THE CLARK LAB
The Clark Research Group
The Clark Research Group develops new materials and analytical methods to identify, quantify, and understand the function of RNA modifications in biological systems.
Our long term goals are to advance sample preparation, chromatographic separation, and mass spectrometry approaches to facilitate the characterization of nucleic acid modifications in the central nervous system, single cells, and subcellular structures.
We leverage neurobiological models and combine techniques in analytical chemistry, molecular biology, and neuroscience to investigate mechanisms of post-transcriptional regulation.
RNA Modifications
Post-transcriptional modifications to RNA are numerous and structurally diverse, with over 150 unique modified nucleosides having been reported to date. This expanded RNA alphabet, or epitranscriptome, is increasingly thought to play important roles in tuning the translation of the cellular proteome, but 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.