Originally apparent in trypanosomes (Benne et al., 1986), RNA alteration is a co-/post-transcriptional action that increases RNA assortment in eukaryotes. The best accepted modification in mammals is the deamination of adenosine to inosine (A-to-I), catalyzed by adenosine deaminases acting on RNA (ADAR) enzymes (Farajollahi & Maas, 2010). Inosine abject pairs with cytosine and is interpreted as guanosine by the cellular accouterment (Bass, 2002; Farajollahi & Maas, 2010). A-to-I alteration occurs in abounding animal tissues and acts on the majority of animal pre-mRNAs (Park et al., 2012; Bahn et al., 2012; Bazak et al., 2014). Best RNA alteration takes abode in Alu repetitive elements. These abbreviate interspersed nuclear elements are ∼300 abject pairs (bp) in length, specific to primates, and generally anchored in introns and 3′ untranslated regions (UTRs). The affluence of Alus in the animal genome—more than one actor copies—makes it actual acceptable to appointment astern pairs of Alus, which can anatomy stem-loop structures that are advantaged substrates of ADAR. Cytosine-to-uracil (C-to-U) alteration is abundant beneath accepted than A-to-I alteration (Blanc & Davidson, 2003) and is advised by APOBEC enzymes. The medical implications of RNA alteration may be all-encompassing as it has been active in diseases alignment from blight and acoustic diseases (Hideyama et al., 2010; Hood & Emeson, 2011; Galeano et al., 2012; Slotkin & Nishikura, 2013) to atherogenesis (Stellos et al., 2016).
Detection of RNA-edited sites is about aboveboard back the sequencing of an RNA-edited archetype (actually cDNA) will abduction the edited abject (Ramaswami & Li, 2016). A alterity in the alignment amid the arrangement and the genomic advertence can be an RNA alteration event, a distinct nucleotide polymorphism (SNP), or an antiquity accompanying to sequencing or abstracts processing. Several computational methods accept been devised to alarm RNA alteration contest from RNA-seq abstracts (Ramaswami et al., 2013; Picardi et al., 2015; Zhang & Xiao, 2015; Kim, Hur & Kim, 2016; Ramaswami & Li, 2016; Tan et al., 2017).
Here, we analyzed transcriptome-wide RNA alteration in one ample accomplice of patients with coronary avenue disease—the Stockholm-Tartu Atherosclerosis About-face Network Engineering Task (STARNET) (Franzén et al., 2016) study. We implemented a atypical apprehension activity with several analytical clarification accomplish to bear a aesthetic set of RNA alteration events. Our activity borrows account from appear methods and it is advised for actuality accomplished on a computer cluster.
First, we focused on patterns of all-around RNA editing. To analyze analytic appearance associated with RNA editing, we mapped RNA alteration quantitative affection loci (edQTLs). Finally, to appraise the ache appliance of RNA editing, we analyzed our edQTLs in the ambience of appear genome-wide affiliation studies (GWAS).
R v.3.2.2 was acclimated for all statistical analyses (R Core Team, 2015). If not contrarily specified, P-values were afflicted with Welch’s t-test. All statistical tests were two-sided.
RNA-seq and genotype abstracts (generated with the Illumina Infinium OmniExpressExome-8 chip) in this abstraction originated from samples calm of up to 7 tissues (artery aorta, centralized mammary artery, accomplished blood, subcutaneous fat, belly fat, liver, and ashen muscle) and 2 corpuscle types (macrophages and cream cells) (Franzén et al., 2016) from 855 animal subjects. Not all tissues/cell types were calm from all subjects. The account for accession these tissues and their role in coronary avenue ache accept ahead been declared (Björkegren et al., 2015). Ethical permits, biopsy and beginning procedures accept ahead been declared (Franzén et al., 2016) (Karolinska Institutet Dnr 154/7 and 188/M-12). The samples from aortic bank (n = 538) and centralized mammary avenue (n = 552) were abandoned able from rRNA-depleted libraries generated with the Illumina RiboZero protocol. The actual samples were about all poly(A)-enriched. Of the 4301 samples included in this study, 52% (2,267/4,301) were sequenced with a strand-specific protocol, and the actual were sequenced with a non-strand-specific protocol. A complete arbitrary of tissues, samples and protocols is apparent in Tables S1 and S2. Alteration calls are listed in Dataset S1.
Metaite and protein abstracts were generated by Olink AB (Sweden) and Nightingale (formerly Brainshake, Finland).
The animal genome GRCh38 and GENCODE (Harrow et al., 2012) v.24 annotations were acclimated throughout this study. RNA alteration sites were mapped to genomic appearance with ANNOVAR (Wang, Li & Hakonarson, 2010) v.2015-03-22. miRBase (Kozomara & Griffiths-Jones, 2014) v.21 was acclimated for miRNA annotations. Scripts acclimated to action abstracts can be retrieved from: https://github.com/oscar-franzen/rnaed.
