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Title: Deletions of a differentially methylated CpG island at SNRPN define a putative imprinting control region

Abstract

Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are associated with paternal and maternal deficiencies, respectively, of gene expression within human chromosome 15q11-q13, and are caused by deletion, uniparental disomy, or other mutations. Four transcripts designated PAR-5, PAR-7, PAR-1 and PAR-4 were isolated and localized to a region within 300 kb telomeric to the gene encoding small nuclear ribonucleoprotein-associated polypeptide N (SNRPN). Analysis of the transcripts in cultured fibroblasts and lymphoblasts from deletion patients demonstrated that SNRPN, PAR-5 and PAR-1 are expressed exclusively from the paternal chromosome, defining an imprinted domain that spans at least 200 kb. All three imprinted transcripts were absent in cells from three PWS patients (one pair of sibs and one sporadic case) with small deletions that involve a differentially methylated CpG island containing a previously undescribed 5{prime} untranslated exon ({alpha}) of SNRPN. Methylation of the CpG island is specific for the maternal chromosome consistent with paternal expression of the imprinted domain. One deletion, which is benign when maternally transmitted, extends upstream <30 kb from the CpG island, and is associated with altered methylation centromeric to SNRPN, and loss of transcription telomeric to SNRPN, implying the presence of an imprinting control region around the CpG island containingmore » exon {alpha}.« less

Authors:
; ;  [1]
  1. Baylor College of Medicine, Houston, TX (United States) [and others
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
133378
Report Number(s):
CONF-941009-
Journal ID: AJHGAG; ISSN 0002-9297; TRN: 95:005313-0106
Resource Type:
Journal Article
Resource Relation:
Journal Name: American Journal of Human Genetics; Journal Volume: 55; Journal Issue: Suppl.3; Conference: 44. annual meeting of the American Society of Human Genetics, Montreal (Canada), 18-22 Oct 1994; Other Information: PBD: Sep 1994
Country of Publication:
United States
Language:
English
Subject:
55 BIOLOGY AND MEDICINE, BASIC STUDIES; GENES; TRANSCRIPTION; HUMAN CHROMOSOME 15; GENETIC MAPPING; CHROMOSOMAL ABERRATIONS; PATIENTS; HEREDITARY DISEASES; NERVOUS SYSTEM DISEASES; DNA; METHYLATION; GENETICS; CENTROMERES; TELOMERES

