ADAR-Deficiency Perturbs the Global Splicing Landscape in Mouse Tissues
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Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press 1 ADAR-deficiency perturbs the global splicing 2 landscape in mouse tissues 3 Running Title: A-to-I RNA editing impacts pre-mRNA splicing 4 5 Authors: 1* 1* 1,2 6 Utkarsh Kapoor , Konstantin Licht , Fabian Amman , Tobias 3 1 3 1 7 Jakobi , David Martin , Christoph Dieterich and Michael F. Jantsch 8 9 10 1. Center of Anatomy & Cell Biology, 11 Department of Cell and Developmental Biology, 12 Medical University of Vienna 13 Schwarzspanierstrasse 17 14 A-1090 Vienna, Austria 15 16 2. Institute of Theoretical Biochemistry 17 University of Vienna 18 Währingerstrasse 17 19 A-1090 Vienna, Austria 20 21 3. Department of Internal Medicine III and Klaus Tschira Institute for 22 Computational Cardiology, 23 Section of Bioinformatics and Systems Cardiology, 24 Im Neuenheimer Feld 669, 25 University Hospital 26 D-96120 Heidelberg, Germany. 27 28 *) equal contribution 29 30 Correspondence to: 31 Michael F. Jantsch 32 Center for Anatomy and Cell Biology 33 Division of Cell- and Developmental Biology 34 Schwarzspanierstrasse 17 35 A-1090 Vienna, Austria 36 Email: [email protected] 37 Tel: +43-1-40160 37510 Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Abstract 2 Adenosine to inosine RNA-editing and pre-mRNA splicing largely occur co-transcriptionally 3 and influence each other. Here we use mice deficient in either one of the two editing 4 enzymes ADAR (ADAR1) or ADARB1 (ADAR2) to determine the transcriptome-wide impact of 5 RNA-editing on splicing across different tissues. We find that ADAR has a 100× higher impact 6 on splicing than ADARB1, although both enzymes target a similar number of substrates with 7 a large common overlap. Consistently, differentially spliced regions frequently harbor ADAR 8 editing sites. Moreover, catalytically dead ADAR also impacts splicing, demonstrating that 9 RNA-binding of ADAR affects splicing. In contrast, ADARB1 editing sites are found enriched 10 5’ of differentially spliced regions. Several of these ADARB1-mediated editing events change 11 splice consensus sequences therefore strongly influencing splicing of some mRNAs. A 12 significant overlap between differentially edited and differentially spliced sites suggests 13 evolutionary selection towards splicing being regulated by editing in a tissue-specific 14 manner. 15 16 2 Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Introduction 2 RNA modifications affect composition, stability, structure and function of messenger RNAs 3 (Licht and Jantsch 2016). In metazoans, adenosine-to-inosine (A-to-I) RNA editing is the 4 most abundant type of RNA editing and is mediated by the adenosine deaminase acting on 5 RNA (ADAR) family of enzymes (Nishikura 2016; Eisenberg and Levanon 2018). During A-to-I 6 editing, an inosine is generated by hydrolytic deamination of adenosines. Inosines are 7 primarily read as guanosines by cellular machines and occasionally as adenosines or uracils 8 (Basilio et al. 1962; Licht et al. 2018). In mammals, two types of active ADARs, ADAR 9 (ADAR1) and ADARB1 (ADAR2) are found that modify different, but partially overlapping 10 substrate sites (Eggington et al. 2011). 11 12 ADARs bind double-stranded RNA (dsRNA) which can be formed between different regions 13 of an RNA. In mRNAs this can involve exon-intron, exon-exon or intron-intron base-pairing. 14 We recently showed that in the mouse most editing-competent structures are formed 15 within introns (intron-intron base-pairing), followed by structures formed within UTRs (Licht 16 et al. 2019). The definition of some editing sites by base-pairing between exonic and intronic 17 sequences has led to the notion that A-to-I editing must occur co-transcriptionally, or before 18 intron removal (O'Connell 1997). Splicing itself occurs mostly co-transcriptional (Merkhofer 19 et al. 2014). Consistently, both pre-mRNA splicing and RNA editing are coordinated (Bratt 20 and Ohman 2003). Moreover, both processes contribute to proteomic diversity (Wang and 21 Burge 2008). 