The central hypothesis of molecular biology depicts RNA as an intermediary conveyor of genetic information. RNA is transcribed from DNA and translated to proteins, the molecular machines of the cell. However, many RNAs do not encode protein and instead function as molecular machines themselves. The most famous examples are ribosomal RNAs and transfer RNAs, which together form the core translational machinery of the cell. Many other non-coding RNAs have been discovered including catalytic and regulatory RNAs. In many cases RNA function is tightly linked to its secondary structure, which is the collection of hydrogen bonds between complimentary RNA sequences that drives these molecules into their three dimensional structure. Over the last decade, technology for determining the sequence of DNA and RNA has advanced rapidly, making transcriptome-wide expression profiling fast and widely available. In this dissertation, I discuss recent efforts to leverage this powerful technology to study, not just RNA expression, but several other aspects of RNA function. In particular, I focus on three tightly linked aspects of RNA biology: RNA-secondary structure, RNA cleavage, and regulatory small RNAs. I introduce a database for integrating, comparing, and contrasting techniques for determining RNA secondary structure including a technique developed in my dissertation laboratory. Additionally, I discuss a newly improved technology capable of detecting RNA cleavage events. Finally, I integrate RNA secondary structure probing and RNA cleavage detection to interrogate a family of genes important for eukaryotic small RNA-mediated silencing. These diverse analyses are just a few examples of the vast promises offered by adapting RNA-sequencing technology to probe RNA function across many cellular processes.