Source:http://linkedlifedata.com/resource/pubmed/id/11807986
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
3
|
| pubmed:dateCreated |
2002-1-24
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| pubmed:databankReference | |
| pubmed:abstractText |
Restriction landmark genome scanning (RLGS) allows comparative analysis of several thousand DNA fragments in the genome and provides a means to identify CpG islands that are altered in tumor cells as a result of amplification, deletion, or methylation changes. We have developed a novel informatics tool, designated virtual genome scan (VGS), that makes it possible to predict automatically the sequence of fragments in RLGS patterns by matching to the human genome sequence. A combination of RLGS and VGS was utilized to identify changes of chromosome 1-derived fragments in neuroblastoma. A NotI-EcoRV fragment was found to be absent frequently in neuroblastoma cell line RLGS patterns. Sequence prediction by VGS as well as cloning of the fragment showed that it contained a CpG island that is part of the human orthologue of the hamster homeobox gene Alx3. Expression analysis in a panel of human and mouse tissues showed predominant expression of ALX3 in brain tissue. Methylation-sensitive sequence analysis of the promoter region in neuroblastoma cell lines indicated that methylation of specific sequences correlated with repression of the ALX3 gene. Expression was re-induced after treatment with the methylation inhibitor 5-aza-2'-deoxycytidine. Promoter methylation analysis of ALX3 in primary neuroblastoma tumors, using methylation-sensitive polymerase chain reaction, found preferential ALX3 methylation in advanced-stage tumors. The VGS approach we have implemented in combination with RLGS is useful for the identification of genomic CpG island-related methylation changes or deletions in cancer.
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| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:citationSubset |
IM
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| pubmed:chemical | |
| pubmed:status |
MEDLINE
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| pubmed:month |
Mar
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| pubmed:issn |
1045-2257
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| pubmed:author |
pubmed-author:AmbrosPeter FPF,
pubmed-author:EckartMarkusM,
pubmed-author:FonatschChristaC,
pubmed-author:HanashSam MSM,
pubmed-author:KuickRorkR,
pubmed-author:LambBarbara JBJ,
pubmed-author:RouillardJean MarieJM,
pubmed-author:WeinhäuslAndreasA,
pubmed-author:WimmerKatharinaK,
pubmed-author:Zhu XxXiao-xiangXX
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| pubmed:copyrightInfo |
Copyright 2002 Wiley-Liss, Inc.
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| pubmed:issnType |
Print
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| pubmed:volume |
33
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| pubmed:owner |
NLM
|
| pubmed:authorsComplete |
Y
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| pubmed:pagination |
285-94
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| pubmed:dateRevised |
2006-11-15
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| pubmed:meshHeading |
pubmed-meshheading:11807986-Adult,
pubmed-meshheading:11807986-Animals,
pubmed-meshheading:11807986-Chromosomes, Human, Pair 1,
pubmed-meshheading:11807986-CpG Islands,
pubmed-meshheading:11807986-Cricetinae,
pubmed-meshheading:11807986-DNA Fragmentation,
pubmed-meshheading:11807986-DNA Methylation,
pubmed-meshheading:11807986-Female,
pubmed-meshheading:11807986-Genes, Homeobox,
pubmed-meshheading:11807986-Genome, Human,
pubmed-meshheading:11807986-Homeodomain Proteins,
pubmed-meshheading:11807986-Humans,
pubmed-meshheading:11807986-Mice,
pubmed-meshheading:11807986-Molecular Sequence Data,
pubmed-meshheading:11807986-Neuroblastoma,
pubmed-meshheading:11807986-Restriction Mapping,
pubmed-meshheading:11807986-Reverse Transcriptase Polymerase Chain Reaction,
pubmed-meshheading:11807986-Sequence Homology, Nucleic Acid,
pubmed-meshheading:11807986-Tumor Cells, Cultured
|
| pubmed:year |
2002
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| pubmed:articleTitle |
Combined restriction landmark genomic scanning and virtual genome scans identify a novel human homeobox gene, ALX3, that is hypermethylated in neuroblastoma.
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| pubmed:affiliation |
Institut für Medizinische Biologie, Universität Wien, Vienna, Austria. katharina.wimmer@univie.ac.at
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| pubmed:publicationType |
Journal Article,
Comparative Study,
Research Support, Non-U.S. Gov't
|