Jun 27 (Wed.), 10:00pm-11:30am
Place: FIT 1-312

Speaker: Dr Russell L. Malmberg, Professor, Associate Dean of Franklin College of Arts & Sciences, University of Georgia
Host: Xuegong Zhang

Title: Computational Searches of Genomes for Non-Coding RNAs

Over the last 30 years there have been dramatic changes in biologists’ understanding of the roles of RNA in cells and organisms, extending beyond the function of mRNA carrying the code for protein synthesis. In the early 1980s, Cech and Altman showed that RNA could had catalytic functions as ribozymes, while in the late 1990s, Voinnet & Baulcombe and Fire & Mello showed that small RNA molecules had regulatory functions. Recently many thousands of long RNAs have been identified, which also play regulatory functions. RNAs which function as RNAs, and not through coding for protein, are referred to as non-coding RNAs; estimates of the total number of different non-coding RNAs in organisms vary widely from thousands to millions.
The sequences of many genomes are becoming available. One bioinformatic problem is that of annotation, identifying the regions of a newly sequenced genome which might lead to either mRNAs that code for protein, or the regions which may produce non-coding RNAs. Identifying the potential non-coding RNAs in the genome is difficult because there are few obvious statistical signals to differentiate DNA which is transcribed into a non-coding RNA from DNA which is not transcribed. One approach is to look for indications of RNA structure. RNA secondary structure can be described as stems and loops formed by internal base-pairing; these stems and loops may be modeled either by thermodynamic or probabilistic methods. However, the use of secondary structure prediction by itself is generally not able to distinguish genomic background DNA from DNA which is transcribed into a non-coding RNA. Our approach has included an analysis of RNA tertiary structure characteristics. These results were then incorporated into the underlying models which are used to detect genomic regions with the potential to give rise to non-coding RNAs. This approach has significantly improved our ability to distinguish potential non-coding RNA genes from the genomic background.

Lab Introduction
Dr Russell L. Malmberg’s research interests are in the broad areas of bioinformatics and plant evolutionary/ecological genetics. Will Rogers and he are studying the genetics, evolution, and ecology, of the insect-eating pitcher plants (Sarracenia species). Most of his bioinformatics work is a collaboration with Liming Cai of the Computer Science Department to develop methods of modeling and searching genomes for non-coding RNAs.