between poly[d(GT).d(CA)] sequences in simian virus 40-infected cultured cells.
    Mol Cell Biol. 1985 Jun;5(6):1247-59 PMID: 2993859
  54. A gene deletion ending within a complex array of repeated sequences 3' to the human beta-globin gene cluster.
    Proc Natl Acad Sci U S A. 1986 Jul;83(14):5194-8 PMID: 2425363
  55. A high affinity topoisomerase I binding sequence is clustered at DNAase I hypersensitive sites in Tetrahymena R-chromatin.
    Cell. 1985 Jun;41(2):541-51 PMID: 2985282
  56. DNA sequence analysis of spontaneous mutations at the aprt locus of hamster cells.
    Mol Cell Biol. 1987 Apr;7(4):1445-9 PMID: 3037319
  57. High-efficiency ligation and recombination of DNA fragments by vertebrate cells.
    Science. 1983 May 6;220(4597):606-9 PMID: 6301012
  58. In vitro study of illegitimate recombination: involvement of DNA gyrase.
    Cold Spring Harb Symp Quant Biol. 1981;45 Pt 1:399-408 PMID: 6271485
  59. Illegitimate recombination mediated in vitro by DNA gyrase of Escherichia coli: structure of recombinant DNA molecules.
    Proc Natl Acad Sci U S A. 1982 Jun;79(12):3724-8 PMID: 6285361
  60. Alu-Alu recombination deletes splice acceptor sites and produces secreted low density lipoprotein receptor in a subject with familial hypercholesterolemia.
    J Biol Chem. 1987 Mar 5;262(7):3354-61 PMID: 3818645
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/mcb.8.9.3748-3754.1988
Published
1988-09-00
Pages
3748-54
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC365432
Subset
IM
Grants
NIGMS NIH HHS · GM30132 · United States
External Links
PubMed source DOI: 10.1128/mcb.8.9.3748-3754.1988 PMC Full Text View journal details
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