RNA Polyadenylation Sites on the Genomes of Microorganisms, Animals, and Plants

Abstract

Pre–messenger RNA (mRNA) 3′-end cleavage and subsequent polyadenylation strongly regulate gene expression. In comparison with the upstream or downstream motifs, relatively little is known about the feature differences of polyadenylation [poly(A)] sites among major kingdoms. We suspect that the precise poly(A) sites are very selective, and we therefore mapped mRNA poly(A) sites on complete and nearly complete genomes using mRNA sequences available in the National Center for Biotechnology Information (NCBI) Nucleotide database. In this paper, we describe the mRNA nucleotide [i.e., the poly(A) tail attachment position] that is directly in attachment with the poly(A) tail and the pre-mRNA nucleotide [i.e., the poly(A) tail starting position] that corresponds to the first adenosine of the poly(A) tail in the 29 most-mapped species (2 fungi, 2 protists, 18 animals, and 7 plants). The most representative pre-mRNA dinucleotides covering these two positions were UA, CA, and GA in 17, 10, and 2 of the species, respectively. The pre-mRNA nucleotide at the poly(A) tail starting position was typically an adenosine [i.e., A-type poly(A) sites], sometimes a uridine, and occasionally a cytidine or guanosine. The order was U>C>G at the attachment position but A>>U>C≥G at the starting position. However, in comparison with the mRNA nucleotide composition (base composition), the poly(A) tail attachment position selected C over U in plants and both C and G over U in animals, in both A-type and non-A-type poly(A) sites. Animals, dicot plants, and monocot plants had clear differences in C/G ratios at the poly(A) tail attachment position of the non-A-type poly(A) sites. This study of poly(A) site evolution indicated that the two positions within poly(A) sites had distinct nucleotide compositions and were different among kingdoms.

A compendium of conserved cleavage and polyadenylation events in mammalian genes

“…Therefore, our genome-wide analysis using conserved PASs does not support the long-standing notion that the CA motif is preferred for 3 ′ end cleavage. Instead, cleavage tends to take place next to an adenosine, which is in good agreement with the biochemical study by Chen et al (1995) and a previous bioinformatic analysis with a much smaller PAS set based on EST sequences from multiple species (Li and Du 2013). In addition, although our sequencing data could not distinguish the two scenarios, we think, based on the biochemical data from Chen et al (1995), pre-mRNA cleavage immediately upstream of an A residue (scenario 1) is more likely to occur.…”

Comparative Analysis of the Base Compositions of the Pre-mRNA 3′ Cleaved-Off Region and the mRNA 3′ Untranslated Region Relative to the Genomic Base Composition in Animals and Plants

“…For example, only 0.3% percentage of mapped mRNAs in plants had 12 A’s [20]. Its potential modification of the content (percentage) of each specific nucleotide (A, C, G, and U) in the whole mRNA pool would be less than 0.1% on average.…”

Cleavage and polyadenylation: Ending the message expands gene regulation

“…The point of cleavage occurs between the hexamer and DSE. In mammals, CA and UA appear to be the most frequent dinucleotides that precede the actual site of cleavage, 22 however, the actual site where cleavage occurs is known to be heterogeneous. Nucleotide composition at the cleavage site has a complex impact on 3′end processing.…”