In silico detection of control signals: mRNA 3 '-end-processing sequences in diverse species

We have investigated mRNA 3'-end-processing signals in each of six eukaryot ic species (yeast, rice, arabidopsis, fruitfly, mouse, and human) through t he analysis of more than 20,000 3'-expressed sequence tags. The use and con servation of the canonical AAUAAA element vary widely among the six species and are especially weak in plants and yeast. Even in the animal species, t he AAUAAA signal does not appear to be as universal as indicated by previou s studies. The abundance of single-base variants of AAUAAA correlates with their measured processing efficiencies. As found previously, the plant poly adenylation signals are more similar to those of yeast than to those of ani mals, with both common content and arrangement of the signal elements. In a ll species examined, the complete polyadenylation signal appears to consist of an aggregate of multiple elements. In light of these and previous resul ts, we present a broadened concept of 3'-end-processing signals in which no single exact sequence element is universally required for processing. Rath er, the total efficiency is a function of all elements and, importantly, an inefficient word in one element can be compensated for by strong words in other elements. These complex patterns indicate that effective tools to ide ntify 3'-end-processing signals will require more than consensus sequence i dentification.