Networks of transcriptional regulation encoded in a grammatical model

The work here presented enriches a previous grammatical model of the transcriptional regulation of gene expression. The previous model is centered on the representation of the regulatory regions upstream of genes, and their internal organization in the DNA. This paper is centered in discussing some alternatives related to the representation of the organization of operons and their alternative states of transcription, as active or inactive units of transcription. Transformational rules can be used to describe the binding and unbinding of regulatory proteins, and the associated representations of (ON/OFF) gene expression. The initial representation of a regulated promoter is linked to that of the operon encoding its regulatory protein. In this way the representation of a regulated operon depends on that of all others regulating its transcription, enabling in principle the encoding of regulatory networks within an expanded grammatical model of gene regulation.