An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands

Zunyan Dai, Dieter Weichenhan, Yue Zhong Wu, Julia L. Hall, Laura J. Rush, Laura T. Smith, Aparna Raval, Li Yu, Daniela Kroll, Joerg Muehlisch, Michael C. Frühwald, Pieter De Jong, Joe Catanese, Ramana V. Davuluri, Dominic J. Smiraglia, Christoph Plass*

*Corresponding author for this work

Research output: Contribution to journalArticle

22 Scopus citations

Abstract

Knudson's two-hit hypothesis postulates that genetic alterations in both alleles are required for the inactivation of tumor-suppressor genes. Genetic alterations include small or large deletions and mutations. Over the past years, it has become clear that epigenetic alterations such as DNA methylation are additional mechanisms for gene silencing. Restriction Landmark Genomic Scanning (RLGS) is a two-dimensional gel electrophoresis that assesses the methylation status of thousands of CpG islands. RLGS has been applied successfully to scan cancer genomes for aberrant DNA methylation patterns. So far, the majority of this work was done using NotI as the restriction landmark site. Here, we describe the development of RLGS using AscI as the restriction landmark site for genome-wide scans of cancer genomes. The availability of AscI as a restriction landmark for RLGS allows for scanning almost twice as many CpG islands in the human genome compared with using NotI only. We describe the development of an AscI-EcoR V boundary library that supports the cloning of novel methylated genes. Feasibility of this system is shown in three tumor types, medulloblastomas, lung cancers, and head and neck cancers. We report the cloning of 178 AscI RLGS fragments via two methods by use of this library.

Original languageEnglish (US)
Pages (from-to)1591-1598
Number of pages8
JournalGenome research
Volume12
Issue number10
DOIs
StatePublished - Oct 1 2002

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Dai, Z., Weichenhan, D., Wu, Y. Z., Hall, J. L., Rush, L. J., Smith, L. T., Raval, A., Yu, L., Kroll, D., Muehlisch, J., Frühwald, M. C., De Jong, P., Catanese, J., Davuluri, R. V., Smiraglia, D. J., & Plass, C. (2002). An AscI boundary library for the studies of genetic and epigenetic alterations in CpG islands. Genome research, 12(10), 1591-1598. https://doi.org/10.1101/gr.197402