Poster abstracts

Poster number 69 submitted by Yingjia Shen

Bioinformatic analyses of alternative polyadenylation and polyadenylation signals of rice and a green alga Chlamydomonas reinhardtii

Yingjia Shen (Department of Botany, Miami University, Oxford, Ohio 45056), Yuansheng Liu (Department of Botany, Miami University), Lin Liu (Department of Botany, Miami University), Brian J. Haas (The Genome Research Institute, Rockville, MD 20850), Chun Liang (Department of Botany, Miami University), Q. Quinn Li (Department of Botany, Miami University)

Abstract:
The 3’-end of a messenger RNA is generally defined by a poly(A) tail. The position of a poly(A) site of an eukaryotic mRNA is determined by sequence signals in the precursor-mRNA. Alternative polyadenylation (APA), in which a poly(A) tail is located at a different location of individual transcripts, allows the same DNA template to produce different isoforms of mRNA. To study poly(A) signals and APA in rice and a model algal species, Chlamydomonas reinhardtii, at a genome level, we constructed two datasets of 55,742 and 16,952 authenticated unique poly(A) sites, respectively. In rice, we identified the poly(A) signals as the typical tripartite cis-elements, including Far-Upstream-Elements (FUE), Near-Upstream-Elements (NUE) and Cleavage Elements (CE) as previously observed in Arabidopsis. When mapped to the genome, however, 15% of these poly(A) sites were found located in the currently annotated intergenic regions. Moreover, an extensive alternative polyadenylation profile was evident where 50% of the genes analyzed had more than one unique poly(A) site. About 4% of analyzed rice genes possessed alternative poly(A) sites at their introns, 5’-UTRs, or protein coding regions. Studies on the poly(A) signals in Chlamydomonas found a unique set of polyadenylation signals that are distinct from that of other organisms. In contrast to the high-AU content in 3’-UTR of rice, Chlamydomonas shows a high-Guanylate content that transits to high-Cytidylate around the poly(A) site. A dominant poly(A) signal, UGUAA, was found in over 50% of NUEs, and its occurrence may be positively correlated with higher gene expression levels. We also observed a high-level APA in the Chlamydomonas draft genome, with a range up to ~33% genes having at least two unique poly(A) sites, and a range of 1% to 11% (depending upon the stringency of the criteria) of the poly(A) sites residing in introns, 5’-UTRs, or protein coding regions. In conclusion, we identified two distinct sets of poly(A) signals from two evolutionarily distant organisms. However, in either case, alternative polyadenylation are found to be significant, which could play an important role in gene expression regulation.

Keywords: Polyadenylaion signal, Alternative polyadenylation, rice Chlamydomonas