Sequencing reads were accumbent with the animal genome application STAR (Dobin et al., 2013) v.2.5.1b, with the best cardinal of alignments set to 1, and the arrangement of mismatches to arrangement breadth set to 0.1. Abandoned abnormally mapped reads were advised (mapping affection = 255). The fiber specificity of sequencing was accepted by counting reads mapped to faculty and antisense transcripts with HTSeq (Anders, Pyl & Huber, 2014) v.0.6.0. For all samples, the predicted strandedness akin the recorded advice from the sequencing facility. Abandoned samples with added than 1,000,000 abnormally mapped reads in genes were analyzed. The aboriginal footfall in our activity was annoyed polymerase alternation acknowledgment (PCR) duplicates with the rmdup command in samtools v.1.2. This footfall banned the cardinal of apocryphal positives from the library architecture action (i.e., amplification of errors alien by the about-face transcriptase). Alignments were again scanned for distinct nucleotide variants (SNVs) by parsing the achievement of the mpileup command in samtools. SNVs were removed if amid aural simple repeats, polymers ≥ 5 bp, aural 5 bp of braid junctions. SNVs amid on the mitochondrial genome, on unplaced contigs, and aural the aloft histocompatibility circuitous were additionally removed. Intersections were alleged with bedtools (Quinlan & Hall, 2010) v.2.21.0. Furthermore, SNVs listed in any of the afterward databases were discarded: NCBI dbSNP b141, b146, and b147; Exome Aggregation Consortium variants v.0.3.1; NHLBI ESP6500 variants; Scripps’ Wellderly (Erikson et al., 2016); and COSMIC (Forbes et al., 2015) v.77. For the actual SNVs, all sequencing reads overlapping the armpit were extracted and realigned with GSNAP (Wu & Nacu, 2010) v.2016-05-25, application settings that acquiesce mismatches and braid junctions. For anniversary sequencing read, the alignment coordinates (chromosome, strand, alpha and stop positions) from STAR and GSNAP were compared, and antagonistic alignments were removed. A accordant alignment was accurate as >99% overlap of the start-stop breach on the aforementioned chromosome and strand. To alarm an RNA alteration event, the abject affection account had to be ≥20. To abstain errors alien from accidental hexamer priming, the SNV had to be >6 bases from the 5′ start position of the sequencing read. SNVs advertence added than one blazon of alternative per armpit were ignored. The final belief appropriate at atomic two non-identical sequencing reads to abutment the RNA alteration event.
121.2 billion single-end reads were mapped to altered locations in the animal genome (median = 27,539,768 reads/sample). Annoyed PCR duplicates bargain the numbers to ∼42.9 billion accumbent reads (median = 9,527,872 reads/sample). In total, 22,124,713 RNA alteration contest were called, mapping to 2,631,392 altered sites. 83.3% (2,866,471/3,438,790) and 92.6% (17,304,283/18,685,923) of the articular contest were A-to-G mismatches in strand-specific and non-strand-specific libraries, respectively. In the non-strand-specific data, these numbers additionally accommodate the about-face accompaniment of A-to-G (i.e., T-to-C).
Sequencing errors are added acceptable to action against the end of reads. We did not acquisition 5′ or 3′ positional biases in sequencing reads for approved contest (A-to-I and C-to-U; Fig. S13). Next, d that G-to-A contest in strand-specific samples were sequencing or mapping errors, we estimated that the apocryphal assay amount (FDR) was 3.1% (89,490/2,866,471). For non-strand-specific samples (assuming all G-to-C contest were sequencing or mapping errors), the FDR was 0.83% (72,500/8,717,781).
Collected RNA samples from macrophages and cream beef are a biological replicates (foam beef are acquired from macrophages by incubating them with acetylated LDL for 48 h). Therefore, we adjourned the reproducibility of RNA alteration in 235 macrophage—foam corpuscle pairs. We aboriginal adjourned the allotment of alteration sites detected in both samples in anniversary pair; the average beyond all pairs was 24%. It may accordingly be believable that abounding RNA alteration sites are not carefully reproducible alike in samples that are aing to biological replicates. This may reflect the academic attributes of RNA alteration or airheadedness in sequencing depth. We additionally bent whether the alteration ratios were abiding for the ∼24% of sites begin in both samples of anniversary pair. Beyond anniversary of the 235 macrophage-foam corpuscle pairs, the average Spearman alternation was 0.83 (Fig. S14). Thus, admitting accepted abstruse and biological confounders, the reproducibility was about aerial for sites that can be detected in both samples.
Gene announcement was afflicted as RPKM (Mortazavi et al., 2008) from reads counted with HTSeq (Anders, Pyl & Huber, 2014).
Association-testing was conducted with the beeline archetypal in MatrixEQTL (Shabalin, 2012) v.2.1.1. Analytic ambit were aboriginal rank-normal adapted with the action rntransform in the R amalgamation GenABEL (Aulchenko et al., 2007) with ties burst randomly. Two biological covariates (age and ) and two abstruse covariates (sequencing accumulation and laboratory) were included in the statistical model. Abandoned sites with non-zero A-to-G(I) alteration ratios in added than 50 samples per tissue were considered. Cogent associations were accurate as those acceptable the afterward criteria: (i) adapted P < 0.05 (10,000 permutations were accomplished for anniversary analytic parameter-tissue combination); (ii) R-sq > 0.4; and (iii) no alternation amid gene announcement (of the overlapping gene) and the activated analytic constant (nominal P > 0.05).
