Poster abstracts

Poster number 10 submitted by Cai Chen

Comparative sequence analysis in insertional RNA editing

Cai Chen (Biophysics Graduate Program, The Ohio State University), Ralf Bundschuh (Departments of Physics and Biochemistry, Biophysics Graduate Program, Center for RNA Biology, The Ohio State University)

Abstract:
RNA editing describes the process in which individual or short stretches of nucleotides in a messenger or functional RNA are inserted, deleted, or substituted. Here we study the mitochondrial genomes of two related organisms with insertional RNA editing, Physarum polycephalum and Didymium iridis. The combination of the two genomes can provide conservation information which is not contained in either of the genomes alone. Sixteen genes and their mRNA sequences from the two organisms are studied: atp1, apt6, atp8, atp9, cox1, cox2, cytb, nad4L, nad6, nad7, rpL2, rpL16, rpS3, rpS7, rpS12, and rpS19. We identify the “C” insertional RNA editing sites shared by the two organisms. Then we calculate the probability for observing increased sequence conservation in the vicinity of the shared insertional editing sites based on the background frequencies. We do not find any statistically significant variations, which implies that the information on editing site is not contained within the sequence in the immediate vicinity of the editing site. In addition, we examine the codon position bias in insertional RNA editing of these two organisms. We find a strong relationship between the strength of the codon bias and the overall sequence conservation in the two organisms: more conserved genes tend to have more significant codon bias. This reinforces the theory that codon bias is a consequence of evolutionary pressure on the protein sequence.

Keywords: RNA editing, sequence conservation, codon bias