Regulatory Pathway Analysis by High-Throughput In Situ Hybridization

Visel A, Carson J, Oldekamp J, Warnecke M, Jakubcakova V, et al. (2007) Regulatory Pathway Analysis by High-Throughput In Situ Hybridization. PLoS Genet 3(10): e178 doi:10.1371/journal.pgen.0030178
I suspected that some simpler then the mouse model organism would be used for such systematic approaches, and Ciona intestinalis was one of my candidates, along with chick. Well, mouse is also quite good :-)
Systematic analysis of gene’s expression to provide spatio-temporal profiles of expression over developmental stages and pathological situations is certainly the best way to have a view of how things work. The most interesting part is that a large part of the work, a large part of the bench work, is automated: robotic-ISH and automated scanning which guarantees large data sets at low cost with high confidence.

10.1371_journal.pgen.003017.jpg

Good news, the works is started, bad news, it will take some time to complete. Data available at Genepaint.

Automated in situ hybridization enables the construction of comprehensive atlases of gene expression patterns in mammals. Such atlases can become Web-searchable digital expression maps of individual genes and thus offer an entryway to elucidate genetic interactions and signaling pathways. Towards this end, an atlas housing ∼1,000 spatial gene expression patterns of the midgestation mouse embryo was generated. Patterns were textually annotated using a controlled vocabulary comprising >90 anatomical features. Hierarchical clustering of annotations was carried out using distance scores calculated from the similarity between pairs of patterns across all anatomical structures. This process ordered hundreds of complex expression patterns into a matrix that reflects the embryonic architecture and the relatedness of patterns of expression. Clustering yielded 12 distinct groups of expression patterns. Because of the similarity of expression patterns within a group, members of each group may be components of regulatory cascades. We focused on the group containing Pax6, an evolutionary conserved transcriptional master mediator of development. Seventeen of the 82 genes in this group showed a change of expression in the developing neocortex of Pax6-deficient embryos. Electromobility shift assays were used to test for the presence of Pax6-paired domain binding sites. This led to the identification of 12 genes not previously known as potential targets of Pax6 regulation. These findings suggest that cluster analysis of annotated gene expression patterns obtained by automated in situ hybridization is a novel approach for identifying components of signaling cascades.

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