Analysis of eighteen deletion breakpoints in the parkin gene

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Abstract

Parkin mutations are responsible for the pathogenesis of autosomal-recessive juvenile parkinsonism (AR-JP). On initial screening of Japanese patients with AR-JP, we had found that approximately half of the parkin mutations are deletions occurring between exons 2 and 5, forming a deletion hot spot. In this study, we investigated the deletion breakpoints of the parkin mutations in 22 families with AR-JP and examined the possible association between these deletion events and meiotic recombinations. We identified 18 deletion breakpoints at the DNA nucleotide sequence level. Almost all these deletions were different, indicating that the deletion hot spot was generated by recurrent but independent events. We found no association between the deletions and specific DNA elements. Recent copy number variation (CNV) data from various ethnic groups showed that the deletion hot spot is overlapped by a highly polymorphic CNV region, indicating that the recurrent deletion mutation or CNV is observable worldwide. By comparing Marshfield and deCODE linkage maps, we found that the parkin deletion hot spot may be associated with a meiotic recombination hot spot, although such association was not found on comparison with recent high-resolution genetic maps generated from the International HapMap project. Here, we discuss the possible mechanisms for deletion hot spot formation and its effects on human genomes.

Introduction

Parkin has been identified as the causative gene of autosomal-recessive juvenile parkinsonism (AR-JP) [1]. It is a gigantic gene occupying a 1.4-Mb genomic DNA sequence and consists of 12 exons with a 1.4-kb coding sequence [2]. The gene encodes a type of ubiquitin ligase (E3), which is associated with ubiquitin-conjugating enzymes (E2s) UbcH7 or UbcH8 [3]. Some proteins such as the O-glycosylated form of α-synuclein [4] and the Pael receptor [5] serve as substrates for parkin and accumulate in parkin-deficient patients.

Parkin mutations frequently cause early onset Parkinson’s disease, especially in the case of a family history and an autosomal-recessive mode of transmission. The frequency of such mutations has been estimated as 40–50% in familial cases and 10–20% in idiopathic cases of early onset Parkinson’s disease [6]. In our initial screening of the parkin mutations in Japanese patients with AR-JP, we found frequent occurrences of exon 3, exon 4, or both exon 3 and exon 4 deletions [7]. To date, 95 different mutations have been reported, and the exonic deletions have been commonly observed worldwide [8]. To precisely analyze the deleted regions, we had previously determined the 1.4-Mb genomic DNA sequence of the parkin gene in collaboration with the Sanger Centre [2]. Thus far, the DNA sequences of deletion breakpoints have been reported for only two cases of exon 4 deletions [9]. In this study, we investigated the deletion breakpoints of parkin mutations in 22 families with AR-JP and examined the possible association between these deletion events and meiotic recombinations.

Section snippets

Materials and methods

AR-JP families. This study included 16 Japanese families, one Korean family, one Taiwanese family, one Israeli family, and three Turkish families, totally comprising 27 individuals with AR-JP. Molecular analysis was performed for the 22 unrelated families, and all the patients showed some exonic deletions of the parkin gene. The findings on five of these families have been reported previously [7]. DNA samples were obtained from the patients following informed consent, and the study was approved

Features of the deletion breakpoints

We designed primer sets of 191 sequence tagged sites (STSs) along with the 1.4-Mb genomic sequence of the parkin gene and examined for the presence or absence of each STS in the DNA samples from 27 patients with AR-JP. PCR analysis revealed that all these patients had homozygous deletion of at least one exon. Therefore, they represented 44 deletions (88 deletion breakpoints). At least half of these deletion breakpoints (44 deletion breakpoints) were located (Fig. 1). We found six patients

Acknowledgments

We thank the patients and their family members for participating in this study and Dr. T Sasaki for his assistance. This study was partly supported by grants from the Research for the Future program by the Japan Society for the Promotion of Science (JSPS); the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT); and the Japanese Ministry of Health, Labor and Welfare.

References (32)

  • S. Kubo et al.

    Recessive Parkinson’s disease

    Movement Disorders

    (2006)
  • N. Hattori et al.

    Molecular genetic analysis of a novel parkin gene in Japanese families with autosomal recessive juvenile parkinsonism: evidence for variable homozygous deletions in the parkin gene in affected individuals

    Annals of Neurology

    (1998)
  • K. Hedrich et al.

    Distribution, type, and origin of parkin mutations: review and case studies

    Movement Disorders

    (2004)
  • J. Clarimon et al.

    Defining the ends of parkin exon 4 deletions in two different families with Parkinson’s disease

    American Journal of Medical Genetics Part B-Neuropsychiatric Genetics

    (2005)
  • C. Nobile et al.

    Analysis of 22 deletion breakpoints in dystrophin intron 49

    Human Genetics

    (2002)
  • K.A. Frazer et al.

    A second generation human haplotype map of over 3.1 million SNPs

    Nature

    (2007)
  • Cited by (0)

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