Genotypic abstracts were candy as declared (Franzén et al., 2016); biallelic markers (MAF > 0.05) were adapted to allele dosages (0, 1, and 2). edQTLs were generated abandoned for anniversary tissue. Abandoned A-to-G(I) sites begin (i.e., editing arrangement > 0) in added than 40 samples were included in the assay (sites on chromosomes were excluded). Site-sample combinations with beneath than <5 reads acknowledging alteration were removed. Alteration ratios were again rank-normal adapted as described, and the absent antecedent of no affiliation amid allele dosages and alteration ratios was activated with a beeline corruption archetypal in MatrixEQTL (Shabalin, 2012). For anniversary hypothesis, we appropriate at atomic 20 capacity in at atomic 2 genotype-allele groups. Thus, the minimum cardinal of individuals for any assay was 40. All accessible genotype-editing armpit combinations were activated behindhand of the complete abiogenetic distance. We adapted for the afterward covariates: age, , laboratory, batch, and citizenry stratification (i.e., cryptic relatedness of abstraction subjects; represented as four abiogenetic multi-dimensional ascent components). The FDR was controlled application a about-face action (Franzén et al., 2016): the RNA alteration cast was accolade 1,000 times, i.e., breaking the articulation amid sample identifiers and agnate measurements. For anniversary alteration site, we generated 1,000 about-face p-values, which were acclimated to acclimatize the complete p-values. An adapted p-value <0.20 was advised significant.
Normalized gene announcement abstracts from (Franzén et al., 2016) were acclimated in a beeline corruption model. P-values were adapted with the Benjamini–Hochberg action and adapted P < 0.05 was advised significant. For anniversary alteration site, all overlapping genes were tested.
The NHGRI-EBI GWAS archive (Welter et al., 2014) (r2018-01-01) and GWASdb (Li et al., 2016) v.2 were downloaded and alloyed into one database, befitting abandoned SNPs with P < 1e − 08. GWAS SNPs that were additionally edSNPs were adored in a new account that was LD-pruned with PLINK (–indep-pairwise 400 kb 1 0.6) (Purcell et al., 2007).
To characterize the animal RNA “editome”, we analyzed RNA-seq abstracts from the STARNET (Franzén et al., 2016) study, in which samples were acquired from up to 9 tissues (atheroscl aortic wall, n = 538; non-atheroscl arterial bank (internal mammary artery), n = 552; liver, n = 545; ashen muscle, n = 533; belly belly fat, n = 533; subcutaneous fat, n = 532; accomplished blood, n = 559; macrophages, n = 256; and cream cells, n = 235). In addition, 18 coronary avenue samples were included. Sequencing was done by application 50-bp single-end reads (these libraries were strand-specific; n = 2, 267) and 100-bp single-end reads (these libraries were non-strand-specific; n = 2,034). Differences in read-length and fiber specificity afflicted the acuteness to ascertain RNA editing, and best analyses were accordingly done abandoned on these two sets of samples. See Table S1 for a arbitrary of analyzed samples. We activated a accurate computational activity that includes centralized and alien filters to analyze RNA alteration in a complete of 4,301 RNA-seq samples (Fig. 1A; Fig. S1). The cardinal of samples per tissue ranged from 235 in cream beef to 559 in accomplished blood. For anniversary accepted alteration site, we afflicted the RNA alteration ratio, accurate as the calculation of edited bases disconnected by the complete cardinal of bases accoutrement the site. The RNA alteration arrangement takes ethics aural the semi-closed breach (0,1].
Most of the articular contest were A-to-G mismatches (Figs. 1B and 1C; Table 1; Tables S2 and S3), constant with A-to-I editing; afterward we accredit to these contest as A-to-G(I) alteration (including the about-face accompaniment back the fiber advice was not preserved). We articular 1,484,357 and 450,002 A-to-G(I) contest in non-strand-specific and strand-specific libraries, respectively; the cardinal of non-redundant A-to-G(I) alteration contest in non-strand-specific and strand-specific libraries was 1,688,815. Added A-to-G(I) contest were detected in non-strand-specific libraries, attributable to added sequencing and best apprehend length. Alarmist had the accomplished cardinal of A-to-G(I) events, possibly absorption college transcriptional complexity. In total, 53.9% (910,943/1,688,815) of articular A-to-G(I) contest had ahead been appear in REDIportal (Picardi et al., 2017) or DARNED (Kiran & Baranov, 2010) (Fig. S2). Aortic bank had the accomplished cardinal of atypical A-to-G(I) sites (n = 117, 493). A-to-G(I) alteration was detected in transcripts from 25,951 genes, of which 62.1% (16,131/25,951) were protein-coding. We intersected RNA alteration contest with genome annotations (Fig. S3), assuming that 56.0% of A-to-G(I) contest were in introns, 18.3% in intergenic regions, and 9.4% in 3′ UTRs; 67.7% of the A-to-G(I) alteration sites were tissue-specific back comparing exact chromosome-positions after because differences in gene announcement (Fig. S4). To exclude bent from differences in gene announcement we again the assay and abandoned advised genes actuality robustly bidding in 7 tissues (defined as average reads per kilobase of archetype per actor mapped reads [RPKM] >10 beyond all samples; 2,639 genes), the aftereffect showed that best contest were tissue-specific (Fig. S4).
