Abstract
The role of cytosine methylation in the regulation of gene expression during normal development and malignant transformation is currently under intense investigation. An ever increasing body of evidence demonstrates that carcinogenesis is associated with aberrant DNA methylation of the promoters of tumor suppressor genes (Chin Med J (Engl) 111:1028-1030, 1998; Leukemia 17:2533-2535, 2003), hypomethylation of oncogenes (Toxicol Appl Pharmacol 206:288-298, 2005; Toxicology 50:231-245, 1988), and concurrent loss of methylation in the intergenic areas and gene bodies, which may lead to genomic instability and chromosomal fragility (Cytogenet Cell Genet 89:121-128, 2000). Single locus methylation assays have focused largely on specific known tumor suppressor genes or oncogenes (Chin Med J (Engl) 111:1028-1030, 1998; Cancer Res 57:594-599, 1997; Hum Genet 94:491-496, 1994; Mol Cell Biol 14:4225-4232, 1994; Gastroenterology 116:394-400, 1999). Such approaches, while being useful, have clear limitations. With the advent of genome-wide microarray-based techniques, it has become possible to perform genome-wide exploratory studies to better understand genomic patterning of DNA methylation and also to discover new potential disease-specific epigenetic lesions (J Cell Biochem 88:138-143, 2003; Genome Res 16:1075-1083, 2006). In order to capture this type of information from primary human tissues, we have adopted and optimized the HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR) to compare and contrast the abundance of cytosine methylation of genomic regions that are relatively enriched for CpG dinucleotides. While we have mainly used a custom NimbleGen-Roche high-density oligonucleotide microarray containing 25,626 HpaII amplifiable fragments, many other microarray platforms or high throughput sequencing strategies can be used with HELP.
| Original language | English (US) |
|---|---|
| Title of host publication | Microarray Methods for Drug Discovery |
| Editors | Sridar V. Chittur |
| Pages | 191-201 |
| Number of pages | 11 |
| DOIs | |
| State | Published - Dec 1 2010 |
| Externally published | Yes |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 632 |
| ISSN (Print) | 1064-3745 |
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Keywords
- DNA methylation
- Epigenomics
- Gene regulation
- Genomic microarray
- HELP assay
ASJC Scopus subject areas
- Molecular Biology
- Genetics
Cite this
HELP (HpaII tiny fragment enrichment by ligation-mediated pcr) assay for dna methylation profiling of primary normal and malignant b lymphocytes. / Shaknovich, Rita; Figueroa, Maria; Melnick, Ari.
Microarray Methods for Drug Discovery. ed. / Sridar V. Chittur. 2010. p. 191-201 (Methods in Molecular Biology; Vol. 632).Research output: Chapter in Book/Report/Conference proceeding › Chapter
}
TY - CHAP
T1 - HELP (HpaII tiny fragment enrichment by ligation-mediated pcr) assay for dna methylation profiling of primary normal and malignant b lymphocytes
AU - Shaknovich, Rita
AU - Figueroa, Maria
AU - Melnick, Ari
PY - 2010/12/1
Y1 - 2010/12/1
N2 - The role of cytosine methylation in the regulation of gene expression during normal development and malignant transformation is currently under intense investigation. An ever increasing body of evidence demonstrates that carcinogenesis is associated with aberrant DNA methylation of the promoters of tumor suppressor genes (Chin Med J (Engl) 111:1028-1030, 1998; Leukemia 17:2533-2535, 2003), hypomethylation of oncogenes (Toxicol Appl Pharmacol 206:288-298, 2005; Toxicology 50:231-245, 1988), and concurrent loss of methylation in the intergenic areas and gene bodies, which may lead to genomic instability and chromosomal fragility (Cytogenet Cell Genet 89:121-128, 2000). Single locus methylation assays have focused largely on specific known tumor suppressor genes or oncogenes (Chin Med J (Engl) 111:1028-1030, 1998; Cancer Res 57:594-599, 1997; Hum Genet 94:491-496, 1994; Mol Cell Biol 14:4225-4232, 1994; Gastroenterology 116:394-400, 1999). Such approaches, while being useful, have clear limitations. With the advent of genome-wide microarray-based techniques, it has become possible to perform genome-wide exploratory studies to better understand genomic patterning of DNA methylation and also to discover new potential disease-specific epigenetic lesions (J Cell Biochem 88:138-143, 2003; Genome Res 16:1075-1083, 2006). In order to capture this type of information from primary human tissues, we have adopted and optimized the HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR) to compare and contrast the abundance of cytosine methylation of genomic regions that are relatively enriched for CpG dinucleotides. While we have mainly used a custom NimbleGen-Roche high-density oligonucleotide microarray containing 25,626 HpaII amplifiable fragments, many other microarray platforms or high throughput sequencing strategies can be used with HELP.
AB - The role of cytosine methylation in the regulation of gene expression during normal development and malignant transformation is currently under intense investigation. An ever increasing body of evidence demonstrates that carcinogenesis is associated with aberrant DNA methylation of the promoters of tumor suppressor genes (Chin Med J (Engl) 111:1028-1030, 1998; Leukemia 17:2533-2535, 2003), hypomethylation of oncogenes (Toxicol Appl Pharmacol 206:288-298, 2005; Toxicology 50:231-245, 1988), and concurrent loss of methylation in the intergenic areas and gene bodies, which may lead to genomic instability and chromosomal fragility (Cytogenet Cell Genet 89:121-128, 2000). Single locus methylation assays have focused largely on specific known tumor suppressor genes or oncogenes (Chin Med J (Engl) 111:1028-1030, 1998; Cancer Res 57:594-599, 1997; Hum Genet 94:491-496, 1994; Mol Cell Biol 14:4225-4232, 1994; Gastroenterology 116:394-400, 1999). Such approaches, while being useful, have clear limitations. With the advent of genome-wide microarray-based techniques, it has become possible to perform genome-wide exploratory studies to better understand genomic patterning of DNA methylation and also to discover new potential disease-specific epigenetic lesions (J Cell Biochem 88:138-143, 2003; Genome Res 16:1075-1083, 2006). In order to capture this type of information from primary human tissues, we have adopted and optimized the HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR) to compare and contrast the abundance of cytosine methylation of genomic regions that are relatively enriched for CpG dinucleotides. While we have mainly used a custom NimbleGen-Roche high-density oligonucleotide microarray containing 25,626 HpaII amplifiable fragments, many other microarray platforms or high throughput sequencing strategies can be used with HELP.
KW - DNA methylation
KW - Epigenomics
KW - Gene regulation
KW - Genomic microarray
KW - HELP assay
UR - http://www.scopus.com/inward/record.url?scp=77953253061&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77953253061&partnerID=8YFLogxK
U2 - 10.1007/978-1-60761-663-4_12
DO - 10.1007/978-1-60761-663-4_12
M3 - Chapter
C2 - 20217579
AN - SCOPUS:77953253061
SN - 9781607616627
T3 - Methods in Molecular Biology
SP - 191
EP - 201
BT - Microarray Methods for Drug Discovery
A2 - Chittur, Sridar V.
ER -