RNA plays indispensable roles in almost every aspect of cell functions. The presence of RNA at the precise location and the designated time is crucial to cell survival and development. Dysregulation of RNA processing, including transcription, splicing, transport, and decay, has emerged as a major contributing factor to neurodegenerative diseases, which are characterized by irreversible neuron loss and gliosis. However, current methods limit our capability to decipher RNA’s biological functions with high spatial and temporal resolution to interrogate the cause and progress of these fatal neurological diseases. The approaches that can assay RNA locations usually involve tedious cell fractionation procedures, which are prone to generate false positives and negatives. Thus it is urgent to assay cellular RNA localization in an unbiased manner.