Computational Analysis Of Ribonucleic Acid Basepairs In Rna Structure And Rna Rna Interactions PDF Download

RNA is ubiquitous in the cellular environment, and it can function in innumerable ways with a variety of interaction partners. A RNA molecule's structure, in particular the set of base pairing interactions between the nucleotides of the molecule known as secondary structure, can help determine its function. Since most proteins can only bind to either single stranded or double stranded RNA, RNA secondary structure can also help determine where and how RNA-protein binding interactions occur. In this work I investigate computational models for RNA-protein interactions in a variety of different contexts. In Chapter 2 I probe the effect of single nucleotide variations on RNA-protein binding as mediated by RNA secondary structure. Single nucleotide variations are single nucleotide changes in an organism's genome that can often cause disease, and may do so through a number of different mechanisms. In this work we propose that sequence changes can affect accessibility to protein binding sites through changes in secondary structure, even when these sequence changes occur tens of nucleotides outside of protein binding sites. We find that single nucleotide variations can have a many fold effect on the binding affinity of proteins for RNA, and characterize the genome-wide effect of single nucleotide variations on HuR binding. HuR is a single-stranded RNA binding protein that binds to AU-rich sequences, and has links to diseases such as cancer. We also find an asymmetry in this effect for HuR, indicating that this effect may be under selection. Following the previous work, which utilizes a model incorporating single stranded RNA binding proteins into RNA secondary structure folding, I introduce a model for incorporating double stranded RNA binding proteins (dsRBPs) into RNA secondary structure partition function calculations in Chapter 3. The dsRBPs are an important but understudied class of proteins that have uses in a wide range of processes. We implement our model in the ViennaRNA package, and validate it by calculating a number of experimental observables for transactivation response element RNA-binding protein. We find that RNA secondary structure can have a many fold effect on the effective binding affinity of dsRBPs, and show that calculated affinities for pre-miRNA-like constructs correlate with experimentally measured processing rates. Our model provides a novel method for interrogating the interplay between dsRBPs and RNA secondary structure. In Chapter 4 I study RNA-protein interactions in a different context, and investigate the role of Shine-Dalgarno (SD) sequences in translation in the Bacteroidetes. The Bacteroidetes are a phylum of bacteria known to rarely use SD sequences, but after performing a survey of SD usage in the phylum we find that certain ribosomal protein genes utilize them, particularly rpsU. A cryo-electron microscopy structure of the ribosome from Flavobacterium johnsoniae, a member of the Bacteroidetes, also shows that S21, which is encoded by the ribosomal open reading frame rpsU, sequesters the anti-Shine-Dalgarno (ASD) sequence. In our survey of SD sequences we also find covariation between the SD sequence of rpsU and the ASD sequence. These observations suggest an autoregulatory model for S21 in the Bacteroidetes.