Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition

Nurit Gal-Mark,Sahar Sweetat,Lea Shallev,Jin Billy Li,Erez Y. Levanon,Michal Barak,Oded Behar,Eli Eisenberg

doi:10.1038/srep43421

Abstract

Adenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level. A-to-I RNA editing is abundant in the brain, and altered editing levels have been reported in various neurological pathologies and following spinal cord injury (SCI). The prevailing concept is that the RNA editing process itself is dysregulated by brain pathologies. Here we analyzed recent RNA-seq data, and found that, except for few mammalian conserved editing sites, editing is significantly higher in neurons than in other cell populations of the brain. We studied A-to-I RNA editing in stab wound injury (SWI) and SCI models and showed that the apparent under-editing observed after injury correlates with an approximately 20% reduction in the relative density of neurons, due to cell death and immune cell infiltration that may account for the observed under-editing. Studies of neuronal and astrocyte cultures and a computational analysis of SCI RNA-seq data further supported the possibility that a reduction in neuronal density is responsible for alterations in the tissue-wide editing patterns upon injury. Thus, our data suggest that the case for a mechanistic linkage between A-to-I RNA editing and brain pathologies should be revisited.

Highlights

Adenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level
Astrocytes, oligodendrocyte precursor cells (OPCs), newly formed oligodendrocytes (NFOs), myelinating oligodendrocytes (MOs), microglia, and endothelial cells were obtained by immunopanning with cell type-specific cell-surface antibodies and FACS of transgenically labeled cell populations
We analyzed RNA-seq data generated from three mouse whole cerebral cortex tissue samples that were sequenced in the same study[40], and RNA-seq data from purchased primary neural stem cells (NSCs) isolated from embryonic mouse cortex (E14.5)[42]

Summary

Introduction

Adenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level. The vast majority of these sites reside within inverted, usually lineage specific, repeats: the Alu element pairs in human[19,20,21,22] and the B1/B2 elements in mouse[15]. These pairs are likely to form long double-stranded RNA (dsRNA) structures, the optimal targets for ADAR enzymes[6]. These long dsRNA structures may often be deaminated at multiple sites. The presence of A-to-I editing events in repetitive elements and other hyper-edited transcripts regulates the structure and stability of dsRNA structures and has been recently shown to play an essential role in regulating the innate immune response[26,27,28]

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Results

Conclusion