NotI subtraction and NotI-specific microarrays to detect copy number and methylation changes in whole genomes
| Autor: | Jingfeng Li, Claes Wahlestedt, Lev L. Kisselev, Olga Vorontsova, Olga V. Muravenko, Lev Petrenko, Alexei Protopopov, Veronika I. Zabarovska, Fuli Wang, Ingemar Ernberg, Michael I. Lerman, V. N. Senchenko, Eugene R. Zabarovsky, George Klein, Valentin N. Petushkov, Vladimir I. Kashuba, Eleonora A. Braga |
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| Jazyk: | angličtina |
| Rok vydání: | 2002 |
| Předmět: |
Lung Neoplasms
Gene Dosage Biology Gene dosage Genome Mice Animals Humans Genetic Testing Carcinoma Small Cell Deoxyribonucleases Type II Site-Specific Gene Carcinoma Renal Cell Oligonucleotide Array Sequence Analysis Genetics Multidisciplinary Methylation DNA Neoplasm Biological Sciences DNA Methylation Kidney Neoplasms CpG site DNA methylation Human genome Chromosomes Human Pair 3 DNA microarray Chromosome Deletion human activities |
| Popis: | Methylation, deletions, and amplifications of cancer genes constitute important mechanisms in carcinogenesis. For genome-wide analysis of these changes, we propose the use of Not I clone microarrays and genomic subtraction, because Not I recognition sites are closely associated with CpG islands and genes. We show here that the CODE (Cloning Of DEleted sequences) genomic subtraction procedure can be adapted to Not I flanking sequences and to CpG islands. Because the sequence complexity of this procedure is greatly reduced, only two cycles of subtraction are required. A Not I-CODE procedure can be used to prepare Not I representations (NRs) containing 0.1–0.5% of the total DNA. The NRs contain, on average, 10-fold less repetitive sequences than the whole human genome and can be used as probes for hybridization to Not I microarrays. These microarrays, when probed with NRs, can simultaneously detect copy number changes and methylation. Not I microarrays offer a powerful tool with which to study carcinogenesis. |
| Databáze: | OpenAIRE |
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