Activity-Dependent A-to-I RNA Editing in Rat Cortical Neurons

Abstract

Changes in neural activity influence synaptic plasticity/scaling, gene expression, and epigenetic modifications. We present the first evidence that short-term and persistent changes in neural activity can alter adenosine-to-inosine (A-to-I) RNA editing, a posttranscriptional site-specific modification found in several neuron-specific transcripts. In rat cortical neuron cultures, activity-dependent changes in A-to-I RNA editing in coding exons are present after 6 hr of high potassium depolarization but not after 1 hr and require calcium entry into neurons. When treatments are extended from hours to days, we observe a negative feedback phenomenon: Chronic depolarization increases editing at many sites and chronic silencing decreases editing. We present several different modulations of neural activity that change the expression of different mRNA isoforms through editing.C HANGES in neural activity can modulate synaptic strength at the level of individual neurons (Burrone et al. 2002) and whole networks , influence developmental and differentiation decisions (Borodinsky et al. 2004), and bias neurons toward inclusion in novel memory formation (Zhou et al. 2009). At the mRNA level, immediate early genes (IEGs) are transcribed rapidly in response to increased neural activity and have been described as a "genomic action potential" (Clayton 2000). The promoter regions of these and other genes involved in neuronal plasticity can undergo activity-dependent alterations in their chromatin structure, such as cytosine demethylation and histone acetylation (Tsankova et al. 2004;Ma et al. 2009). In addition to the major, genome-wide epigenetic changes known to occur during early development, recent studies have found activity-driven epigenetic modifications in post-mitotic neurons during fear memory recall, exposure to drugs of abuse, and emotional stress (Renthal et al. 2007). We sought to understand if neural activity influences a post-transcriptional genetic modification, adenosine-toinosine (A-to-I) RNA editing.A-to-I RNA editing is an enzymatically catalyzed, sitespecific nucleotide change (deamination) in pre-mRNA that changes adenosine into inosine, which reads as guanosine during translation (Bass 2002;Nishikura 2010). The bestknown example is the developmentally regulated editing of the glutamate receptor subunit Gria2, where A-to-I editing at a single site controls whether GRIA2-containing AMPA receptors are permeable to Ca 2+ ions (Sommer et al. 1991). In neurons, many transcripts undergo editing: Previous large-scale genomic screens in Drosophila and human cells found that synapse-related transcripts are enriched in RNA-editing sites (Paul and Bass 1998;). More generally, inosine is greatly enriched in brain tissue compared to other tissues (Paul and Bass 1998) and the mammalian adenosine deaminases acting on RNA (ADARs) tend to be preferentially or exclusively expressed in the brain (Melcher et al. 1996). Knockout of ADARs in mice, Drosophila, and Caenorhabditis elegans leads to aberrant neurological and b...

Dynamic regulation of RNA editing in human brain development and disease

“…Indeed, a similar increasing editing pattern is reported in Drosophila at several genes 40 . We also note that several sites with increasing editing patterns have previously been shown to be edited in an activity-dependent manner 41,42 , which is further evidence for functionality. In addition, while we found that the increasing editing pattern was evolutionarily conserved, our results with post-mortem and in vitro human samples enabled us to identify developmentally regulated RNA editing sites not found in other model organisms.…”

Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease

“…However, RNA-seq is generally less accurate in quantifying RNA editing levels due to the moderate read coverage currently available (Ramaswami et al 2013). Several attempts have been made to couple targeted amplification and next-generation sequencing for accurate quantification of RNA editing with limited success (Li et al 2009;Sanjana et al 2012;Ramaswami et al 2013). Very recently, a more robust experimental system which combines microfluidics-based multiplex PCR has been presented by Zhang et al (2014).…”

Accumulation of nuclear ADAR2 regulates adenosine-to-inosine RNA editing during neuronal development

“…This may be important not only for neuronal development but also for neuronal plasticity. Indeed, acute and chronic neuronal activation of both hippocampal and cortical neurons alters the editing of several substrates Sanjana et al, 2012). However, differences in nuclear concentration of ADAR2 upon neuronal activation remain to be investigated.…”