My research aims to identify functional RNA elements in transcriptomes through genome-wide detection of RNA structures. RNA play an important role in regulating cellular gene expression. Its ability to fold into complex secondary and tertiary structures is fundamental to its function in the cell. In almost every step of its life cycle, RNA structure has been found to influence diverse processes including transcription, translation mRNA transcript and decay. Alterations in RNA structure have been implicated in several diseases. Despite the importance of RNA structure, structural information for most cellular RNAs, such as mRNAs, is lacking due to the low throughput nature of RNA structure probing and difficulties in probing long RNAs. To fully assess the impact of RNA structure in biology, I aim to utilize and extend high throughput ways to probe RNA structures in solution by coupling structure probing to high throughput sequencing. This enables us to probe RNA structures for thousands of RNAs simultaneously. This expansion of RNA structural data will likely enhance our understanding of how RNA function in different cellular systems, as well as open doors to potentially targeting these structural elements in diseases.