INTERFERING CONTEXTS OF REGULATORY SEQUENCE ELEMENTS

Motivation: Although one would normally expect a given regulatory elem ent to perform best when it fully matches its consensus sequence, this is generally far from being the case. Usually, almost none of the act ual sites fits the consensus exactly, and some of those that do fit do not perform well. The main reason for that is the very nature of the sequences and the messages (codes) they contain. Normally, any given s tretch of the sequence with one or another regulatory site not only ca rries this regulatory message, but several more messages of various ty pes as well. These messages overlap with the regulatory element in suc h a way that the letter (base) which actually appears in any given seq uence position simultaneously belongs to one or more additional codes. Apart from numerous individual codes (sequence patterns) specific for a given species or gene, there are many different general (universal) sequence codes all interacting with one another. These are the classi cal triplet code, DNA shape code, chromatin code, gene splicing code, modulation code and many more, including those that have not yet been discovered. Examples of overlapping of different codes and their inter action are discussed, as well as the role of degeneracy of the codes a nd the sequence complexity as a function of code density.