Genome tiling array

The combination of chromatin immunoprecipitation with DNA microarrays allows the genome-wide analysis of the distribution of an antigen. The immunoprecipitated DNA is quantitatively amplified, labeled and used to probe DNA microarrays. In principle ChIP-on-chip methods can be divided into two basic groups, depending on the content of the microarrays which are used (i) microarrays/promoter tiling arrays and (ii) genome tiling arrays. 

In microarrays the probes are designed with a focus on specific genomic elements such as promoters. These promoter tiling arrays have the advantage that costs are reduced, but they are biased since array design relies on known aimotation. Thus, relevant regions may not be covered [20]. 

Methyl-DNA immunoprecipitation (MeDip) can be used to identify methylated CpG islands in the genome. MeDip utilizes either antibodies against methylated CpG or the MBD (GpG methylation binding) proteins for immunoprecipitation of methylated DNA. Analysis of the DNA by tiling arrays or sequencing makes DNA methylation mapping across the genome possible [25]. 

Kapranov P, Drenkow J, Cheng J, et al. (2005). Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15 987-997. 

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