Summary of abstracts and RNA alteration events.
In strand-specific samples, the added best accepted change was noncanonical T-to-C alteration (16.2%, 116,318/714,372). Interestingly, in strand-specific libraries the cardinal of A-to-G(I) contest activated with the cardinal of T-to-C contest (Spearman’s ρ = 0.67, P < 2.2e−16). T-to-C contest accept been appear in studies utilizing high-throughput sequencing abstracts but it is alien whether T-to-C contest are accurate or artifacts (Bahn et al., 2012).
The accord amid sequencing abyss and cardinal of alteration contest was about beeline (Fig. 1D and Fig. S5; alarmist samples: Spearman’s ρ = 0.86, P < 2.2e−16), suggesting that apprehension of RNA alteration per sample was not saturated or that the mechanisms mediating RNA alteration are nonspecific. If RNA alteration is nonspecific, it can be afflicted that added sequencing does not bathe detection. Assay of the accumulative cardinal of altered A-to-G(I) sites as a action of added samples did not acknowledge a bright addiction against assimilation (Fig. S6A). It is additionally accessible that assimilation cannot be detected because best alteration takes abode in introns, which are abundant beneath captured with RNA-seq. However, assay of the cardinal of genes in which RNA alteration occurred did acknowledge a trend against assimilation (Fig. S6B).
In the present adaptation of the animal genome accumulation (GRCh38) there are 1,186,920 Alus accoutrement 10.2% (315,412,481 bp/3,088,269,832 bp). Alu was the sole aspect decidedly accomplished in alteration contest (Fig. 1E; Figs. S7–S9). Overall, 70.3% (1,187,358/1,688,815) of all A-to-G(I) contest were in Alus. Of the Alus in the animal genome, 20.3% (241,226/1,186,920) had at atomic one A-to-G(I) alteration event. Admitting accoutrement 20.7% (641,953,033 bp/3,088,269,832 bp) of the genome (Lander et al., 2001), LINE elements independent abandoned 4.0% (67,810/1,688,815) of the A-to-G(I) events. The beggarly alteration arrangement per sample was hardly lower in non-Alu A-to-G(I) compared to alteration sites in Alus (meannon−Alu = 0.54, meanAlu = 0.57, P = 3.5e−15), acceptable absorption the able alternative of ADAR for double-stranded folds. Back Alu elements were aggregate by subfamilies (Y, J, and S) according to their accustomed phylogeny (Bennett et al., 2008), it showed that 42.5% (718,653/1,688,815) of A-to-G(I) alteration contest were amid aural the AluS subfamily, followed by AluJ (23.2%) and AluY (4.5%), see Fig. 1F. The beggarly alteration arrangement per sample was accomplished in AluY (meanAluS = 0.56, meanAluJ = 0.56, meanAluY = 0.64, P < 2.2e−16; Fig. 1G). Beggarly alteration levels were additionally decidedly college aural nongenic Alus compared to genic Alus (meangenicAlus = 0.56, meannongenicAlus = 0.66, P < 2.2e−16), conceivably because antibacterial alternative bargain alteration levels in mRNAs.
ADAR1 and ADAR2 activate A-to-I alteration (Macbeth et al., 2005; Nishikura, 2016). ADAR3 is catalytically abeyant and may accept authoritative backdrop (Chen et al., 2000). The announcement of ADAR1, ADAR2, and ADAR3 was compared beyond the tissues/cell types (Fig. 2; Fig. S10). ADAR1 was analogously bidding in all tissues (median = 31 RPKM, average complete aberration [MAD] = 14); the everyman levels empiric were in ashen beef (median = 5 RPKM, MAD =1 ), see Fig. 2A. The closing was additionally empiric in GTEx (Melé et al., 2015). Announcement of ADAR1 activated with A-to-G(I) alteration contest in every tissue except cream beef (q-value < 0.05), added acceptance the actuality of alleged RNA alteration events. Accomplished claret showed the arch alternation amid A-to-G(I) alteration contest and ADAR1 announcement (strand-specific samples, Spearman’s ρ = 0.85, P < 2.2e−16; Fig. S11). Although -specific differences in ADAR1 announcement accept been appear in bump samples (Paz-Yaacov et al., 2015), we begin abandoned bashful -specific differences in cream beef (P = 0.015), alarmist (P = 0.049), and subcutaneous fat (P = 0.017; Fig. S12).
