Upstream sequence elements enhance poly(A) site efficiency of the C2 complement gene and are phylogenetically conserved.

Abstract

Poly(A) signals of mammalian pre‐mRNA have been defined as an AAUAAA sequence 10–30 nt upstream of the cleavage/poly(A) site followed by a GU/U‐rich element immediately downstream. However, a number of viral poly(A) signals have been shown to possess additional signals upstream of AAUAAA that increase poly(A) site efficiency. We describe the first non‐viral example of such an upstream sequence element (USE) for the poly(A) site of the human C2 complement gene. As this gene is very closely spaced to the related Factor B gene [the C2 poly(A) site is only 421 bp from the transcription start site of Factor B] we have isolated this same intergenic sequence from four other mammals (mouse, cat, rabbit and cow). We show that the USE of the C2 poly(A) site is highly conserved between these five different mammals. Furthermore, extensive mutagenesis of the human USE indicates that most of the 53 nt sequence is required for full activity. The human C2 poly(A) site does not possess any obvious downstream GU/U‐rich sequences, although sequences immediately 3′ to AAUAAA as well as 13 nt of sequence following the cleavage site are both required for full activity. Interestingly the other mammalian C2 poly(A) sites do possess significant downstream GU/U‐rich sequences. Finally we show that all five mammalian C2 poly(A) signals are immediately followed by conserved signals for transcriptional termination, consistent with the close proximity of the downstream Factor B gene.

RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates

“…Conserved regions around poly(A) signals upstream for those used by the shark were identified in two of the genes and may indicate sites of alternative poly(A). Previous work on comparisons among mammalian genomes identified conserved areas around poly(A) signals that direct the positioning of the poly(A) tail (21)(22)(23). Two reports extended this approach to identify short regions of 3Ј UTR conservation surrounding poly(A) signals in nonmammalian species (24,25).…”

Ending the message: poly(A) signals then and now

“…In particular, the GUrich sequence (or downstream sequence element, DSE) present just past the mRNA 39 end in the immediate gene 39 flanking region was shown to enhance 39-end formation Proudfoot 1984, 1987;McLauchlan et al 1985). Similarly, the sequence immediately upstream of AAUAAA (upstream sequence element, USE) (Carswell and Alwine 1989;DeZazzo et al 1991;Valsamakis et al 1991;Moreira et al 1995;Brackenridge and Proudfoot 2000;Venkataraman et al 2005;Danckwardt et al 2007) can in some cases act as an enhancing element for 39-end processing efficiency. Finally, the actual nucleotides at the site of 39-end cleavage can also influence the efficiency of this process (Chen et al 1995).…”

Protein factors in pre-mRNA 3′-end processing

“…1A), does not have a consensus sequence, but often consists of a U-rich element (UUUU) [2] or similar sequences (UGUA, UAUA) [54]. The efficiency of cleavage and polyadenylation is enhanced by the presence of this auxiliary element, as it promotes the binding of other polyadenylation factors to the cleavage site [55][56][57][58]. Most auxiliary upstream elements have been identified with the enhanced expression of intronless genes, which are normally expressed at lower levels than transcripts that contain introns [59].…”