Sm proteins are a family of highly conserved RNA binding proteins present in all three domains of life. These proteins form oligomeric rings and play important roles in many aspects of RNA metabolism. In archaea and bacteria, Sm proteins associate with mRNAs and small RNAs to regulate translation and stability. In eukaryotes, Sm proteins together with their associated RNAs form several distinct complexes to control splicing, histone mRNA processing, and mRNA degradation. Recent studies suggested that canonical Sm proteins, core components of spliceosomal small nuclear ribonucleoproteins (snRNPs), have functions beyond splicing. The goal of this dissertation is therefore to develop new experimental and computational tools to identify Sm-associated RNPs, and study their structure and function on the molecular, cellular and organismal levels. To identify Sm-associated RNAs, I developed a multi-targeting RNA immunoprecipitation sequencing (RIP-seq) method (Chapter 2). RIP-seq in <italic>Drosophila<italic> ovaries and human HeLa cells revealed three categories of Sm-associated RNAs: snRNAs, small Cajal body RNAs (scaRNAs) and mRNAs. Specifically, I identified a newly evolved yet highly conserved snRNA, <italic>Like-U (LU)<italic>. More importantly, I found that snRNPs mediate the interaction between Sm proteins and mature mRNAs, suggesting a splicing-independent function for snRNPs. I developed a computational method, Vicinal, for the accurate determination of ncRNAs ends using chimeric reads from RNA-seq (Chapter 3). Applying Vicinal to hundreds of RNA-seq datasets, I defined the ends of numerous ncRNAs in fly, mouse and human transcriptomes, including the newly identified LU snRNA. Most snRNAs in higher eukaryotes exist in multi-gene families, however, little is known about their contribution to splicing regulation. In Chapter 4, I analyzed expression of snRNA paralogs during vertebrate and invertebrate development. Surprisingly, I identified a developmental switch in the expression of snRNA paralogs that is conserved in evolution, despite a lack of stable orthologous groups. This work lays the foundation for genetic analysis of snRNA paralog functions. In Chapter 5, I describe our discovery of SMN bodies in <italic>Drosophila<italic> testes. Our analysis of SMN bodies and U body-like RNPs suggests a concerted pathway for snRNP assembly in the cytoplasm, blockage of which leads to granule formation.