Tiling array
Like traditional microarrays, they function by hybridizing labeled DNA or RNA target molecules to probes fixed onto a solid surface.
[1] In addition to detecting previously unidentified genes and regulatory sequences, improved quantification of transcription products is possible.
The two main ways of synthesizing tiling arrays are photolithographic manufacturing and mechanical spotting or printing.
The first method involves in situ synthesis where probes, approximately 25bp, are built on the surface of the chip.
ChIP-chip experiments have been able to identify binding sites of transcription factors across the genome in yeast, drosophila and a few mammalian species.
The method of sequencing cDNA to find transcribed genes also runs into problems, such as failing to detect rare or very short RNA molecules, and so do not detect genes that are active only in response to signals or specific to a time frame.
The overlapping nature of the probes also allows detection of non-polyadenylated RNA and can produce a more precise picture of gene structure.
[6] Earlier studies on chromosome 21 and 22 showed the power of tiling arrays for identifying transcription units.
[9] Methyl-DNA immunoprecipitation followed by tiling array allows DNA methylation mapping and measurement across the genome.
Mapping these sites can add to the knowledge of expressed genes and also epigenetic regulation on a genome-wide level.
DNase chip is an application of tiling arrays to identify hypersensitive sites, segments of open chromatin that are more readily cleaved by DNaseI.
These hypersensitive sites have been shown to accurately predict regulatory elements such as promoter regions, enhancers and silencers.
On the other hand, fine-tiled array CGH would produce ultrahigh resolution to find other abnormalities such as breakpoints.
The RNA is copied into double stranded DNA, which is subsequently amplified and in vitro transcribed to cRNA.
Various software and algorithms are available for data analysis and vary in benefits depending on the manufacturer of the chip.
[2] Furthermore, the approach provides no clearly defined start or stop to regions of interest identified by the array.
