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Accumulation of Nuclear ADAR2 Regulates Adenosine-To-Inosine

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Accumulation of Nuclear ADAR2 Regulates Adenosine-To-Inosine © 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 745-753 doi:10.1242/jcs.200055 RESEARCH ARTICLE Accumulation of nuclear ADAR2 regulates adenosine-to-inosine RNA editing during neuronal development Mikaela Behm, Helene Wahlstedt*, Albin Widmark, Maria Eriksson‡ and Marie Öhman§ ABSTRACT Owing to structural similarities, inosine is recognized as Adenosine to inosine (A-to-I) RNA editing is important for a functional guanosine (G) by the cellular machineries. Hence, A-to-I editing brain, and most known sites that are subject to selective RNA editing has the capacity to diversify neuronal gene expression through have been found to result in diversified protein isoforms that are alteration of protein sequences, splicing patterns and base-pairing involved in neurotransmission. In the absence of the active editing properties. Editing within coding sequences mostly occurs in genes enzymes ADAR1 or ADAR2 (also known as ADAR and ADARB1, involved in neurotransmission, such as in the transcript coding for respectively), mice fail to survive until adulthood. Nuclear A-to-I the GluA2 subunit of the AMPA glutamate receptor, where editing editing of neuronal transcripts is regulated during brain development, is essential for survival (Brusa et al., 1995; Higuchi et al., 2000). with low levels of editing in the embryo and a dramatic increase after Another example of a recoding editing event occurs in the Gabra-3 α birth. Yet, little is known about the mechanisms that regulate editing transcript, encoding the 3 subunit of the inhibitory GABA during development. Here, we demonstrate lower levels of ADAR2 in receptor, where editing leads to an isoleucine to methionine (I/M) the nucleus of immature neurons than in mature neurons. We show that change in the translated protein (Ohlson et al., 2007). Here, the importin-α4 (encoded by Kpna3), which increases during neuronal edited isoform is necessary for proper trafficking and recycling α maturation, interacts with ADAR2 and contributes to the editing properties of the 3 subunit during brain development (Daniel et al., efficiency by bringing it into the nucleus. Moreover, we detect an 2011). Most sites edited within coding sequences are inefficiently increased number of interactions between ADAR2 and the nuclear edited in the embryonic brain, while they are edited to much greater isomerase Pin1 as neurons mature, which contribute to ADAR2 protein extents in the adult brain (Dillman et al., 2013; Hwang et al., 2016; stability. Together, these findings explain how the nuclear editing of Lomeli et al., 1994; Wahlstedt et al., 2009). substrates that are important for neuronal function can increase as the Just like edited sites within coding sequences, editing within brain develops. repetitive elements in introns and untranslated regions (UTRs) is lower in embryonic tissue than in adult human tissue, including the KEY WORDS: A-to-I RNA editing, ADAR2, Importin-α4, Pin1 brain (Shtrichman et al., 2012). Although most A-to-I editing sites within these repetitive elements have not been assigned specific INTRODUCTION functions, there are examples where editing leads to alternative Diversification of the neuronal transcriptome through co- and splicing and exonization of introns (Lev-Maor et al., 2007). The post-transcriptional events is crucial for proper function of the non-coding microRNAs (miRNAs) are also edited, particularly in mammalian brain. One of the most common modifications of the targeting seed sequence (Alon et al., 2012; Ekdahl et al., 2012; neuronal transcripts is deamination of adenosine to inosine (A-to-I) in Kawahara et al., 2007; Vesely et al., 2014). The ADAR enzymes double-stranded RNA (dsRNA), which is catalyzed by one of two target the nuclear miRNA precursors and can affect their maturation active adenosine deaminases that act on RNA (ADARs), ADAR1 or mRNA-targeting capacity. The frequency of miRNA editing is and ADAR2 (also known as ADAR and ADARB1, respectively) also a regulated event during brain development (Ekdahl et al., (Bass, 2002; Bass et al., 1997; Nishikura, 2010; Paul and Bass, 2012). 1998). Most ADAR substrates depend on intronic sequences to To date, mechanisms for how A-to-I editing is regulated have been form the dsRNA structure required for editing (reviewed in sparse. We have previously seen that the protein levels of ADAR1 and Wahlstedt and Öhman, 2011). Thus, editing of many substrates has ADAR2 are constant during mouse brain development, not following to occur in the nucleus before splicing. Both ADAR1 and ADAR2 thegradual increase ofA-to-I editing (Wahlstedt et al.,2009). A number have been shown to accumulate in the nucleolus, where the enzymes ofediting enhancerandrepressorcandidates have been identified by the bind but do not edit ribosomal RNA (Desterro et al., 2003; Sansam Jantsch laboratory (Garncarz et al., 2013; Tariq et al., 2013), and work et al., 