ADAR2 announcement was low in all tissues (Fig. 2B; average = 3 RPKM, MAD = 2) except the three vascular tissues (atheroscl aortic wall, centralized mammary artery, and coronary artery; average = 23 RPKM, MAD = 14); announcement was accomplished in centralized mammary avenue (median = 42 RPKM, MAD = 12). ADAR2 announcement activated with the cardinal of A-to-G(I) contest abandoned in atheroscl aortic bank (Spearman’s ρ = 0.18, P = 2.6e−05) and was stronger in females (females: ρ = 0.19, P = 0.012; males: ρ = 0.17, P = 5.2e−04). However, there were no -specific differences in alteration in any tissues (P > 0.05). ADAR3 was about beneath the apprehension akin in all tissues (median = 0.01 RPKM, MAD = 0.02).
RNA alteration provides a apparatus for beef to accomplish added protein assortment (Nishikura, 2010). However, atypical protein recoding events—those that account amino acerbic changes—are rare. We systematically searched for A-to-G(I) alteration contest causing recoding. We begin that 3.9% (67,429/1,688,815) of A-to-G(I) contest were aural accepted protein-coding exons (variants arising from antisense archetype were excluded), and abandoned 3.0% (50,883/1,688,815) were non-synonymous substitutions. The closing appeared in a complete of 9,739 protein-coding genes. The average cardinal of non-synonymous substitutions per sample was 18 (MAD = 19).
Editing ratios had a long-tailed skewed administration (median = 0.14), suggesting that these variants are present in a baby cardinal of transcripts. Best of the non-synonymous sites (90.8%, 46,245/50,883) were begin in distinct samples. Thus, although variants are accepted on a all-around scale, abounding reflect accomplishments noise.
To focus on acceptable anatomic sites, we looked for conserved non-synonymous substitutions, that were present in >20 tissue samples and had a average alteration arrangement >0.1 in any tissue. Application these criteria, we begin 65 conserved alteration sites in 44 genes (Table S4). Six sites were predicted to be deleterious according to PROVEAN (Choi et al., 2012) and SIFT (Ng & Henikoff, 2001) (chr4:57,110,146, chr6:44,152,612, chr9:33,271,197, chr16:5,044,722, chr16:57,683,958 and chr17:1,534,142). As expected, conserved alteration sites had college alteration ratios (medianconserved = 0.30, mediannotconserved = 0.05, P < 2.2e−16, Mann–Whitney U test). Moreover, 80% (52/65) of these sites had been appear in REDIportal (Picardi et al., 2017), and 35% (23/65) had been appear in the abstract (Table S4). The classical archetype of recoding in GRIA2 (glutamate ionotropic receptor AMPA blazon subunit 2) was begin at the accepted armpit (chr4:157,336,723; p.Q607R) (Wright & Vissel, 2012) in aortic bank and centralized mammary artery. The average alteration arrangement in anniversary tissue was 1, advertence that all transcripts agitated the adapted base.
Eleven recoding sites were atypical (Table 2). Seven had low alteration ratios (<0.5; average = 0.24), which in allotment may explain why they were not detected previously. This award highlights the ability of ample RNA-seq datasets such as STARNET.
Novel A-to-G(I) mRNA-recoding sites.
Two recoding sites (one ahead appear Zhang et al., 2014a and one novel) resided in IGFBP7 (insulin-like advance factor-binding protein 7). The aboriginal site, chr4:57,110,062 changes a codon encoding lysine to arginine (amino acerbic 97); it was begin specific to the centralized mammary avenue and had been appear in academician (Zhang et al., 2014a). The second, chr4:57,110,146, changes a codon encoding glutamic acerbic to glycine (amino acerbic 69); it was begin in both atheroscl aortic bank and the centralized mammary artery. Both recoding sites were in the IGF-binding area of IGFBP7, possibly highlighting a atypical authoritative mechanism.
Two recoding sites (chr2:219,483,602 in SPEG and chr3:179,375,226 in MFN1) were ahead appear abandoned in abrasion (Danecek et al., 2012), suggesting these mRNA-recoding sites are of age-old agent back they were present in the accepted antecedent of actual animal and abrasion lineages (diverged ∼65 to 110 actor years ago (Emes et al., 2003)).
Next, we advised A-to-I recoding contest consistent in the accident of stop codons (the opposite, the accepting of stop codons, is not biologically accessible by A-to-I editing). Application the aforementioned belief declared above, we begin one recoding site, at chr10:101,017,585 in PDZD7 (PDZ area absolute 7). It was specific to belly belly fat and modifies the stop codon UAG to UGG (encodes tryptophan), extending PDZD7 by 18 amino acids (WSQIPGLKLSTRLSLPKC). This recoding armpit was afresh appear in animal academician tissue (Hwang et al., 2016). To our ability this is the aboriginal and conceivably abandoned recoding armpit in bodies that causes protein extension. We arrested if the change was associated with abstinent ancestry (e.g., LDL-C) and we did not acquisition any association.
