Muscle actin genes: a first step towards computational classification of tissue specific promoters

Tissue-specific gene expression is governed by enhancer and promoter sequences determining the specificity most probably by their internal organization of transcription factor binding sites. In case of muscle-specific gene expression excellent compilations of sequence regions responsible for the tissue-specificity are available. We took advantage of such a compilation in order to elucidate organizational features that are directly correlated with promoter specificity. We chose a systematic approach solely based on a sequence collection known to consist of specific regulatory regions which can in principle be applied to every precompiled set of such sequences. We were able to show that these sequences contained a detectable subgroup (actin promoters) for which it was possible to construct a highly specific promoter model recognizing the majority of all known actin sequences. The model was robust with respect to different training sets, almost 100% specific and sensitive enough to be suitable for database searches. We believe this pilot study demonstrates the general applicability of our approach as well as the concept of modular promoter organization.