Poster abstracts
Poster number 145 submitted by Yingdong Zhu
Analysis of novel 5’-UTR polyadenylation sites in Arabidopsis thaliana
Yingdong Zhu (Biology Department, Miami University), Cheng Guo (Biology Department, Miami University), Chun Liang (Biology Department, Miami University), Qingshun Q. Li (Biology Department, Miami University), Jack C. Vaughn (Biology Department, Miami University)
Abstract:
Precursor mRNA processing including polyadenylation serves as an important basis for posttranscriptional regulation. The poly(A) site is generally located several tens or hundreds of nucleotides downstream of the mRNA termination codon. However, many eukaryotic genes have more than one poly(A) site, which results in a set of mRNA isoforms with different length. The usage of one poly(A) site over another is mainly owing to the relative strength as well as the availability of the site, which is known as alternative polyadenylation (APA). For many years, polyadenylation was only observed in the 3’-UTR and lack of poly(A) signal sequence conservation made its exact position difficult to predict. The first evidence that the 5’-UTR of some mRNAs could encode peptides and potentially control translation of the downstream ORF came from studies on upstream open reading frames (uORFs). The importance of uORF was recently highlighted in an analysis of the uORF among angiosperms, which showed that ~1% of them are evolutionarily conserved among related species. Arabidopsis thaliana is an important model plant for analyzing the transcriptomics, and remarkably, ~30% of its protein coding mRNAs possess a 5’-UTR with one or more uORF. Recently, we profiled the transcriptomes of roots, flowers and leaves in Arabidopsis (wild-type Columbia), and our bioinformatics analysis predicted that a portion of poly(A) sites are located in the 5’-UTR in addition to the conventional 3’-UTR. Verification of a predicted poly(A) site located in the 5’-UTR should meet three conditions: first, it cannot come from the 3’-UTR of another adjacent gene or neighboring regions of the DNA sequence; second, it should contain a poly(A) tail; third, it can maintain a certain expression level. Considering that polyadenylation in the 5’-UTR can produce novel short peptides, and perhaps reduce or eliminate the original transcripts, we hypothesize that it may be related to an unknown regulation mechanism of the corresponding genes. To confirm our predictions from large scale and computational analysis, we are investigating several predicted uORFs for presence of an AUG start codon, a conventional stop codon, and also using 3’-RACE for evidence of a poly(A) tail.
Keywords: alternative polyadenylation, upstream open reading frame, Arabidopsis thaliana