Nature Reviews Genetics 7, 200-210 (March 2006) | doi:10.1038/nrg1809
I have spent nearly three days reading this review on microarray. It is partly because this paper involves too many new concepts for me to digest, partly because, I have to admit, I have wasted too much time on BBS, films and music ^_^. Even until now I still cannot declare to absorb all materials in this paper, but i think it is better to take some notes here for it may urge me to concentrate on research.
This paper describe the following microarray development
| Process | Status* |
|---|---|
*From most to least developed: mature, in progress, under development, early stages, pilot phase, idea. CGH, comparative genomic hybridization; ChIP-on-chip, on-chip chromatin immunoprecipitation. | |
| Transcriptional profiling | Mature, but still to be improved |
| Genotyping | Mature, but still to be improved |
| Splice-variant analysis | In progress |
| Identification of unknown exons | Early stages |
| DNA-structure analysis | Pilot phase |
| ChIP-on-chip | In progress |
| Protein binding | Under development |
| Protein–RNA interaction | Idea |
| Chip-based CGH | In progress |
| Epigenetic studies | Under development |
| DNA mapping | Mature |
| Resequencing | In progress |
| Large-scale sequencing | Under development |
| Gene/genome synthesis | Early stages |
| RNA/RNAi synthesis | Pilot phase |
| Protein–DNA interaction | Under development |
| On-chip translation | Under development |
| Universal microarray | Under development |
He thoughts transcriptional profiling is relative in technique but the data analysis and interpretation. Some organization are take effect in this path, such as Microarray Gene Expression Data (MGED) Society, Gene Ontology Consortium and Bioconductor.
Expanding RNA studies the transcried RNA profile is a mixture of pre-mRNA, various form of alternative spliced mature mRNA, non-coding RNA and regualatory RNA. If we think about the effect of alternative splicing, it is possible that we may ignorant other forms and exons in the genome sequence which is not seen in our experiement samples. Then how to know other exons and what condition they are retained in mature mRNA, we can built an array consisting of oligonucleotide representing all known exons from genome annotation analysis. This array can then be used for the above condition.
Another question arising is that how can we find exons that escape the notice of genome annotation analysis. "One option is to synthesize oligonucleotides that correspond to the sequences at the exon–intron boundaries with their 5' ends attached to the chip surface "
Another approach is the entire genome microarray (tiling path), but the fragment is rather long which may miss some active sites of interest.
ChIP-on-chip on-chip chromatin immunoprecipitation. But, how this technique get high throughput if only one kind of protein can be precipitated due to the specificity of antibody binding? Needs more reading to understand this technique.
The author also predicted that " all analyses that are carried out with DNA are feasible at the level of RNA also."
comparative genomic hybridization (CGH), a method that is used to analyse variations in DNA copy number
The following part of this paper describes on demand sythesis based on microfluidic microarray, such as probe production (parallel production of large amount of different of oligomers), gene synthesis, RNAi production and protein in situ synthesis. Finally he introduced universal microarray platform based on L-DNA with great enthusiasm.
Conclusions:
1. To some extent, microarray technique means a new data-driven method e.g placing data production before intellectual concepts. This method is different from traditional hypothesis driven research in biology but is successful in physics.
2. The global view obtained by microarray approaches might lead researchers to appreciate more complexity of biological systems.
3. Experimental multiplexing by analysing different processes on a single system platform will become important. The in vitro systems biology will emerge competing (or complementing) in silico systems biology.
Here is a list of notable research project about microarray analysis
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