Talk abstracts

Talk on Friday 02:00-02:15pm submitted by Shrabani Basu

Global analysis of small non coding RNAs in malaria pathogen

Shrabani Basu (Department of Chemistry and Center For Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213), Will Foran (Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue Pittsburgh, PA 15213), Ben Sauerwine (Department of Physics, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213), Michael Widom (Department of Physics, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213), Kausik Chakrabarti (Department of Chemistry and Center For Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213)

Abstract:
Noncoding RNAs (ncRNAs) play a pivotal role in the function and regulation of essential cell processes. Small RNA repertoire, biogenesis and function are largely unknown in malaria parasite Plasmodium falciparum that kills 3-5 million people worldwide, each year. We are particularly interested in understanding the specific role of ncRNAs in malaria parasite P. falciparum. Towards this end, we have performed a genome wide single stranded and a double stranded RNA high throughput sequencing. This allowed us to catalog all small RNAs that are overrepresented in the genome and to initiate investigation on their function. Our studies indicate antisense small RNA transcription as a major event that can regulate essential genes in malaria parasites. Additionally, we are in the process of in vivo structure probing by hydroxyl radical footprinting, which provides information on tertiary structure and intermolecular interface with a single nucleotide resolution. We have included tight controls to validate some of our genome wide RNA sequencing and structure probing data. All results tie up to enlighten our understanding of the properties and function of small RNAs in malaria parasite P. falciparum at a genome wide scale.

Keywords: ncRNA, hydroxyl radical footprinting, ss and dsRNA-Seq