CRACS Seminar by Dale Richardson

02 December 2011

Seminar: Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing

By Dale Richardson, CIBIO, Univ. Porto

Date: 2.December.2011
Time: 11:30h
Room: S2
Location: Dep. Ciencia de Computadores/FCUP

Abstract

Alternative splicing (AS) of pre-mRNA is a fundamental molecular process that generates diversity in the transcriptome and proteome of eukaryotic organisms. SR proteins, a family of splicing regulators with one or two RNA recognition motifs (RRMs) at the N-terminus and an arg/ser-rich domain at the C-terminus, function in both constitutive and alternative splicing. We identified SR proteins in 27 eukaryotic species, which include plants, animals, fungi and ‘‘basal’’ eukaryotes that lie outside of these lineages. Using RNA recognition motifs (RRMs) as a phylogenetic marker, we classified 272 SR genes into robust sub-families. The SR gene family can be split into five major groupings, which can be further separated into 11 distinct sub-families. Most flowering plants have double or nearly double the number of SR genes found in vertebrates. The majority of plant SR genes are under purifying selection. Moreover, in all paralogous SR genes in Arabidopsis, rice, soybean and maize, one of the two paralogs is preferentially expressed throughout plant development. We also assessed the extent of AS in SR genes based on a splice graph approach (http://combi.cs.colostate.edu/as/gmap_SRgenes). AS of SR genes is a widespread phenomenon throughout multiple lineages, with alternative 39 or 59 splicing events being the most prominent type of event. However, plant-enriched sub-families have 57%–88% of their SR genes experiencing some type of AS compared to the 40%–54% seen in other sub-families. The SR gene family is pervasive throughout multiple eukaryotic lineages, conserved in sequence and domain organization, but differs in gene number across lineages with an abundance of SR genes in flowering plants. The higher number of alternatively spliced SR genes in plants emphasizes the importance of AS in generating splice variants in these organisms.

Short bio:
Dale Richardson completed his Bachelor's and Master's degrees at Colorado State University in Biology and Botany, respectively. In the fall of 2010, he completed his PhD studies at the International Graduate School in Genetics and Functional Genomics at the University of Cologne, where he studied the implications of whole genome duplication and alternative splicing on evolution and gene expression in Arabidopsis. Currently, he holds a post-doctoral position at CIBIO where he works with Dr. Harald Meimberg and  Dr. Nuno Fonseca to incorporate RNA-seq technology into genome wide mapping of key SR protein binding sites in transcribed mRNA. His goal is to contribute to the development and understanding of the "plant splicing code", or the set of rules and conditions that regulate alternative splicing in plants.