Affiliations: Department of Biotechnology and Environmental
Chemistry, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido
090-8507, Japan | Toyo Engineering Corporation, 2-8-1 Akanehama,
Narashino, Chiba 275-0024, Japan
Abstract: A large-scale analysis of human polyadenylation signals was carried
out in silico. The most canonical AAUAAA hexamer and its 11
single-nucleotide variants that are most frequent in human genes were used to
search for polyadenylation signals in the terminal sequences. Out of 18,277
poly(A) sites that were identified from 26,414 human genes, 82.5% of the
sites were found to contain at least one of these 12 hexamers as a
polyadenylation signal within 40 nucleotides upstream of the poly(A) site. The
rest (17.5%) did not contain any of these hexamers, which suggests the
existence of yet unknown signals. A total of 20,347 terminal sequences in close
proximity to 12 polyadenylation signals were collected using modified EST
clustering technique to establish a large-scale database of polyadenylation
signals. To characterize the 12 hexamers, the locations of polyadenylation
signals that were identified as "authentic" and the uracil contents of the
downstream region of the signal were examined. Based on this analysis, the 11
variants of the canonical AAUAAA were identified as possibly forming
"functional" signals as AAUAAA. Moreover, the observed frequency of 41.9%
for AAUAAA was significantly lower than those of other reports, suggesting that
the non-canonical variants are more important in the polyadenylation process
than frequently recognized. Since the poly(A) sites processed by those
non-canonical variants have not been generally annotated in major gene
databases, it is important to determine whether the variant hexamers could work
as polyadenylation signals that may be responsible for generating heterogeneity
of mRNAs by alternative polyadenylation.
