Introduction:

Transcription factors (TF) regulate gene transcription through DNA-protein interaction such as direct binding with DNA. In order to mediate a specific gene transcription, TFs bind in a sequence-specific manner to certain promoter sequences usually located upstream from its target gene. By combining chromatin immunoprecipitation using TF specific antibodies, also known as the ChIP assay, then labeling IP-captured promoter-DNA as a probe for hybridization with an array that is pre-spotted with various promoter sequences, it is possible to determine many genetic targets for a given TF. The first generation technology called "ChIP-on-chip" has demonstrated its success (Ren, B. et al., (2000) Science 290:2306-2309).

Selected by NIH ENCODE project, and invented by UCSD researchers, ChIP-GLAS (Chromatin Immunoprecipitation-Guided Ligation And Selection) is a new generation of ChIP-Chip technology with greatly increased sensitivity and specificity. It provides a complete product solution for the discovery of virtually all promoters that bind a specific transcription factor. Aviva Systems Biology is pleased to introduce its new products of ChIP-GLAS system.

The new invention of the ChIP-GLAS method is significantly different from conventional ChIP-on-chip technology. The major advantages include high sensitivity, high specificity, simplified protocol and low cost. Some of the key differences are summarized below:

Oligo based array chips: the GLAS-chip is a high-density oligo based human promoter array, which coats 20,000 40-mer-oligonucleotides representing a unique sequence in the promoter region of 20,000 genes in the genome. Corresponding to the chip, H20K-oligo-mix is a pool of 20,000 paired oligos. Each pair of oligo corresponds to a 40-mer spotted on the chip and contains a pair of universal primer-landing site (T7 and T3).

Use of ligated oligonucleotides as templates for the PCR reaction: GLAS assay utilizes IP-captured DNA to guide ligation of specific paired oligos and the ligated oligos instead of directly amplifying IP DNA. In the GLAS assay, the immunoprecipitated DNA and total input DNA are annealed with H20K-oligo-mix. Aligned oligo pairs are then ligated, selected, amplified, and labeled with fluorescent dyes. The selected oligos are hybridized to H20K-chips and the array is then scanned. By computing the ratio of corrected red/green dye intensities in each spot, the enrichment can then be determined at each promoter location.

High specificity and sensitivity: the ChIP-GLAS technology has significantly improved the conventional ChIP-on-Chip assay in terms of sensitivity and specificity. First, it increases the sensitivity by 2-log units. This improvement made the technology more feasible for most studies in gene regulation. A second improvement is that the new technology has greatly increased the specificity of analysis. All microarray-based approaches face the specificity issue. GLAS assay utilizes IP-captured DNA as templates to guide specific paired oligos annealing and ligation. As the result, the complexity is significantly reduced during hybridization on microarray chips.

More convenient protocol: ChIP-GLAS comes with a detailed protocol and as a set of kits. This increases convenience and consistency. The experiment procedure has also been simplified to increase the success of the experiment.

Low cost: ChIP-GLAS system has largely reduced experimental cost. The calculated expense for conventional ChIP-on-Chip is more than $150 excluding chips. However, the price for ChIP-GLAS kits is only $60 per assay.