Citation Formats

Sutcliffe, J.S.,, Nakao, M., and Beaudet, A.L.. Deletions of a differentially methylated CpG island at SNRPN define a putative imprinting control region. United States: N. p., 1994. Web. doi:10.1038/ng0994-52.
Sutcliffe, J.S.,, Nakao, M., & Beaudet, A.L.. Deletions of a differentially methylated CpG island at SNRPN define a putative imprinting control region. United States. doi:10.1038/ng0994-52.
Sutcliffe, J.S.,, Nakao, M., and Beaudet, A.L.. 1994. "Deletions of a differentially methylated CpG island at SNRPN define a putative imprinting control region". United States. doi:10.1038/ng0994-52.
@article{osti_133378,
title = {Deletions of a differentially methylated CpG island at SNRPN define a putative imprinting control region},
author = {Sutcliffe, J.S., and Nakao, M. and Beaudet, A.L.},
abstractNote = {Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are associated with paternal and maternal deficiencies, respectively, of gene expression within human chromosome 15q11-q13, and are caused by deletion, uniparental disomy, or other mutations. Four transcripts designated PAR-5, PAR-7, PAR-1 and PAR-4 were isolated and localized to a region within 300 kb telomeric to the gene encoding small nuclear ribonucleoprotein-associated polypeptide N (SNRPN). Analysis of the transcripts in cultured fibroblasts and lymphoblasts from deletion patients demonstrated that SNRPN, PAR-5 and PAR-1 are expressed exclusively from the paternal chromosome, defining an imprinted domain that spans at least 200 kb. All three imprinted transcripts were absent in cells from three PWS patients (one pair of sibs and one sporadic case) with small deletions that involve a differentially methylated CpG island containing a previously undescribed 5{prime} untranslated exon ({alpha}) of SNRPN. Methylation of the CpG island is specific for the maternal chromosome consistent with paternal expression of the imprinted domain. One deletion, which is benign when maternally transmitted, extends upstream <30 kb from the CpG island, and is associated with altered methylation centromeric to SNRPN, and loss of transcription telomeric to SNRPN, implying the presence of an imprinting control region around the CpG island containing exon {alpha}.},
doi = {10.1038/ng0994-52},
journal = {American Journal of Human Genetics},
number = Suppl.3,
volume = 55,
place = {United States},
year = 1994,
month = 9
}
  • The small nuclear ribonucleoprotein-associated protein SmN (SNRPN) gene is located in the Prader-Willi syndrome (PWS) critical region in chromosome 15q11-q13. We have previously shown that it is functionally imprinted in humans, being only expressed from the paternal allele and differentially methylated on parental alleles. Therefore, SNRPN may have a role in PWS, although genetic studies suggest that at least two genes may be necessary for the classical PWS phenotype. We have characterized the SNRPN genomic structure, and shown that it comprises ten exons. Surprisingly, we identified an open reading frame (ORF) in the first three exons, 190-bp 5{prime} to themore » SmN ORF. Notably, the majority of base substitutions bewteen human and rodents in the upstream ORF occurred in the wobble position of codons, suggesting selection for a protein coding function. This ORF, which we name SNURF (SNRPN upstream reading frame) encodes a putative polypeptide of 71 amino acids. By analogy to prokaryotic operons that encode proteins with related functions, it is possible that SNURF may have a role in pre-mRNA splicing.« less
  • Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are associated with paternal and maternal deficiencies respectively, of gene expression within human chromosome 15q11-q13, and are caused by deletion, uniparental disomy (UPD), or other mutations. The SNRPN gene maps in this region, is paternally expressed, and is a candidate gene for PWS. Southern blotting using methylation-sensitive enzymes and a genomic DNA probe from the CpG island containing exon {alpha} of the SNRPN gene reveals methylation specific for the maternal allele. In cases of the usual deletions or UPD, the probe detects absence of an unmethylated allele in PWS and absence of amore » methylated allele in AS. We have analyzed 21 nondeletion/nonUPD AS patients with this probe and found evidence for an imprinting mutation (absence of a methylated allele) in 3 patients. Southern blotting with methylation-sensitive enzymes using the exon {alpha} probe, like use of the PW71 probe, should detect abnormalities in all known PWS cases and in 3 of the 4 forms of AS: deletion, UPD and imprinting mutations. This analysis provides a valuable diagnostic approach for PWS and AS. In efforts to localize the imprinting mutations in AS, one patient was found with failure to inherit a dinucleotide repeat polymorphism near probe 189-1 (D15S13). Analysis of this locus in AS families and CEPH families demonstrates a polymorphism that impairs amplification and a different polymorphism involving absence of hybridization to the 189-1 probe. The functional significance, if any, of deletion of the 189-1 region is unclear.« less
  • Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are distinct clinical disorders resulting from deficiency of paternal (PWS) or maternal (AS) expression of imprinted genes within chromosome 15q11-q13. 15 refs., 1 fig.
  • The Miller-Dieker syndrome (MDS), composed of characteristic facial abnormalities and a severe neuronal migration disorder affecting the cerebral cortex, is caused by visible or submicroscopic deletions of chromosome band 17p13. Twelve anonymous DNA markers were tested against a panel of somatic cell hybrids containing 17p deletions from seven MDS patients. All patients, including three with normal karyotypes, are deleted for a variable set of 5-12 markers. Two highly polymorphic VNTR (variable number of tandem repeats) probes, YNZ22 and YNH37, are codeleted in all patients tested and make molecular diagnosis for this disorder feasible. By pulsed-field gel electrophoresis, YNZ22 and YNH37more » were shown to be within 30 kilobases (kb) of each other. Cosmid clones containing both VNTR sequences were identified, and restriction mapping showed them to be <15 kb apart. Three overlapping cosmids spanning >100 kb were completely deleted in all patients, providing a minimum estimate of the size of the MDS critical region. A hypomethylated island and evolutionarily conserved sequences were identified within this 100-kb region, indications of the presence of one or more expressed sequences potentially involved in the pathophysiology of this disorder. The conserved sequences were mapped to mouse chromosome 11 by using mouse-rat somatic cell hybrids, extending the remarkable homology between human chromosome 17 and mouse chromosome 11 by 30 centimorgans, into the 17p telomere region.« less
  • We previously reported that loss of heterozygosity (LOH) of 1p is found in all pheochromocytomas from patients with the Multiple Endocrine Neoplasia type 2 syndromes and in 40% of sporadic pheochromocytomas. We used 24 polymorphic DNA markers to map the deleted region in 27 tumors and found that in all tumors with 1p LOH, the deletion involves the entire short arm. LOH of 1q has not been found. The common breakpoint in these tumors is between D1S514 and D1S442 which defines a 2 centiMorgan interval which includes the centromere. To determine whether genomic imprinting plays a role in 1p deletionmore » in these tumors, parental DNA was obtained for eight individuals with pheochromocytomas and the parental DNA was obtained for eight individuals with pheochromocytomas and the parental origin of allelic loss determined. In four cases the paternal allele was lost and in four cases, the maternal allele was lost. In addition, allelic loss was examined in multifocal or bilateral tumors from five individuals. 1p LOH was demonstrated in all tumors examined, but in two patients, tumors from different sites demonstrated opposite patterns of allelic loss, indicating that either maternal or paternal alleles may be lost in different tumors from the same individual. These data show that deletion of 1p is a significant event in the development of human pheochromocytomas, and involves a common breakpoint in the pericentromeric area. Allelic deletion is not influenced by the parent of origin.« less