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Comparative Study
. 2000 Jul;10(7):1001-10.
doi: 10.1101/gr.10.7.1001.

Patterns of variant polyadenylation signal usage in human genes

E Beaudoing  1 , S Freier, J R Wyatt, J M Claverie, D Gautheret
Affiliations
Comparative Study

Patterns of variant polyadenylation signal usage in human genes

E Beaudoing et al. Genome Res. 2000 Jul.

Abstract

The formation of mature mRNAs in vertebrates involves the cleavage and polyadenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA signal sequence. The extensive cDNA data now available shows that these hexamers are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3' untranslated sequences to 157,775 polyadenylated expressed sequence tags (ESTs), used as markers of actual mRNA 3' ends. About 5600 EST-supported putative mRNA 3' ends were collected and analyzed for significant hexameric sequences. Known polyadenylation signals were found in only 73% of the 3' fragments. Ten single-base variants of the AAUAAA sequence were identified with a highly significant occurrence rate, potentially representing 14.9% of the actual polyadenylation signals. Of the mRNAs, 28.6% displayed two or more polyadenylation sites. In these mRNAs, the poly(A) sites proximal to the coding sequence tend to use variant signals more often, while the 3'-most site tends to use a canonical signal. The average number of ESTs associated with each signal type suggests that variant signals (including the common AUUAAA) are processed less efficiently than the canonical signal and could therefore be selected for regulatory purposes. However, the position of the site in the untranslated region may also play a role in polyadenylation rate.

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Figures

Figure 1
Figure 1
Average position of observed polyadenylation sites on 3′ UTRs in function of the number of observed alternate sites. From top to bottom: mRNAs with a single poly(A) site identified (3377 RNAs), mRNAs with two poly(A) sites identified (724 RNAs), mRNAs with three poly(A) sites identified (182 RNAs), and mRNAs with four poly(A) sites identified (43 RNAs). Position 1 on the X-axis is the first base following the Stop codon. Error bars indicate standard deviations.
Figure 2
Figure 2
Distribution of polyadenylation signal types at each site on the UTR. From top to bottom: mRNAs with a single poly(A) site identified, mRNAs with two poly(A) sites identified, mRNAs with three poly(A) sites identified, and mRNAs with four poly(A) sites identified. Poly(A) sites are numbered from 5′ to 3′.
Figure 3
Figure 3
Number of revealing ESTs per poly(A) site, in function of the position of sites in the UTR. From top to bottom: mRNAs with a single poly(A) site identified, mRNAs with two poly(A) sites identified, mRNAs with three poly(A) sites identified, and mRNAs with four poly(A) sites identified. Poly(A) sites are numbered from 5′ to 3′.
Figure 4
Figure 4
The 12 putative human polyadenylation signals and their 90% consensus sequence (N = any nucleotide). The consensus does not take into account the relative frequency of signals. Positions conserved in more than 90% of the variants are highlighted.
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