Principles and challenges of genome-wide DNA methylation analysis

@article{Laird2010PrinciplesAC,
  title={Principles and challenges of genome-wide DNA methylation analysis},
  author={Peter W. Laird},
  journal={Nature Reviews Genetics},
  year={2010},
  volume={11},
  pages={191-203}
}
  • P. Laird
  • Published 2 February 2010
  • Biology
  • Nature Reviews Genetics
Methylation of cytosine bases in DNA provides a layer of epigenetic control in many eukaryotes that has important implications for normal biology and disease. Therefore, profiling DNA methylation across the genome is vital to understanding the influence of epigenetics. There has been a revolution in DNA methylation analysis technology over the past decade: analyses that previously were restricted to specific loci can now be performed on a genome-scale and entire methylomes can be characterized… 

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...

References

SHOWING 1-10 OF 177 REFERENCES

Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion.

A genome-wide DNA methylation profiling technology employing a novel amplification step for DNA subjected to bisulfite-mediated cytosine conversion, which is more cost-effective than mCIP and requires as little as 100 ng of Arabidopsis DNA.

DNA methylation: a profile of methods and applications.

A review of methods designed to yield quantitative and qualitative information on genomic DNA methylation hopes to be a valuable tool in selecting the best techniques to address particular questions concerning the cytosine methylation status of genomic DNA.

Epigenomics: Mapping the Methylome

Comparisons between cancer and non-cancer cell types yielded differential methylation patterns that link genetic and epigenetic instability offering a new approach to decipher misregulation in cancer.

Genome-scale DNA methylation maps of pluripotent and differentiated cells

Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.

The MIRA method for DNA methylation analysis.

The methylated-CpG island recovery assay (MIRA), which is based on the high affinity of the MBD2b/MBD3L1 complex for double-stranded CpG-methylated DNA, has been used in combination with microarray platforms to map DNA methylation patterns across the human genome.

DNA methylation profiling of human chromosomes 6, 20 and 22

Analysis of six annotation categories showed that evolutionarily conserved regions are the predominant sites for differential DNA methylation and that a core region surrounding the transcriptional start site is an informative surrogate for promoter methylation.

Finding the fifth base: genome-wide sequencing of cytosine methylation.

Advanced "next-generation" DNA sequencing technologies are now enabling the global mapping of this epigenetic modification at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes.

Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets.

Six new targets of epigenetic inactivation are reported, including IRX3, WNT10A, W NT6, RARalpha, BMP7 and ZGPAT, which displayed cell line and tumor specific differential methylation when compared with normal brain samples, suggesting they may have utility as biomarkers.
...