“The Evolutionary Impact of Functional RNA Secondary Structures within Protein- Coding Regions in Yeast”

Literature Review Previous use of duplicate genes produced by whole genome duplication in yeast Because analysis of gene duplicates provides some insight into determining if the predicted fRNAs from this study are genuine, it is useful to review the significance of gene duplication and previous studies investigating the evolutionary patterns resulting from a whole genome duplication in yeast. Gene (and genome) duplication is a very important source of novel genetic information (Ohno 1970, Lynch and Conery 2000). Following gene duplication, the duplicate pair can undergo 1) nonfunctionalization – one duplicate becomes nonfunctional (typically via accumulation of mutations), 2) subfunctionalization – the functions of the predecessor gene are divided amongst the duplicates or 3) neofunctionalization – one of the duplicates evolves a novel function. Assuming both pairs are conserved, the duplicates may show asymmetric divergence, which means that one duplicate accumulates substitutions in the nucleotide sequence more quickly than the other duplicate. This phenomenon can be explained if the more slowly evolving duplicate is under greater functional constraint. However, the more rapidly evolving duplicate can either be under lesser constraint than the other duplicate or undergoing rapid change due to adaptive benefits produced in the duplicate gene. This study will examine how functional RNA (fRNA) structures differ in duplicate genes created by a whole genome duplication (WGD) in yeast (Kellis et al. 2004). The purpose of this project is to gain some preliminary data that may illuminate the role of RNA secondary structures in gene regulation and expression and how genomic duplication affects these important biological processes. 3 The large number of duplicate gene pairs in post-WGD species of yeast has already proven useful in comparative studies investigating functional asymmetry of gene duplicates (see Kim and Yi 2006). There has also been a recent study to investigate differences in the evolution of duplicates produced by the whole genome duplication versus duplicates produced by smaller scale duplications (SSD) in Saccharomyces cerevisiae (Guan et al. 2006). One reason that this study may be useful for my research project the list of WGD and SSD paralogs used in this study may be useful in comparing the proportion of fRNA secondary structures found in and around duplicate versus non-duplicate genes. However, synonymous sites show saturation in Saccharomyces cerevisiae (Guan et al. 2006), and there are other epistemological problems, such as long-branch attraction, with dating ancient events using phylogenetic analysis of molecular data from related yeast …