Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures

Abstract

Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3#-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3#-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a singlenucleotide profile scan on the 3#-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3#-ends for gene annotation.Messenger RNA polyadenylation is a crucial step during the maturation of most eukaryotic mRNA, in which a polyadenine [poly(A)] tract is added to the cleaved 3#-end of a precursor mRNA (pre-mRNA) posttranscriptionally. Such a modification of mRNA has been shown to affect its stability, translatability, and nuclear-to-cytoplasmic export (Zhao et al., 1999). The posttranscriptional processing of mRNA is an event that has also been found tightly coupled with splicing and transcription termination (Proudfoot et al., 2002;Proudfoot, 2004). Thus, it is an essential processing event and the integral part of gene expression.The polyadenylation process requires two major components: the cis-elements or poly(A) signals of the pre-mRNA, and the trans-acting factors that carry out the cleavage and addition of the poly(A) tail at the 3#-end. These trans-acting factors are a complex of about 25 to 30 proteins involved in signal recognition, cleavage, and polyadenylation (Proudfoot, 2004). These proteins seem to be conserved among eukaryotic organisms. However, the poly(A) signals have been found to differ widely among yeast (Saccharomyces cerevisiae), animals, and plants in terms of signal locations and sequence content. The highly conserved AAUAAA element in mammals becomes a minor signal in plant and yeast genes, and the ubiquitous downstream elements of mammalian pre-mRNAs are nowhere to be found in yeast and plants. The latter two possess an enhancing element located far upstream of the cleavage site (Zhao et al., 1999).Previous understanding of these signal elements was derived mostly...

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

“…Other than this, the base composition profiles of 3′-UTR (as in Fig. 2B) and intronic PACs are indistinguishable from those published by others (17,19).…”

“…1). To gain further insight into PACs that lie within some of these different genomic regions, the relative base composition of the sequences surrounding these sites was studied; such analyses have proven effective in identifying important sequence trends and probable cis elements (17,19). For this process, PACs located in 3′-UTRs were chosen as the "default," and the position-by-position variations from the relative nucleotide compositions surrounding these sites were assessed using a χ 2 test.…”

“…Plant poly(A) site datasets (3,17) have been assembled from the analysis and curation of the results of EST and full-length cDNA sequencing projects. Unfortunately, these projects are not specially targeted to the identification of poly(A) sites, nor are they high-throughput.…”

Cassandraretrotransposons carry independently transcribed 5S RNA

“…S2). Although the signal differs from the canonical AATAAA, it resembles other noncanonical signals and its distance from the terminator is quite typical (22). Hence, Cassandra polyadenylation more likely represents RNA maturation than turnover.…”

A Simple Decision Rule for Recognition of Poly(A) Tail Signal Motifs in Human Genome

“…This problem is important for functional analysis of genomic sequences. Generally, the sequences in the primary genomic sequence that correspond to actual poly(A) signal sequences (poly(A) tail motifs) are known, although their composition varies across species [2], [3]. In addition, there are typically several motifs indicating the true poly (A) signal, with varying degree of prominence.…”