General Technique
The Microarray Facility is central to the mission of the ISB. In the Microarray Facility, ISB scientists carry out high-throughput experiments interrogating the inputs and outputs of information to the genome. The input of information to the genome is interrogated in chromatin-immunoprecipitate-to-chip (ChIP-chip) experiments that probe the interactions of DNA-binding proteins with genome sequences. Genomic information input from protein-DNA binding patterns control the information output (expression) of the genome. These patterns of gene expression determine the properties of cells, in both normal and disease states. The prediction and prevention of disease will require an understanding of the regulation and consequences of normal and dysfunctional gene-expression patterns.
Microarray technology is based on the synthesis or deposition of nucleic-acid probes for genomic sequences on a small chemically modified glass slide (a chip). The probes are laid out in specific positions in a small array of thousands of probes on the chip (a microarray). Either protein-bound DNA fragments, or the expressed form of genes, mRNA, is extracted from biological samples and converted to fluorescently labeled copies. The microarray is coated with the labeled copies which hybridize to the probe spots. A laser scanner detects the level of fluorescence of each probe spot to detect protein binding or gene expression.
Purpose/use/application of the technique:
Microarray-based genomic analyses are a mainstay of systems biology research at the ISB. A relatively mature technology, it comes closer than any other to providing quantitative data with the quality, amounts, and fully genomic scale demanded for systems biology research. The gene-binding and gene-expression patterns revealed by microarray technology implicate information-flow pathways in complex molecular networks that control the expression of genes and the properties of cells. The understanding of these pathways will enable successful interventions to predict and prevent diseases. For example, if a dysfunctional pathway for a disease is identified, inhibitors of a gene in that pathway can be developed to prevent disease.
Example(s) of projects at ISB that use this technique:
Genomic expression arrays provide a key source of data for many ISB projects, including:
- GLUE grant (Aderem Lab)
- Peroxisome biogenesis (Aitchison Lab)
- Functional genetics of susceptibiltiy to prions (Hood Lab)
- Modeling predictive biological networks in Halobacteria (Baliga Lab)
Ongoing area of technology development:
Various projects and strategic partners at the ISB are pursuing the development of advanced technologies aimed at solving fundamental scientific problems at the forefront of genomic expression biology. These include single-cell genomic expression, ultra-high throughput, digital genomics (direct molecule counting), and full genome tiling. Often these efforts involve technologies that differ radically from microarray-based techniques.
Representative publication(s):
Carter GW, Rupp S, Fink GR, Galitski T. (2006) Disentangling information flow in the Ras-cAMP signaling network. Genome Research 16:520-6.
Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova I, Lange PH, Goodlett DR, Zhou D, Vasicek TJ, Hood L. Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. (2005) Cancer Res. 65:3081.
Read Publication
Oudes AJ, Roach JC, Walashek LS, Eichner LJ, True LD, Vessella RL, Liu AY. (2005) Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression. BMC Cancer 5:86.
Read Publication
|
home
