UC San Diego

Nearly all eukaryotic RNAs have a continual tract of polyadenosine at their end, called a poly(A) tail. Unlike the main portion of the RNA, this addition is added after transcription has occurred and is not genomically encoded. Poly(A) tails have been implicated in a wide range of roles such as protecting the RNA and facilitating translation. In a cellular environment, RNAs are covered with an array of proteins that influence how an RNA is used and ultimately determine its fate. The poly(A) tail is bound primarily by the nuclear and cytoplasmic poly(A) binding proteins, PABPN and PABPC. These proteins play integral roles in the creation and subsequent protection of the poly(A) tail, partnering with numerous other proteins along the way. Chapter 2 summarizes recent discoveries and technological advances in understanding poly(A) tail dynamics. Sequencing of poly(A) tails is challenging due to their repetitive nature, but advances made in the last ten years have begun to make this possible. This has enabled genome-wide approaches to understanding native poly(A) tail lengths in numerous organisms, leading to profound discoveries about the range of poly(A) tail sizes that can exist on an RNA. Chapter 3 presents an in-depth study of poly(A) binding proteins PABPN and PABPC, and the RNAs that they are bound to at steady state in human cells. Although PABPN and PABPC are likely binding to nearly all RNAs at some point in their life cycle, they each have a unique enrichment and depletion binding profile. PABPC tends to be enriched with well-translated RNAs with long half-lives and shorter poly(A) tails. PABPN tends to be enriched with poorly translated RNAs with longer poly(A) tails. To advance these types of studies in another organism, I have developed tools and approaches for investigating the roles of PABPN, PABPC, and the poly(A) tail in Caenorhabditis elegans. In chapter four, I will discuss these resources. This includes the introduction of Nanopore long-read sequencing to our lab, and details how this was used to look at poly(A) tail length in C. elegans. Overall, this work deepens our understanding of the roles of PABPN and PABPC throughout the lifetime of an RNA.