Structure, function and evolution of small RNAs in unicellular eukaryotes

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Ribonucleic acid (RNA) molecules called non-coding RNAs (ncRNAs) have diverse functions, controlling a variety of cellular processes in all organisms. Many eukaryotic genomes contain more genomic DNA sequence specifying the production of ncRNAs than specifying proteins and yet, the detailed function of most of these ncRNAs remains unknown. Consequently, identifying and determining functions of ncRNAs is becoming an increasingly important area of functional genomics - relating genomic DNA sequence to biological function - and is a primary objective of my research program. We will study ncRNAs in the unicellular eukaryotes called protists, organisms that comprise the bulk of eukaryotic evolutionary diversity. Nobel prize-winning discoveries were the result of first characterizing ncRNAs and their cellular functions in protists, such as self-splicing (autocatalytic) introns and telomerase RNA, both first identified in Tetrahymena thermophila. Two main classes of ncRNAs that we will investigate are the small nucleolar (sno) and small nuclear (sn) RNAs. SnoRNAs are known to have a functional role in the synthesis of ribosomes - the complexes responsible for protein synthesis in the cell. We will use an in vivo approach to determine the specific roles of individual snoRNAs during ribosome synthesis in the protist Euglena gracilis, an organism with a particularly complex ribosome assembly pathway. SnRNAs are core components of the eukaryote-specific cellular structure(s) termed the spliceosome. Spliceosomes are required for the removal of intervening sequences (introns) from protein-coding RNAs, a process called splicing. We will characterize splicing and spliceosome components in the early-diverging protist Giardia lamblia. This organism is particularly interesting because it possesses a very unusual splicing system, contains relatively few introns, and appears to be undergoing intron loss as it reduces its genome size and further adapts to its parasitic lifestyle. We will also characterize gene expression pathways and cellular components used for ncRNA synthesis in these protists, and exploit their evolutionary positions to derive insights about ncRNA and spliceosome evolution in eukaryotes.