Scholarly article on topic 'The contribution of Alu exons to the human proteome'

The contribution of Alu exons to the human proteome Academic research paper on "Biological sciences"

CC BY
0
0
Share paper
Academic journal
Genome Biology
OECD Field of science
Keywords
{""}

Academic research paper on topic "The contribution of Alu exons to the human proteome"

Lin et al. Genome Biology (2016) 17:15 DOI 10.1186/s13059-016-0876-5

Genome Biology

RESEARCH

Open Access

The contribution of Alu exons to the human proteome

CrossMark

Lan Lin1*1, Peng Jiang21, Juw Won Park13,41, Jinkai Wang1+, Zhi-xiang Lu1, Maggie P. Y. Lam5, Peipei Ping5,6 and Yi Xing1*

Abstract

Background: A/u elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some A/u exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of A/u exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as A/u elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins.

Results: We adopt a proteotranscriptomics approach to systematically assess the contribution of A/u exons to the human proteome. Using RNA sequencing, ribosome profiling, and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of A/u exons and the presence of A/u exon derived peptides in human proteins. These A/u exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances between humans and closely related primates. In the case of the RNA editing enzyme ADARB1, which contains an A /u exon peptide in its catalytic domain, RNA sequencing analyses of A-to-I editing demonstrate that both the A /u exon skipping and inclusion isoforms encode active enzymes. The A/u exon derived peptide may fine tune the overall editing activity and, in limited cases, the site selectivity of ADARB1 protein products.

Conclusions: Our data indicate that A /u elements have contributed to the acquisition of novel protein sequences during primate and human evolution.

Keywords: A /u, Transposable element, Exon, Alternative splicing, RNA editing, RNA-seq, Ribo-seq, Transcriptome, Proteome, Evolution, Primate

Background

Transposable elements have played important roles in the evolution of gene regulation and function [1]. The primate-specific Alu retrotransposon is the most abundant class of transposable elements in the human genome, with over 1 million copies occupying over 10 % of the human genomic DNA [2]. Although Alu elements were historically considered as 'junk DNA, extensive research in the past two decades has revealed significant contributions of Alu to the evolution of the human genome and gene regulatory networks [1-3].

* Correspondence: linlan@ucla.edu; yxing@ucla.edu +Equalcontributors

department of Microbiology, Immunology & Molecular Genetics, University

of California, Los Angeles, Los Angeles, CA 90095, USA

Fulllist of author information is available at the end of the article

Alu is a major contributor to de novo origination of lineage-specific exons in primates [4]. Because the Alu element contains multiple sites that resemble the consensus donor and acceptor splice site signals, the insertion of Alu elements into intronic regions of existing genes produces preferable substrates for subsequent mutations that create and establish new exons [4, 5]. The exonization of Alu elements is frequent during primate and human evolution - thousands of human genes contain Alu-derived exon segments in their mRNA transcripts [6, 7]. Although the majority of Alu exons have low splicing activities and probably represent non-functional evolutionary intermediates, a subset of Alu exons have acquired ubiquitously strong or tissue-specific splicing activities in human tissues, as demonstrated by recent tran-scriptome studies using splicing-sensitive exon microarray

O© 2016 Lin et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 BnlVled Central International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and

reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

and deep RNA sequencing [8, 9]. These 'established' A/k exons are preferentially located in the mRNA 5' untranslated regions (5'-UTR) and may play a role in regulating mRNA translational efficiency [6, 8, 9]. A/k exons inserted into coding regions of protein-coding genes frequently contain premature termination codons (PTCs) and may provide a mechanism for fine-tuning steady-state mRNA levels by inducing mRNA nonsensemediated decay (NMD) [10]. Together, these data have established the regulatory roles of A/k exons in multiple aspects of RNA metabolism including translation and degradation.

Despite the prevalence of A/k exons in the human transcriptome, the contribution of A/k exons to the human proteome remains unclear and controversial [11-15]. In the 1990s and early 2000s, Makalowski and others carried out large-scale discoveries of A/k exons in human genes using cDNA sequences and expressed sequence tags (ESTs) [11, 12, 16]. They identified numerous instances of 'in-frame' A/k exons in the coding region of human mRNAs that are predicted to add A/k-derived peptides to the protein products. However, the presence of an in-frame A/k exon in the mRNA coding sequence does not guarantee its translation and incorporation into stable protein products. Additionally, since most A/k exons have low splicing activities [6, 16], even a 'translatable' coding-region A/k exon may only be incorporated into a small fraction of the gene's transcript products and consequently become largely undetectable and negligible on the protein level. In fact, in these studies there was little experimental evidence to support the existence of A/u-derived peptides in vitro or in vivo. In 2006, Makalowski and colleagues revisited this question by searching for transposable elements derived peptides in non-redundant protein entries in the Protein Databank (PDB) [13]. Since all proteins in PDB have solved 3D structures, Makalowski and colleagues reasoned that PDB provides a high-confidence collection of stable, functional proteins. They did not identify any A/k derived peptides in PDB protein entries. On the basis of this result, Makalowski and colleagues concluded that exons derived from A/k or other young repetitive elements do not have adequate evolutionary time to be incorporated into stable protein products, and the role of A/k exons should be almost entirely regulatory [13]. Since then, this has become the prevailing view on the contribution of A/k exons to the human proteome [3, 14, 15, 17]. However, this PDB-based study also has major drawbacks. Most importantly, PDB has very limited coverage of alternatively spliced protein isoforms, and less than 10 protein isoforms had structures deposited in PDB by the time of this study [18]. When structural biologists select proteins for structural characterization, there is an inherent bias towards selecting evolutionarily

conserved protein isoforms and against protein isoforms with non-conserved (lineage-specific) exon segments such as A/k exons. Therefore, the presence of A/k exon peptides in the human proteome may be significantly underestimated in the PDB-based analysis. Indeed, in gene-specific studies, researchers have found evidence for the expression of A/k exon peptides in vitro or in vivo -two examples being the A/k exons in genes encoding the RNA editing enzyme ADARB1 [19] and DNA methyl-transferase DNMT1 [20]. Neither case was recapitulated in the PDB study [13]. In summary, despite substantial interest in this topic, the real contribution of A/k exons to the human proteome remains unclear, and past studies may have reached dramatically different conclusions due to inherent limitations of their data sources.