2003). However, the nucleolar association is highly dynamic from the O’Connell laboratory has revealed that ADAR2 is post- and the ADAR enzymes shuttle between the nucleolus and translationally regulated by the phosphorylation-dependent peptidyl- nucleoplasm. prolyl isomerase Pin1 (Marcucci et al., 2011). Pin1 recognizes a conserved phosphorylated Ser/Thr-Pro motif in the N-terminal region Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm of ADAR2, and this interaction is required for nuclear localization of University, Svante Arrheniusväg 20C, Stockholm, 106 91, Sweden. ADAR2. Nevertheless, there are no indications that these factors *Present address: Department of Oncology-Pathology, Cancer centrum Karolinska, regulate editing specifically during brain development. Karolinska Institutet, Stockholm 171 76, Sweden. ‡Present address: BioArctic AB Warfvinges väg 35, Stockholm 112 51, Sweden. Here, we show that developmentally regulated RNA editing in neurons can be explained by an increasing presence of the ADAR2 §Author for correspondence ([email protected]) enzyme in the nucleus. We show that ADAR2 is imported into the α M.O., 0000-0002-6636-5841 nucleus by importin- 4 and is stabilized by a nuclear interaction with Pin1. These factors increase the accessibility of ADAR2 to the Received 23 November 2016; Accepted 30 December 2016 editing substrates during neuronal maturation. Journal of Cell Science 745 RESEARCH ARTICLE Journal of Cell Science (2017) 130, 745-753 doi:10.1242/jcs.200055 RESULTS DIV, the amounts of transcripts edited resembled those detected in the RNA editing increases in cultured primary cortical neurons adult mouse brain. Gabra-3 and pri-miR-376b are substrates for both as they mature ADAR1 and ADAR2 (Fig. S1B; Ohlson et al., 2007). Editing at the We have previously shown that A-to-I RNA editing increases in both +4 site in the ADAR1-specific non-coding substrate pri-miR-381 coding and non-coding substrates in the developing mouse brain also increased as the neurons matured (Fig. 1B; Fig. S1B). (Ekdahl et al., 2012; Wahlstedt et al., 2009). To study the mechanisms Interestingly, editing at the lysine-to-glutamate (K/E) site in the that regulate A-to-I editing during neuronal maturation, we isolated cytoplasmic FMR1 interacting protein 2 (Cyfip2), appeared later in cortical neural progenitor cells from mouse cortices at embryonic day the developing neurons than editing at the other sites – only after 6 16 and cultured them for up to 14 days in vitro (DIV). During this DIV a clear G peak was visible in the chromatogram (Fig. 1B). At 12 timeframe, neural progenitors matured and formed an extensive DIV, 50% of the Cyfip transcripts were edited at the K/E site, which neurite network (Fig. 1A; Fig. S1A). To determine if editing has been shown to be exclusively edited by ADAR2 (Nishimoto increased in a similar way in developing cultured neurons as in the et al., 2008; Rueter et al., 1999). To determine if this is a specific brain, coding as well as non-coding RNA substrates with both pattern for ADAR2-mediated editing, we analyzed auto-editing at the specific and overlapping specificity for ADAR1 and ADAR2 editing −1 site in the ADAR2 pre-mRNA. Editing at the −1sitegaveriseto were selected for analyses after 1–12 days in culture (Ekdahl et al., alternative splicing and a subsequent inclusion of 47 nucleotides in 2012; Nishimoto et al., 2008; Ohlson et al., 2007). Similar to that in exon 5 (Fig. 1C) (Rueter et al., 1999). Editing-induced alternative the embryonic brain, low levels of editing were observed at the I/M splicing was measured by performing semi-quantitative reverse- site in the coding region of the Gabra-3 transcript and at the +6 site in transcriptase (RT)-PCR, using exonic primers that amplify both the miRNA precursor transcript pri-miR-376b after 1 DIV (Fig. 1B). normal and alternatively spliced ADAR2 transcripts. Using this As the neurons matured, editing levels gradually increased, and at 12 approach, we could confirm that editing mediated by ADAR2 Fig. 1. Editing levels increase in developing cortical neurons. (A) Neurites were visualized by βIII-tubulin immunoreactivity (green) in primary mouse cortical neurons cultured for up to 14 days in vitro (DIV). DAPI staining (blue) was used to visualize the nuclei. Scale bar: 50 μm. (B) Sanger sequencing chromatograms showing editing levels as a dual A and G peak after RT-PCR analysis of the I/M site in the Gabra-3 transcript, the +6 site in pri-miR-376b, the +4 site in pri-miR-381 and the lysine-to-glutamate (K/E) site in Cyfip2 in neurons cultured for 1, 3, 6 and 12 DIV. Arrows indicate the edited sites. (C) Schematic illustration of alternative ADAR2 pre-mRNA processing of exon 4 and 5 due to editing at the −1 site in intron 4. Editing at the −1 site creates an alternative 3′ splice site, which results in the inclusion of 47 nucleotides. The illustration is not drawn to scale. (D) Semi- quantitative RT-PCR of alternative ADAR2 pre- mRNA processing of exon 4 and 5 using exonic primers in neurons cultured for 1, 3, 6 and 12 DIV.
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