In advancing the sequencing libraries, we acclimated the Ribo-Zero agreement to annihilate ribosomal RNA, which enabled us to investigate baby non-coding RNAs in 996 RNA-seq samples from atheroscl aortic bank and centralized mammary artery. We articular A-to-G(I) alteration sites in 102 altered microRNAs (miRNAs; annotations amount the absolute predicted stem-loop region) and 73 baby nucleolar RNAs (snoRNAs). Stringent alteration belief (recurrence in > 50 samples) articular 18 alteration sites in 10 miRNAs (mir-24-2, mir-27a, mir-27b, mir-605, mir-641, mir-1254, mir-1285-1, mir-1304, mir-3126, and mir-3138; Table S5) and 2 snoRNAs (U88 and SNORD17). RNA alteration sites in mir-24-2, mir-605, mir-3126, and U88 had not ahead been appear in REDIportal (Picardi et al., 2017) or DARNED (Kiran & Baranov, 2010). Six alteration sites occurred in complete miRNAs: three in mir-605-3p and one anniversary in mir-3138, mir-605-5p, and mir-24-2-3p. Two alteration sites were associated with college HDL cholesterol levels: chr9:95,085,457, which was amid alfresco the complete miRNA (pri-mir-27b; P = 2.2e−05; FDR = 8.5%) and chr10:51,299,636 (mir-605-3p; P = 1.6e−06; FDR = 0.65%).
Next, we looked for associations amid 18,458 RNA alteration sites and 208 analytic ambit (Franzén et al., 2016). Thirty-nine associations were begin cogent (FDR < 5%; 10,000 permutations) and complex 25 genes in bristles tissues (Table S6). 52% (13/25) of these were amid in 3′ UTRs, implying they could affect archetype regulation. Of the actual sites, eight were in introns, two were in accepted authoritative elements, one was exonic, and three were intergenic. A subset of all cogent associations is listed in Table 3.
A-to-G(I) RNA alteration sites associated with analytic parameters.
Although none of the 25 genes had been anon associated with coronary avenue disease, 22 of 25 sites were associated with claret lipoprotein levels. Two of the afflicted genes may accept roles in lipid metaism: LRP11 (low body lipoprotein receptor-related protein 11) and PLIN5 (lipid accumulator atom protein 5). In subcutaneous fat, the LRP11 alteration armpit (chr6:149,822,432), amid in the best 3′ intron of the best isoform, was associated with claret low body lipoprotein (LDL) levels. RNA alteration of two genes accepted for their roles in congenital allowed response—C3 (complement basic 3) and C1RL (complement C1r subcomponent like)—occurred in alarmist and were both associated with claret HDL levels.
To bare accessible abiogenetic adjustment of RNA alteration (Kurmangaliyev, Ali & Nuzhdin, 2015), we looked for RNA alteration quantitative affection loci (edQTLs; Fig. 3A). Application abstracts from the 1000 Genome Project (Durbin et al., 2010), allegation resulted in 6,246,842 accepted variants with accessory allele abundance >5%. Next, we articular 17,718 edQTLs at FDR <20% (i.e., associations amid allele dosages and RNA alteration ratios; Fig. 3B) by assuming ∼2.6 billion antecedent tests (comprising 11,280 altered alteration sites). We advised whether articular edQTLs were additionally announcement QTLs (eQTLs). 19.5% (3,465/17,718) of RNA alteration sites in edQTLs were eQTLs with account to the overlapping gene. Beyond all tissues, we begin 890 basis edQTLs—the best cogent affiliation for anniversary RNA alteration armpit (Dataset S2). A complete of 77% (690/890) of the basis edQTLs were auto (the authoritative SNP and the alteration armpit are amid on altered chromosomes).
Most of the alteration sites with edQTLs were accomplished in Alu elements (87%, 783/890); the Alu-subtype administration was the aforementioned as apparent in Fig. 1F. A complete of 95% (853/890) of the edQTLs accept ahead appear alteration sites (Kiran & Baranov, 2010; Picardi et al., 2017); 47% (425/890) were in 3′ UTRs, 25% (230/890) were in introns, and 12% (113/890) were in intergenic regions. RNA alteration sites of edQTLs overlapped 417 genes (Dataset S2).
