+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Comprehensive DNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay

Comprehensive DNA methylation profiling of human repetitive DNA elements using an MeDIP-on-RepArray assay

Methods in Molecular Biology 859: 267-291

Hypomethylation of repetitive DNA elements is a common epigenetics event in cancer. Although it is believed that this hypomethylation impacts chromosomal and transcriptional stability of the genome, the extent of repetitive sequences contribution to the development and progression of human cancers remains to be clarified. Repetitive sequences have largely been ignored by genome-wide studies, and thus little is known about the DNA methylation profiles of different repetitive DNA elements types. As a step toward investigating epigenetic landscape of repetitive DNA, we have developed a repeat-specific DNA microarray called RepArray. The RepArray comprises 236 prototypic oligonucleotides that span the main repetitive elements families found in the human genome. Combined to a methylated DNA immunoprecipitation (MeDIP) approach, RepArray allows depicting simultaneously the global trends that affect multiple repeat classes through the analysis of a restricted number of targets. Here, we present the MeDIP-on-RepArray protocol as it was established in our laboratory to delineate DNA methylation changes after chemical or genetic disruption of DNA methyltransferase activity in cells. It might serve as a workflow guideline for screening DNA methylation changes on repetitive elements during development and aging, among tissues and in various types of stress or pathological situations.

Please choose payment method:

(PDF emailed within 1 workday: $29.90)

Accession: 052269593

Download citation: RISBibTeXText

PMID: 22367878

Related references

MeDIP-on-Chip for methylation profiling. Methods in Molecular Biology 1249: 281-290, 2015

Comprehensive analysis of DNA-methylation in mammalian tissues using MeDIP-chip. Methods 53(2): 175-184, 2011

Epigenetic alterations in TRAMP mice: epigenome DNA methylation profiling using MeDIP-seq. Cell and Bioscience 8: 3, 2018

Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots. Clinical Epigenetics 8: 81, 2016

DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation. Genome Research 23(12): 2030-2041, 2014

Su1863 Genome-Wide Identification of Epstein-Barr Virus (EBV) Driven Gastric Cancer-Related DNA Methylation by Medip-Chip Profiling of EBV Infected AGS Cells. Gastroenterology 142(5): S-521-S-522, 2012

Genome-Wide Methylation Patterns in Androgen-Independent Prostate Cancer Cells: A Comprehensive Analysis Combining MeDIP-Bisulfite, RNA, and microRNA Sequencing Data. Genes 9(1), 2018

Comprehensive DNA Methylation and Gene Expression Profiling in Differentiating Human Adipocytes. Journal of Cellular Biochemistry 117(12): 2707-2718, 2016

Methylation profile of DNA repetitive elements in human testicular germ cell tumor. Molecular Carcinogenesis 51(9): 711-722, 2012

Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 27(12): 2409-2423, 2006

DNA methylation of stress-related genes and LINE-1 repetitive elements across the healthy human placenta. Placenta 33(3): 183-187, 2012

Genome-wide dynamic changes of DNA methylation of repetitive elements in human embryonic stem cells and fetal fibroblasts. Genomics 99(1): 10-17, 2012

In utero exposures, infant growth, and DNA methylation of repetitive elements and developmentally related genes in human placenta. Environmental Health Perspectives 120(2): 296-302, 2012

In Utero Exposures, Infant Growth, and Dna Methylation of Repetitive Elements and Developmentally Related Genes in Human Placenta. Environmental Health Perspectives 120(2): 296-302, 2012

Methylation-level inferences and detection of differential methylation with MeDIP-seq data. Plos One 13(8): E0201586, 2018