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Tiling Arrays
GeneChip® Tiling Arrays
GeneChip®Tiling Arrays are the most comprehensive array tools available for discovering novel RNA transcripts or mapping sites of protein/DNA interaction in chromatin immunoprecipitation experiments. GeneChip Tiling Arrays feature 25-mer oligonucleotides for optimal hybridization specificity, and high-resolution arrays for the most accurate detection of protein/DNA interactions and novel transcript discovery. The GeneChip Tiling Arrays cover the entire genome, with probes every 35 bases along the genome for the highest resolution yet.
Figure illustrates array design for a 35-base pair resolution tiling array. Probes are tiled at approximately 35-base pair intervals as measured from the central position of adjacent oligos, leaving approximately 10-base pair gaps between oligos.
With the completion of many whole genome sequences, new types of genome wide experiments are now possible. Tiling Arrays offer a physical readout of a genome and can be used as a discovery tool for mapping sites of protein/DNA interaction in chromatin immunoprecipitation (ChIP) experiments, discovering new RNA transcripts, or understanding global epigenomic changes like methylation or acetylation.
- The GeneChip Human Tiling 1.0R Array Set is comprised of 14 arrays designed for transcript mapping experiments.
- The GeneChip Human 2.0R Array Set is a seven-array set designed for chromatin immunoprecipitation experiments. The Human 2.0R Array Set includes all perfect match probes from the Human 1.0R Array Set.
- The GeneChip Human Promoter 1.0R Array is a subset of probes from the Human 2.0R Array Set and is designed for chromatin immunoprecipitation experiments on promoter regions.
Human Tiling 1.0R Array Set
The Human Tiling 1.0R Array Set is designed specifically for transcript mapping experiments. This 14-array set contains approximately 45 million oligonucleotide probes to interrogate the human genome. Each array in the set contains over 3.25 million Perfect Match/Mismatch probe pairs to specifically interrogate genomic regions.
The sequences were selected from build 34 of NCBI genome assembly. Repetitive elements were removed using RepeatMasker and the probes are tiled on average every 35 bp of genomic sequence.
Human Tiling 2.0R Array Set
Affymetrix has released a tiling array specifically for ChIP-Chip studies. The GeneChip® Human Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments. This set of seven arrays contains approximately 45 million oligonucleotide probes. Each array in the set contains over 6.5 million perfect match probes to specifically interrogate genomic regions. The sequences used in the design of the Human Tiling 2.0R Array Set were selected from NCBI human genome assembly (Build 34). The Human Tiling 2.0R Array Set is available either as a whole-genome set of seven arrays or individual arrays from the set may be purchased separately. The GeneChip® Human Promoter 1.0R Array is a subset of the Human Tiling 2.0R Tiling Array Set, and the content was chosen specifically to analyze protein/DNA interactions within promoter regions
Human Promoter 1.0R Array
The GeneChip® Human Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. The Human Promoter Array is a single array comprised of over 4.6 million probes tiled through over 25,500 human promoter regions. Sequences used in the design of the Human Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker. Promoter regions were selected using sequence information from:
- 35,685 ENSEMBL genes (version 21_34d, May 14, 2004)
- 25,172 RefSeq mRNAs (NCBI GenBank®, February 7, 2004)
- 47,062 complete-CDS mRNA (NCBI GenBank, December 15, 2003)
Probes are tiled at an average resolution of 35 bp, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10 bp between probes. Each promoter region covers approximately 7.5 kb upstream through 2.45 kb downstream of 5' transcription start sites. For over 1,300 cancer-associated genes, coverage of promoter regions was expanded to include additional genomic content. This more extensive coverage spans from 10 kb upstream through 2.45 kb downstream of transcriptional start sites.
The array interrogates regions proximal to transcription start sites and contains probes for approximately 59 percent of CpG islands annotated by UCSC in NCBI human genome assembly (Build 34). The probes selected for the Human Promoter 1.0R Array are a subset of the probes used in the whole-genome ChIP array set, the GeneChip® Human Tiling 2.0R Array Set.
Background Information
Tiling Arrays
Microarrays designed to evaluate gene expression generally use few probes to represent each gene and depend on annotation of the public data bases for the design of the probes. More recently oligonucleotide arrays representing the entire genome are emerging as an alternative to simple annotated gene expression to further illuminate the characteristics of the whole genome. Due to their decreased feature size and increased resolution on the real estate of the array and superior reproducibility, oligonucleotide arrays fabricated in silico, such as Affymetrix arrays are the most favorable platform for WGA (Mockler and Ecker, 2005). With the advent of these arrays it became clear that the paradigm supporting the doctrine that genes encoding proteins and their upstream regulatory elements were the only important genetic elements and all other DNA constituted junk DNA was suddenly shattered. WGAs allowed an unbiased assessment of transcriptional events.
At the time of this writing, there were no publications using this technology but collectively, the studies using the Nimblegen ENCODE arrays and the Chromosome 21 and 22 arrays on the Affymetrix platform provide compelling evidence that we have barely approached the whys and wherefores of our understanding of the genomes of humans and other organisms and to term this stage in science as the “post genomic era” was somewhat impulsive and in fact, our understanding of the transcriptome is still very much evolving.
ChIP on CHIPS
The interaction between DNA and protein arbitrate many critical and diverse processes including DNA repair, transcription DNA replication and recombination. Recent advancements in technology have permitted a more in depth analysis of the protein DNA interaction. A technique which amalgamates chromatin immunoprecipitation (ChIP) and microarray technogies (Chip) has recently emerged. Traditional global scanning methods such as ChIP cloning, ChIP Display and Differential Chromatin Scanning on one hand had an advantage because they provided an unbiased evaluation of specific interactions and may identify RNAs that are not currently in the public data bases, however, on the other hand these methods are arduous very time consuming and not quantitative (see Hanlon and Lieb, 2004 for a comprehensive review). ChIP-Chip was developed originally using yeast to globally identify the binding partners of various transcription factors (Ren et al, 2000, Iyer et al, 2001, Lieb et al 2001). These early array platforms were constructed using PCR amplified open reading frames and other intragenic probes.
Collectively these studies discussed have shown that transcription factor binding is not restricted to canonical annotated upstream promoter regions. At the time of this writing there were no publications that had used the whole genome tiling arrays; however, one can forecast that we should anticipate full genome coverage of large eukaryotic genomes in the foreseeable future. The use of such arrays will, in all probability, presage a paradigm shift in our present understanding of transcriptional regulation.
Some useful transcription factor binding sites include:
METAMEME http://metameme.sdsc.edu/
MOTIF Search http://motif.genome.jp/