To appraise a accessible mechanistic role of edSNPs in disease, we intersected edSNPs with advance SNPs from GWAS. 90 edSNPs coincided with GWAS SNPs, encompassing 59 traits. LD-pruning burst the 90 SNPs to 30 non-linked SNPs. rs2573346 is associated with sarcoidosis (Hofmann et al., 2008) and had an edQTL in the 3′ UTR of FAM213A in belly fat (Fig. 3C). rs2028299 is associated with blazon 2 diabetes (Kooner et al., 2011) and had two edQTLs in belly fat (both amid in the 3′ UTR of ARPIN). rs2028299 is associated with announcement of ARPIN in fat tissue (P < 1e−10) (Kooner et al., 2011). A abrogating alternation was begin amid ARPIN announcement in belly fat and claret levels of VLDL (r = − 0.2; P < 1e−06). rs78579285 has been associated with collective advancement (Beighton score) (Pickrell et al., 2016) and we detected an edQTL in belly fat aural the intron of PIEZO1 (encodes a mechanosensitive ion-channel component). rs7546668 is associated with branch action (glomerular filtration rate) (Gorski et al., 2017) and it formed an edQTL with an alteration armpit detected in alarmist (Fig. 3D). The alteration armpit overlapped DNAJC16 (encodes DnaJ Heat Shock Protein Family (Hsp40) Member C16) and AGMAT (encodes Agmatinase). rs4073054 is associated with HDL (Chasman et al., 2009) and had an edQTL with an RNA alteration armpit in the 3′ UTR of F11R in liver. Announcement of F11R was associated with claret levels of VLDL (r = − 0.2, P < 1e−08) and HDL (r = − 0.2, P < 1e−07). rs1127311 is a pleiotropic locus and it is associated with C-reactive protein and triglyceride levels (Ligthart, Vaez & Hsu, 2016). Interestingly, rs1127311 is anchored in the 3′ UTR of ADAR, and it forms an edQTL with an alteration armpit in the added to the aftermost intron of FGG. rs3947, anchored in the 3′ UTR of the protease-encoding gene CTSB, is associated with claret protein levels (Suhre et al., 2017). rs3947 forms an edQTL with an alteration armpit amid in the 3′ UTR of CTSB. rs3947 is in able LD with rs2740594 (R-sq = 0.86), which is associated with Parkinson’s ache (Chang et al., 2017). rs4957048 is associated with assorted sclerosis/ulcerative colitis (De Lange et al., 2017), and it was associated with an alteration armpit amid after of SLC22A25 (Fig. 3E). rs6756513 is associated with platelet calculation (Astle et al., 2016) and it had an edQTL in an intron of C3P1. rs10847434 is associated with coronary avenue ache (Lee et al., 2013) and had an edQTL with an alteration armpit in the best 3′ exon of APOC1P1 in liver. APOC1P1 encodes a continued non-coding RNA after any accepted action or role. However, its locus (Jeemon et al., 2011) has been abundantly affiliated to coronary avenue ache (neighboring genes are APOE, APOC1, and TOMM40). In liver, there was a abrogating alternation amid announcement of APOC1P1 and APOE (r = − 0.3; P = 7e−13) as able-bodied as APOC1P1 and APOC1 (r = − 0.22; P = 1e−07). The abrogating alternation may announce a authoritative action of APOC1P1. rs1883350 is associated with blubbery alarmist ache (Feitosa et al., 2013) and we articular one alarmist edQTL hardly after of PNPLA3 (Patatin-like phospholipase domain-containing protein 3). PNPLA3 is associated with blubbery alarmist ache (Speliotes et al., 2010) and encodes a protein accepted to be complex in alarmist fat storage. Finally, rs4739066 is associated with myocardial infarction (Wakil et al., 2016) and we begin this SNP to accept two edQTLs with alteration sites in the 3′ UTR of the α-tocopherol alteration protein gene (TTPA). The alteration sites are amid 64 bp afar and are arresting back they accept adverse aftereffect sizes. TTPA is associated with the severity of atheroscl lesions in the adjacent aorta (Terasawa et al., 2000).
We analyzed RNA alteration by revisiting RNA-seq abstracts from the STARNET abstraction (Franzén et al., 2016). The abstraction aimed to characterize the RNA alteration mural of animal tissues and articulation RNA alteration contest with phenotypic traits. We analyzed several thousand RNA-seq samples application a atypical apprehension activity for RNA editing. Our assay covered 855 subjects, seven animal tissues and two corpuscle types. We articular ∼1.6 actor RNA alteration events, apery a able A-to-I alteration signal. The articular contest constituted atypical alteration sites and ahead appear sites (Picardi et al., 2017). Abounding atypical contest originated from intergenic regions and non-coding RNAs, advertence that abounding transcripts of the animal genome are still uncharacterized. The A-to-I alteration levels ranged from about ephemeral to 100%, suggesting that anonymous factors adapt the backbone of alteration at abandoned sites. As expected, the added blazon of approved editing, C-to-U, was abundant beneath accepted (∼3.5% of articular events). Similar to antecedent studies (Park et al., 2012; Ramaswami et al., 2012; Ramaswami et al., 2013) we articular a ample cardinal of noncanonical edits, which may be accurate alteration events, ultra-rare abiogenetic variants or artifacts from sequencing and abstracts processing. Noncanonical U-to-C was the added best accepted accident (Fig. 1B) as apparent by assay of strand-specific data, acknowledging a antecedent address (Bahn et al., 2012). This award may point to a atypical alteration apparatus in humans. The actuality of accepted U-to-C alteration charcoal uncertain, and informatics abandoned is absurd to achieve this question.
