ChIP-chip ChIP-chip is one of the most popular usages of tiling arrays.
Chromatin immunoprecipitation allows binding sites of
proteins to be identified. A genome-wide variation of this is known as ChIP-on-chip. Proteins that bind to
chromatin are cross-linked
in vivo, usually via fixation with
formaldehyde. The chromatin is then fragmented and exposed to
antibodies specific to the protein of interest. These complexes are then precipitated. The DNA is then isolated and purified. With traditional DNA microarrays, the immunoprecipitated DNA is hybridized to the chip, which contains probes that are designed to cover representative genome regions. Overlapping probes or probes in very close proximity can be used. This gives an unbiased analysis with high resolution. Besides these advantages, tiling arrays show high reproducibility and with overlapping probes spanning large segments of the genome, tiling arrays can interrogate protein binding sites, which harbor repeats. ChIP-chip experiments have been able to identify binding sites of transcription factors across the genome in yeast, drosophila and a few mammalian species.
Transcriptome mapping Another popular use of tiling arrays is in finding expressed genes. Traditional methods of
gene prediction for annotation of genomic sequences have had problems when used to map the transcriptome, such as not producing an accurate structure of the genes and also missing transcripts entirely. 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. Tiling arrays can solve these issues. Due to the high resolution and sensitivity, even small and rare molecules can be detected. The overlapping nature of the probes also allows detection of non-polyadenylated RNA and can produce a more precise picture of
gene structure. Earlier studies on chromosome 21 and 22 showed the power of tiling arrays for identifying transcription units. The authors used 25-mer probes that were 35bp apart, spanning the entire chromosomes. Labeled targets were made from polyadenylated RNA. They found many more transcripts than predicted and 90% were outside of annotated
exons. Another study with Arabidopsis used high-density
oligonucleotide arrays that cover the entire genome. More than 10 times more transcripts were found than predicted by ESTs and other prediction tools. Also found were novel transcripts in the
centromeric regions where it was thought that no genes are actively expressed. Many noncoding and natural
antisense RNA have been identified using tiling arrays. Historically, the method uses Southern blotting to find digested fragments. Tiling arrays have allowed researchers to apply the technique on a genome-wide scale.
Comparative genomic hybridization (CGH) Array-based CGH is a technique often used in diagnostics to compare differences between types of DNA, such as normal cells vs. cancer cells. Two types of tiling arrays are commonly used for array CGH, whole genome and fine tiled. The whole genome approach would be useful in identifying copy number variations with high resolution. On the other hand, fine-tiled array CGH would produce ultrahigh resolution to find other abnormalities such as breakpoints. == Procedure ==