A large-scale analysis of mRNA polyadenylation of human and mouse genes

Abstract

mRNA polyadenylation is a critical cellular process in eukaryotes. It involves 3′ end cleavage of nascent mRNAs and addition of the poly(A) tail, which plays important roles in many aspects of the cellular metabolism of mRNA. The process is controlled by various cis-acting elements surrounding the cleavage site, and their binding factors. In this study, we surveyed genome regions containing cleavage sites [herein called poly(A) sites], for 13 942 human and 11 155 mouse genes. We found that a great proportion of human and mouse genes have alternative polyadenylation (∼54 and 32%, respectively). The conservation of alternative polyadenylation type or polyadenylation configuration between human and mouse orthologs is statistically significant, indicating that alternative polyadenylation is widely employed by these two species to produce alternative gene transcripts. Genes belonging to several functional groups, indicated by their Gene Ontology annotations, are biased with respect to polyadenylation configuration. Many poly(A) sites harbor multiple cleavage sites (51.25% human and 46.97% mouse sites), leading to heterogeneous 3′ end formation for transcripts. This implies that the cleavage process of polyadenylation is largely imprecise. Different types of poly(A) sites, with regard to their relative locations in a gene, are found to have distinct nucleotide composition in surrounding genomic regions. This large-scale study provides important insights into the mechanism of polyadenylation in mammalian species and represents a genomic view of the regulation of gene expression by alternative polyadenylation.

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

“…2B) was generally conserved across eukaryotes, even though in budding yeast greater variation in these cis elements appears to be tolerated (Graber et al 1999). One notable feature of PAS is that, depending on exactly how the AAUAAA and DSE signals are positioned and defined, the actual site of poly(A) addition can vary by several to tens of nucleotides (Zhang et al 1986;Sheets et al 1990;Tian et al 2005). This is especially evident in yeast PAS, which, perhaps due to lower sequence conservation, do not accurately define the position of polyadenylation (Zhao et al 1999).…”

“…However, a significant part of mRNA size variation derives not from alternative splicing, but rather from alternative PAS selection. Thus, it is calculated that well over half of all mRNAs have variable PAS selection, meaning that they will possess mRNA isoforms differing by the extent of their 39 UTRs (Edwalds-Gilbert et al 1997;Tian et al 2005). Since mRNA 39-end processing occurs cotranscriptionally and is stimulated by Pol II CTD (Proudfoot 2004), it is clear that once a particular PAS has been selected and mRNA 39 cleavage occurs with consequent release from chromatin-associated Pol II, then further cleavage of more proximal PAS on the mRNA will not occur.…”

“…Bioinformatic analysis of PAS usage in higher eukaryotes has revealed the remarkable fact that well over 50% of genes display APA site usage (Tian et al 2005). In general, where APA is clearly evident, then the downstream PAS appear to have sequence features that more closely match the canonical AAUAAA and DSE sequence elements (Legendre and Gautheret 2003).…”

“…Here, again, the selective recognition of an intronic PAS results in the formation of a truncated mRNA encoding calcitonin gene-related peptide (CGRP) rather than full-sized calcitonin (Amara et al 1982;Zhao et al 1999). Interestingly, genome-wide analysis of this type of APA suggests that the regulated formation of mRNAs encoding different C-terminal protein sequences may be quite widespread (Tian et al 2005;Wang et al 2008).…”

Protein factors in pre-mRNA 3′-end processing

“…A study of over 4,000 human ESTs found that 77% contained a PAS, and of these 75% contained the AAUAAA sequence and 20% contained the AUUAAA sequence [36]. A more recent study of over 13,000 human and mice ESTs showed that the number of ESTs that did not contain a PAS is only about 4% [35]. AAUAAA (70%) and AUUAAA (15%) are the most common hexamers in the PAS.…”