Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction

Gangning Liang, Mark L Gonzalgo, Carol Salem, Peter A. Jones

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

The ability to detect methylation changes associated with oncogenic transformation is of critical importance in understanding how DNA methylation may contribute to tumorigenesis. We have developed a simple and reproducible fingerprinting method called methylation-sensitive arbitrarily primed polymerase chain reaction (AP-PCR) to screen for DNA methylation changes. This technique relies on digesting genomic DNA with methylation-sensitive and -insensitive restriction enzymes (e.g., HpaII and MspI) prior to AP-PCR amplification. Matched normal and tumor DNAs were compared to identify differential methylation. After the PCR products were resolved on high-resolution polyacrylamide gels, regions of genomic DNA that showed hypo- and hypermethylation associated with tumors were detected. These fragments were then isolated, cloned, and sequenced. Novel CpG islands were found to be frequently hypermethylated in bladder and colon tumors. We have demonstrated that this technique is a rapid and efficient method that can be used to screen for altered methylation patterns in genomic DNA and to isolate specific sequences associated with these changes.

Original languageEnglish (US)
Pages (from-to)150-155
Number of pages6
JournalMethods
Volume27
Issue number2
DOIs
StatePublished - 2002
Externally publishedYes

Fingerprint

Methylation
Polymerase chain reaction
DNA Methylation
Carcinogenesis
Polymerase Chain Reaction
Tumors
DNA
CpG Islands
Urinary Bladder Neoplasms
Neoplasms
Colon
Amplification
Enzymes

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction. / Liang, Gangning; Gonzalgo, Mark L; Salem, Carol; Jones, Peter A.

In: Methods, Vol. 27, No. 2, 2002, p. 150-155.

Research output: Contribution to journalArticle

@article{1ca45e68d7cd43f9bbe84e660c3fd229,
title = "Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction",
abstract = "The ability to detect methylation changes associated with oncogenic transformation is of critical importance in understanding how DNA methylation may contribute to tumorigenesis. We have developed a simple and reproducible fingerprinting method called methylation-sensitive arbitrarily primed polymerase chain reaction (AP-PCR) to screen for DNA methylation changes. This technique relies on digesting genomic DNA with methylation-sensitive and -insensitive restriction enzymes (e.g., HpaII and MspI) prior to AP-PCR amplification. Matched normal and tumor DNAs were compared to identify differential methylation. After the PCR products were resolved on high-resolution polyacrylamide gels, regions of genomic DNA that showed hypo- and hypermethylation associated with tumors were detected. These fragments were then isolated, cloned, and sequenced. Novel CpG islands were found to be frequently hypermethylated in bladder and colon tumors. We have demonstrated that this technique is a rapid and efficient method that can be used to screen for altered methylation patterns in genomic DNA and to isolate specific sequences associated with these changes.",
author = "Gangning Liang and Gonzalgo, {Mark L} and Carol Salem and Jones, {Peter A.}",
year = "2002",
doi = "10.1016/S1046-2023(02)00068-3",
language = "English (US)",
volume = "27",
pages = "150--155",
journal = "Methods in Enzymology",
issn = "0076-6879",
publisher = "Academic Press Inc.",
number = "2",

}

TY - JOUR

T1 - Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction

AU - Liang, Gangning

AU - Gonzalgo, Mark L

AU - Salem, Carol

AU - Jones, Peter A.

PY - 2002

Y1 - 2002

N2 - The ability to detect methylation changes associated with oncogenic transformation is of critical importance in understanding how DNA methylation may contribute to tumorigenesis. We have developed a simple and reproducible fingerprinting method called methylation-sensitive arbitrarily primed polymerase chain reaction (AP-PCR) to screen for DNA methylation changes. This technique relies on digesting genomic DNA with methylation-sensitive and -insensitive restriction enzymes (e.g., HpaII and MspI) prior to AP-PCR amplification. Matched normal and tumor DNAs were compared to identify differential methylation. After the PCR products were resolved on high-resolution polyacrylamide gels, regions of genomic DNA that showed hypo- and hypermethylation associated with tumors were detected. These fragments were then isolated, cloned, and sequenced. Novel CpG islands were found to be frequently hypermethylated in bladder and colon tumors. We have demonstrated that this technique is a rapid and efficient method that can be used to screen for altered methylation patterns in genomic DNA and to isolate specific sequences associated with these changes.

AB - The ability to detect methylation changes associated with oncogenic transformation is of critical importance in understanding how DNA methylation may contribute to tumorigenesis. We have developed a simple and reproducible fingerprinting method called methylation-sensitive arbitrarily primed polymerase chain reaction (AP-PCR) to screen for DNA methylation changes. This technique relies on digesting genomic DNA with methylation-sensitive and -insensitive restriction enzymes (e.g., HpaII and MspI) prior to AP-PCR amplification. Matched normal and tumor DNAs were compared to identify differential methylation. After the PCR products were resolved on high-resolution polyacrylamide gels, regions of genomic DNA that showed hypo- and hypermethylation associated with tumors were detected. These fragments were then isolated, cloned, and sequenced. Novel CpG islands were found to be frequently hypermethylated in bladder and colon tumors. We have demonstrated that this technique is a rapid and efficient method that can be used to screen for altered methylation patterns in genomic DNA and to isolate specific sequences associated with these changes.

UR - http://www.scopus.com/inward/record.url?scp=0036315414&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036315414&partnerID=8YFLogxK

U2 - 10.1016/S1046-2023(02)00068-3

DO - 10.1016/S1046-2023(02)00068-3

M3 - Article

C2 - 12095274

AN - SCOPUS:0036315414

VL - 27

SP - 150

EP - 155

JO - Methods in Enzymology

JF - Methods in Enzymology

SN - 0076-6879

IS - 2

ER -