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Prediction of tissue-specific cis-regulatory sequences: application to the ascidian Ciona intestinalis and the anterior neurectoderm

Prédiction des séquences cis-regulatrices tissu-spécifiques: application à l'ascidie Ciona intestinalis et au neurectoderme antérieur

Abstract : The detection and annotation of cis-regulatory sequences is a difficult problem. There is currently no generally applicable experimental procedure or computational algorithm to identify the non-coding regions of the genome that serve to activate gene expression in a given cell type. The only indicator of cis-regulatory function is the conservation of a sequence in other genomes. Regions can then be tested one-by-one in transgenic assays but this is time-consuming in vertebrates. Only a limited number of these already validated cis-regulatory sequences have been curated in biological databases. One of the main advantages of the model organism Ciona intestinalis is that cis-regulatory tests can be conducted very easily and the result is observable after one day while the animal follows the chordate body plan. However, a sequence found to be active in this organism can currently not be mapped to genomes of other animals.