# Neuronal ciRNA characterization and impact upon channel functioning

> **NIH NIH R01** · UNIVERSITY OF PENNSYLVANIA · 2020 · $642,682

## Abstract

The cellular requirement for mRNA diversity is apparent, as the evolutionarily conserved process of
mRNA splicing generates mRNA and protein diversity through alternative mRNA splicing. Indeed it has
been established that >90% of mammalian genes are alternatively spliced. The abundance of the
alternatively spliced forms varies extensively, but a large fraction (~85%) of these alternatively spliced
RNAs exist in the range of 5-15% of that particular gene's mRNA transcript population. The biological
roles of alternatively spliced mRNAs are varied for example different spliced forms of channels and
receptors give rise to differentially responsive proteins, spliced cadherin RNAs facilitate specific cell-cell
interactions and distinct splice forms of individual transcription factors modulate distinct gene sets. With
such examples of molecular diversity, there has been increased effort to characterize additional splicing
events resulting in the recent discovery of three different types of alternatively spliced RNAs including
1) circular RNAs, 2) exitrons and 3) a complex population of alternatively spliced RNAs containing
retained introns (ciRNAs) that was identified in the cytoplasm of cells through the use of highly sensitive
NextGen sequencing on isolated neuronal dendrite RNA populations. This last class of RNAs is the
topic of this proposal. The discovery of a large population of ciRNAs was unexpected, yet led to the
hypothesis that they may exert a here to for unknown biological function. An example of a ciRNA that
provides insight into functionality of this class of RNAs is one that comprises part of BKCa mRNA
population. Preliminary evidence suggests a physiological role for the ciRNA in BK channel functioning
but little is known about the intrinsic mechanisms involved and whether multiple ciRNAs that possess
different retained introns for a particular RNA exert similar or distinct functions. The robust biological
impact of this ciRNA isolated from dispersed cultured neurons highlights the need to identify and
characterize the ciRNAs from cells in their native tissue microenvironment to explore how they may
regulate the cells' natural physiological responsiveness. We propose to investigate these events in situ
using our newly developed Transcriptome In Vivo Analysis (TIVA) to isolate RNA from individual
dendrites resident in the live mouse brain slice. The identity of dendritically localized ciRNAs (including
depolarization induced ciRNAs) will be determined by single cell RNAseq. A second goal is to start to
dissect the mechanism(s) of action of ciRNAs by manipulating their expression and measuring function.
While we expect to discover new ciRNAs in the course of this project, the ciRNAs encoding channels
are among the most easily examined for a functional role and provide a starting point for functional
assessments of this novel class of RNAs.

## Key facts

- **NIH application ID:** 9892047
- **Project number:** 5R01MH110180-05
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** JAMES H EBERWINE
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $642,682
- **Award type:** 5
- **Project period:** 2016-07-01 → 2021-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9892047

## Citation

> US National Institutes of Health, RePORTER application 9892047, Neuronal ciRNA characterization and impact upon channel functioning (5R01MH110180-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9892047. Licensed CC0.

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