The Role of Retained Intron Sequences in Neuronal Dendritic mRNA
University of Pennsylvania School of Medicine, Philadelphia, PA
Department of Pharmacological Sciences
James H. Eberwine, Mentor
Defended October 8th, 2009
Abstract
Gene expression is regulated by a number of well-characterized processes from transcription to translation. While normally considered as being confined to the nucleus, recent publications have identified retained introns in cytoplasmic mRNA. In both neuronal dendrites and anucleate platelets, retained intronic sequences have been associated with cellular function, proper protein expression and responsiveness to external stimuli. Here we report that the retention of introns in the mRNA of neuronal dendrites occurs far more broadly than previously reported, and may serve as an important component of post-transcriptional gene expression regulation.
Dendritically localized mRNA with retained introns were detected by microarray, and confirmed for localization by in situ hybridization and next generation sequencing. Computational analysis of these introns revealed that a number of common sequence clusters can be identified across retained introns. One such sequence found in many retained introns is the rodent ID element that we show can confer dendritic targeting capacity to exogenous transcripts and is capable of blocking targeting of particular endogenous RNAs. Using a combination of the PNA-assisted identification of RNA-binding proteins (PAIR) method and a nucleic acid-binding protein microarray, we also identify a large number of proteins capable of binding retained intron sequences. These studies highlight a new subclass of RNA transcripts in dendrites, a novel mechanism for dendritic targeting of mRNAs, and suggest a functional role for retained introns in hippocampal neurons.