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

Abstract

We have investigated mRNA 3'-end-processing signals in each of six eukaryotic species (yeast, rice, arabidopsis, fruitfly, mouse, and human) through the analysis of more than 20,000 3'-expressed sequence tags. The use and conservation of the canonical AAUAAA element vary widely among the six species and are especially weak in plants and yeast. Even in the animal species, the AAUAAA signal does not appear to be as universal as indicated by previous studies. The abundance of single-base variants of AAUAAA correlates with their measured processing efficiencies. As found previously, the plant polyadenylation signals are more similar to those of yeast than to those of animals, with both common content and arrangement of the signal elements. In all species examined, the complete polyadenylation signal appears to consist of an aggregate of multiple elements. In light of these and previous results, we present a broadened concept of 3'-end-processing signals in which no single exact sequence element is universally required for processing. Rather, 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 identify 3'-end-processing signals will require more than consensus sequence identification.

Figure 1

Single-nucleotide frequencies preceding the 3′-end-processing sites as determined by alignment of 3′-ESTs generated from yeast (1,352), rice (1,246), arabidopsis (4,069), fruitfly (3,236), mouse (6,029), and human (4,427) cDNAs. Positions are given relative to the putative 3′-end-processing site. (A) Sequences aligned on the 3′-most end of the ESTs. (B) Sequences aligned to a 6-nt profile, via an iterative procedure as described in Methods.

Figure 2

Single-nucleotide frequencies that describe the two principal signal elements of the fruitfly 3′-end-processing signal, as determined by analysis of 882 ESTs that were successfully aligned to contig sequences. By using the iterative profiling procedure defined in Methods, the sequences were successively aligned on (A) the PE (approximate position −20) and (B) DE (approximate position +14).

Figure 3

A comparison of the occurrences (in 327 contig-aligned fruitfly EST sequences that did not contain AAUAAA) with in vitro measured [in human HeLa cells (21)] processing efficiencies of sequences similar to the canonical PE AAUAAA. The processing efficiencies are plotted as a percentage of the efficiency of AAUAAA, whereas the occurrences are plotted as a fraction of the total number of sequences examined.

Figure 4

Graphical representations of the proposed alignment of 3′-end-processing signals for (A) yeast, (B) plants, and (C) animals, including the most common words found for each subelement.