We additionally begin RNA alteration to be acerb accomplished in Alu elements, as ahead appear (Athanasiadis, Rich & Maas, 2004; Kim et al., 2004; Ramaswami et al., 2012). Aural and alfresco of Alu elements the arrangement of alteration was stochastic, absorption the abridgement of specificity of the RNA alteration machinery. The accord amid the cardinal of contest and sequencing abyss additionally appropriate that alteration is unspecific, back there was no addiction to saturation. Best of the contest were tissue-specific, acceptable absorption differences in gene announcement amid tissues. Anatomic RNA alteration sites accept been appear in several studies, e.g., (Sommer et al., 1991). We took advantage of our multi-sample accomplice to analyze anatomic sites. Remarkably, beyond 1.6 actor RNA alteration sites, we apparent abandoned 11 new sites that adapt the amino acerbic sequence. Such recoding sites were accepted from their accident in assorted subjects. Arrangement assay appear that best of them were neutral, advertence the role of antibacterial alternative in removing adverse sites. Notably, GRIA2 mRNAs were edited in aortic bank and centralized mammary artery. GRIA2 alteration converts a codon for glutamine to arginine, which renders ion-channels closed to calcium ions. GRIA2 is ubiquitously bidding in academician tissues as able-bodied as in the aortic wall, fallopian tubes, pituitary gland, and uterus (Melé et al., 2015). The role of these receptors alfresco the axial afraid arrangement is arresting yet unknown.
We begin that 39 RNA alteration sites were associated with traits, adopting the achievability of phenotypic consequences. In best cases alteration was begin in the 3′ UTR or an intron. The above is a ambition for archetype regulation, and may advance disruption of bounden sites of miRNAs or RNA-binding proteins. Several sites were begin in introns, after accessible affirmation for abashed authoritative elements. While we are not able to aphorism out that some of these associations may accept arisen due to abysmal abashing factors, we accept added analysis is warranted.
Several A-to-I alteration contest were in important miRNA families, possibly as a apparatus to adapt miRNA action through modification of bounden specificity. We begin an affiliation amid claret HDL levels and alteration of pri-mir-27b/mir-605. mir-27b has been affiliated to progression of atherosclerosis (Li et al., 2011a; Zhang et al., 2014b), and mir-605 is active in achievement (Yuan et al., 2016) and hypertension (Li et al., 2011b). These abstracts highlight the charge to added accommodate A-to-I alteration abstracts with account to the abbreviate non-coding transcriptome. Added specialized sequencing assays will be bare to abduction the abounding admeasurement of A-to-I alteration in miRNAs and added baby non-coding RNAs.
Finally, to appraise the abiogenetic adjustment of RNA editing, we generated and advised edQTLs. edQTLs articulation RNA alteration to abiogenetic loci and accept been declared in Drosophila melanogaster (Kurmangaliyev, Ali & Nuzhdin, 2015; Ramaswami et al., 2015) and bodies (Park et al., 2017). Intersecting authoritative SNPs with accepted disease-associated variants appear accepted causal links for several GWAS SNPs. We begin 30 disease-associated authoritative SNPs, several of which accept been affiliated to cardiometaic traits. For example, rs2028299, ahead associated with blazon 2 diabetes, was an edQTL in the archetype of ARPIN, suggesting dysregulation of RNA alteration as the account of added ache risk.
Our abstracts announce that RNA alteration contest are acutely common, but rarely of biological significance. Nevertheless, in assertive instances such as amid distinct nucleotide polymorphisms from genome-wide affiliation studies, and for specific genes in disease-relevant tissues, RNA alteration appears acceptable to comedy an important and potentially causal role in ache pathobiology. These allegation highlight a atypical apparatus of abiogenetic addition to cardiometaic disease, and advance that added analysis of this action is warranted.
Figures S1–S14, Tables S1–S5.
Supplementary material, RNA alteration in metaic and vascular animal tissues The table is tab separated. The columns accord to: (1) three letter tissue abbreviation; (2) library blazon (N = non-strand- specific, Y = strand-specific); (3) chromosome; (4) position; (5) DNA base; (6) RNA base; and (7) cardinal of samples in this tissue-library aggregate area this accident was detected. Coordinates are in GRCh38.
Supplementary material, RNA alteration in metaic and vascular animal tissues The table is tab separated. The columns accord to: (1) three letter tissue abbreviation; (2) authoritative SNP; (3) the encoded (effect) allele of the authoritative SNP; (4) genomic alike of the RNA alteration armpit (GRCh38); (5) atomic alternation blazon (cis = the authoritative SNP and the alteration armpit are on aforementioned chromosome, auto = the authoritative SNP and the alteration armpit are on altered chromosomes); (6) beta coefficient; (7) p-value of the affiliation amid RNA alteration and the authoritative SNP; (8) adapted (permutation-based) p-value; (9) the gene overlapping the RNA alteration site; (10) aforementioned as previous, but giving the gene attribute instead; (11) gene biotype according to GENCODE; (12) the echo type, if any, overlapping the RNA alteration site; (13) the trait, if this authoritative SNP is a appear GWAS advance SNP; (14) gene region; (15) if the gene has ahead appear as complex in cardiometaic traits; (16) if the RNA alteration armpit has been appear in DARNED; (17) if the RNA alteration armpit has been appear in REDIportal; and (18) if the overlapping gene has an eQTL. Abbreviations: (Y)es, (N)o. This table is accustomed as an alien file.
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