Arun Manoharan, Ph.D.

11

The 3’ untranslated regions (3’UTRs) of mRNAs have recently been shown to play major roles in gene regulation by interaction with small (21-26nt length) RNAs, such as microRNAs and small interfering RNAs (siRNAs). Recent studies highlight dynamic expression of small RNAs and provide limited evidence of utilization of alternative 3’UTR lengths (3’UTR isoforms) across development and specific cell types. However a comprehensive catalogue of 3’UTRome of an organism had been unavailable. By computational analysis of traditional and novel high-throughput sequence data, chapter two of this dissertation provides annotated 3’UTRs for more than 75% of the genes in the model organism Caenorhabditis elegans across the major stages of development. At the whole-transcriptome level, 3’UTRs express remarkable diversity in utilization of alternative poly-adenylation sites, which define the alternative 3’UTR isoforms, in ~40% of genes in the genome. We identified many isoforms are developmentally stage-specific and many genes show evidence of length switching between longer and shorter isoforms over development to maybe include or escape regulation from small RNAs or other RNA binding proteins. Thus, our study reveals the diversity and temporally regulated expression of 3’UTR isoforms as a complex mechanism in gene regulation at an unprecedented scope. The analysis provides large-scale evidence for multiple alternative 6nt sequence elements (PAS sites) near 3’ ends of 3’UTRs that are enriched in shorter, alternative isoforms. Chapter three of my dissertation also compared and combined the results of a parallel study of 3’UTRs in C. elegans further expanding transcriptome coverage of 3’UTRs. As an example of biological relevance for 3’UTR isoform usage, in chapter four we identified a potential connection between the synaptogenesis pathway and specific 3’UTR isoform usage in C. elegans. In related work described in chapter five, I analyzed small RNA sequences from isolated sperm and oocytes and identified and characterized a new class of germline-specific siRNAs, 26G-RNAs, which target coding regions and 3’UTRs of genes to regulate their target gene expression. These have been classified into two subclasses: 26G-RNAs generated in the male germline targeting genes involved in spermatogenesis, and maternally inherited 26G-RNAs targeting genes that function in zygotic development.

Current Placement

The Microbiome Discovery Company