RNA Modifications
Post-transcriptional modifications of RNA are numerous and structurally diverse, with more than 170 unique modified nucleosides having been reported to date. The expanded RNA alphabet is known as the epitranscriptome, and is increasingly thought to play important roles in tuning the translation of the cellular proteome. However, the identification and quantification of RNA modifications remains challenging. Conventional approaches rely on large amounts of RNA and typically focus the detection of a single type of modification. Our lab develops new methods that leverage the power of liquid chromatography-mass spectrometry (LC-MS) to simultaneously detect dozens of RNA modifications in a single experiment. We combine these LC-MS-based methods with multivariate statistical analysis to quantitatively profile RNA modifications in biological samples.
Single-Cell Analysis of the Epitranscriptome
Cells are the individual units of life from which complex functions arise. In the brain, cell morphology can tell us only part of the story: when scrutinized with highly sensitive analytical methods, single cells from an otherwise homogeneous population display unique chemical compositions. Single-cell RNA sequencing measurements have substantially contributed to our knowledge of single-cell heterogeneity, but these approaches are unable to detect the full complement of RNA modifications. In our lab, we are pursuing a new frontier in single-cell analysis, focused on simultaneous quantification of multiple RNA modifications in single cells. Our approach involves the development of new sample preparation strategies and highly sensitive mass spectrometry techniques that facilitate the characterization of low abundance RNA modifications, enabling investigations into the intriguing possibility of cell-specific mechanisms of post-transcriptional regulation.
New Methods for Characterizing Modified Ribonucleosides
Characterizing modified ribonucleosides is important for understanding their myriad roles in downstream biology as well as investigating their significance as biomarkers for disease. Since modified ribonucleosides are chemically diverse and often present at extremely low concentrations in complex biological samples, new approaches are needed to purify and preconcentrate these analytes prior to instrumental analysis. We leverage a class of compounds known as ionic liquids (ILs) to address these challenges. ILs are molten salts that exhibit melting temperatures below 100 C and in some cases, below room temperature. The chemical structure of ILs can be designed to incorporate specific functional groups that facilitate interactions with modified ribonucleosides, rendering these compounds ideal for selective extraction of modified ribonucleosides from complex samples.