UCLA

Coding and noncoding RNAs (ncRNAs) are essential molecules of life. While the roles of RNA have been extensively studied inside the cell, RNA has also been detected outside of the cell and stably expressed in body fluids. These extracellular RNAs (exRNAs) are packaged inside vesicles, lipoproteins, or in ribonucleoprotein complexes which protect them from degradation by ribonucleases. exRNAs are thought to be involved in cell-to-cell communication by sending messages via extracellular vesicles. Previous studies primarily focused on total expression of exRNAs, especially microRNAs whose presence in the extracellular space is now well established. Other aspects of the transcriptome, such as RNA modifications, were rarely investigated in exRNA profiles. In addition to microRNAs, a plural of recent studies reported the detection of mRNA fragments in the extracellular space. However, many questions remain about the mechanisms that enable their stability, sorting, and function. In this dissertation, leveraging a large amount of public and in-house exRNA-seq data, we develop and apply bioinformatic tools to analyze the patterns of post-transcriptional modifications, mRNA fragments, and repeat-derived RNAs.We developed miNTA, a highly accurate bioinformatic method to identify 3’ end non-templated additions (NTAs) on microRNAs, a type of post-transcriptional modification. We observed enriched levels of 3’ uridylation across 4 biofluids, consistent with previous findings. We demonstrated that 3’ uridylation levels enabled improved segregation of biofluids relative to miRNA expression levels. Next, we analyzed mRNA fragments, repeat-derived RNAs and another type of post-transcriptional modifications, RNA editing, in exRNA-seq data of 17 human biofluids. We observed enrichment of RNA binding protein (RBP) binding sites in mRNA fragments, supporting the hypothesis that RBPs play a role in selection and stability of mRNA fragments. Additionally, we reported hundreds of RNA editing sites across biofluids. Expanding upon examples of RNA editing across biofluids, we probed RNA editing differences in Alzheimer’s Disease and control individuals using plasma-derived exRNA-seq data. Editing levels of differential editing sites were elevated in Alzheimer’s Disease patients, including three sites whose levels correlated with patient cognitive scores. These findings support the potential to uncover useful information via RNA editing analysis in exRNA profiling.