22 23 Splicing efficiency can control editing levels. Both, mini-gene reporter assays as well as 24 analyses of endogenous targets, demonstrated that exon-intron dependent editing sites are 25 strongly affected by the efficiency of splicing (Licht et al. 2016). Conversely, A-to-I RNA 26 editing may affect splicing by creating or disrupting splice sites or branch points (Rueter et 27 al. 1999). Similarly, ADARs may alter binding sites for splicing factors and compete with 28 splicing factors for binding and/or access to the same RNA. Several studies have shown an 29 impact of RNA editing on splicing for selected substrates. For instance, inhibition of editing 30 of the glutamate receptor subunit Gria2 impairs splicing of intron 11 and affects alternative 31 splicing at intron 13/14 (Higuchi et al. 2000; Schoft et al. 2007; Penn et al. 2013). Similarly, 3 Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press 1 global studies performed in human tissue culture cells, flies, and mouse brains lacking 2 ADARB1 have provided insights into the impact of editing on splicing (Solomon et al. 2013; 3 St Laurent et al. 2013; Mazloomian and Meyer 2015; Dillman et al. 2016; Hsiao et al. 2018). 4 However, a transcriptome-wide splicing analysis comparing different tissues within a mouse 5 genetic deletion model of Adar remains elusive. 6 7 In mice, both ADARs are essential but can be rescued to different extents. Adar null mice are 8 embryonic lethal and die at stage E11.5 and show defects in erythropoiesis, elevated 9 interferon signaling and widespread apoptosis (Hartner et al. 2004; Wang et al. 2004; 10 Hartner et al. 2009; Liddicoat et al. 2015). It has been shown that a deletion in Adar can be 11 rescued by a concomitant deletion of the cytoplasmic RNA sensor MDA5 (Ifih1) or its 12 downstream signaling mediator MAVS (Mavs). The extent to which Adar deficiency can be 13 rescued depends strongly on the Adar allele used and ranges from complete viability, over 14 reduced growth to post-natal death (Mannion et al. 2014; Liddicoat et al. 2015; Pestal et al. 15 2015; Bajad et al. 2020). Similarly, Adarb1 null mice die within a few weeks after birth 16 accompanied by seizures and epilepsy. Adarb1 deficiency can be rescued by a pre-edited 17 version of the AMPA glutamate receptor subunit 2 (Gria2) (Higuchi et al. 2000). These mice 18 have been extensively studied and appear phenotypically normal under standard laboratory 19 conditions (Higuchi et al. 2000). The Adar deletion mice rescued by a concomitant Mavs 20 deletion exhibit a minute phenotype (Bajad et al. 2020). 21 In this study, for the first time, we use Adar-deficient, rescued mice to characterize the 22 ADAR-mediated impact on the transcriptome-wide splicing landscape in different mouse 23 tissues and compare their splicing landscape with that of Adarb1-deficient rescued mice 24 (Higuchi et al. 2000). 25 26 Results 27 RNA-seq and Global Splicing Analysis 28 To determine the impact of ADAR on splicing, we interbred Mavs-/- mice with Adar+/- 29 (AdarΔ7-9) mice to generate Adar+/- ; Mavs-/- mice (Bajad et al. 2020). Offspring of these mice 30 with genotype Adar+/+ ; Mavs-/- (Adar WT) and Adar-/- ; Mavs-/- (Adar KO) were collected at 31 P14. In the Adar-/- mice used here a truncated, editing-deficient ADAR protein is expressed 4 Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press 1 (Bajad et al. 2020). To assess the impact of ADARB1 on splicing, we crossed heterozygous 2 Adarb1+/- ; Gria2R/R mice and collected Adarb1+/+ ; Gria2R/R (Adarb1 WT) and Adarb1-/- ; 3 Gria2R/R (Adarb1 KO) pups at P14. 4 Since A-to-I RNA editing events are enriched in tissues of neuronal origin, we sequenced 5 poly(A) selected RNA of cortices isolated from Adar WT, Adar KO, Adarb1 WT and Adarb1 6 KO mice in biological triplicates in 125-bp paired-end mode on a Illumina HiSeq 2500 7 (Supplemental Figure 1A, 1B). Editing sites were detected in these RNA-seq data sets using a 8 machine learning algorithm RDDpred (Kim et al. 2016). Editing levels for each site were 9 calculated by dividing the number of edited reads by the total number of reads spanning the 10 editing site. Following removal of known SNPs and stringent filtering, we compiled a list of 11 differentially edited sites where we observed a significant change (Welch’s t-test; p ≤ 0.1) in 12 RNA editing levels between WT and KO cortex samples. We detected 9,382 editing sites in 13 Adar WT out of which 1,459 were found to be differentially edited in the Adar KO cortex. 14 Similarly, we detected 8,161 editing sites in Adarb1 WT out of which 1,413 were found to be 15 differentially edited in the Adarb1 KO cortex. As expected, most differentially edited sites 16 showed reduced editing upon Adar or Adarb1 deletion. In contrast, editing levels were 17 increased for a small number of editing sites upon depletion of one of the two ADARs 18 (Figure 1A). In the Adar-/- cortex, 117 sites showed an increase in editing between 1% and 19 83%. Similarly, in Adarb1-/- cortex, 107 sites showed an increase in editing between 1% and 20 54% (Supplemental Figure 2A, 2B and Supplemental Dataset 1). This observation suggests 21 competition between ADAR and ADARB1 for access to the same editing site that hints 22 towards a regulatory mechanism to keep editing levels in check.