In this work, we adopted a proteotranscriptomics approach to systematically assess the contribution of A/k exons to the human proteome. Using RNA sequencing (RNA-seq), ribosome profiling (Ribo-seq), and mass spectrometry data of diverse human tissues and cell lines, we evaluated the evidence for the translational activities of A/k exons and the presence of A/k exon derived peptides in human proteins.

Results

RNA-seq discovery of putative coding Alu exons with high splicing activities

RNA-seq has become a powerful approach for quantitative analyses of exon splicing [21]. We previously used an RNA-seq dataset of human cerebellum to characterize the splicing profiles of A/k exons [9]. Among A/k exons with high splicing levels (>50 % exon inclusion) in the cerebellum according to this RNA-seq analysis, the vast majority (over 80 %) were located in the mRNA 5'-UTR, and only a handful were located within the protein-coding region [9]. In the present work, to comprehensively identify putative coding A/k exons and characterize their splicing activities, we used a much larger RNA-seq dataset with approximately 1.8 billion RNA-seq reads covering 19 human tissues, including 16 tissues from the Illumina Human Body Map 2.0 dataset and three tissues from different anatomical compartments of the human placenta (see Materials and Methods).

We implemented a computational pipeline to identify putative coding A/k exons with high splicing activities (Fig. 1a and Materials and Methods). Briefly, from Ensembl transcript annotations, we extracted 1,996 A/u-derived internal (spliced) exons. Of these, 911 A/k exons were located within the coding sequences (CDS). To remove A/k exons that would trigger transcript degradation via mRNA nonsense-mediated decay (NMD), we further identified 262 coding-region A/k exons that would not introduce premature termination codons (PTCs) within or downstream of the A/k exons when

1,996 Ensembl-annotated Alu exons

PRIDE peptide

911 Alu exons

No NMD

262 coding Alu exons

MaxJCalO . y>0.33/

MaxJC>10

|AV|aio% i

In PRIDE

..Archive

48 coding 27 coding 85 coding

Alu exons Alu exons Alu exons

MaxJCilO

v|/>0.33 (48),'

MaxJC£10

|&V|>10% (27)

NEK4 —£

_Alu exon_

Alu exon

ISSLKTLFRKEKPLFNWMETF......VSVLIDSAIGKTKKQ*

Alu exon

lUCIIPGSSQWIIESIHVaGQWIJ?

KMFffl™fyi]SICillLraNI)SEEFffi«]M[»N(]«ClfLP

Fig. 1 Identification and analysis of putative coding Alu exons in human genes. a The bioinformatics work flow to identify and characterize putative coding Alu exons using RNA-seq and proteomics data. b The Venn diagram illustrating the number of putative coding Alu exons with different types of RNA-seq or proteomic evidence. c The splicing patterns and deduced peptide sequences of putative coding Alu exons with supporting peptide sequences from the PRIDE database. The stop codon of each isoform is indicated by a STOP sign

included into the transcripts. Specifically, PTCs were defined as stop codons located more than 50 bp upstream of the last exon-exon junction of the mRNA [22]. These 262 non-PTC exons were considered as candidate protein-coding A/k exons that had the potential to add A/u-de-rived peptides to the protein products. Of note, 69 % (182/262) of these candidate protein-coding A/k exons were divisible by 3 in exon length while only 24 % (159/649) of the putative NMD-inducing A/k exons were divisible by 3 (Fisher's exact test P =2e-36). Next, we performed detailed RNA-seq analyses on these exons to identify those with moderate-to-high levels of splicing or differential splicing activities among human tissues. For each exon, we calculated its transcript inclusion level (denoted as percent-spliced-in, or Y [23]) in a given tissue using RNA-seq reads uniquely mapped to the upstream, downstream, and exon-skipping splice junctions (see Materials and Methods). To ensure accurate estimation of the transcript inclusion level, we required that at least one splice junction (upstream, downstream, or exon-skipping) had at least 10 reads. We identified 48 A/k exons with transcript inclusion levels of at least 33 % in one of the human tissues, indicating moderate-to-high levels of exon splicing. In parallel, we performed pairwise tissue comparisons using the MATS algorithm for differential splicing analysis [24] and identified 27 A/k exons with at least 10 % change in transcript inclusion levels (that is, |AY| >10 %) between at least one pair of tissues (false discovery rate

(FDR) <10 %), indicating differential splicing among human tissues. The vast majority of these differentially spliced A/k exons (23/27) were also among the 48 exons with at least 33 % transcript inclusion levels in at least one of the human tissues. In total, we obtained 52 A/k exons by combining these two exon lists (Fig. 1b and Additional file 1: Table S1). These results indicate that although A/k exons with high splicing levels are preferentially located within the 5'-UTR [6, 8, 9], there is a reasonably large number of putative protein-coding A/k exons with high splicing activities in human tissues.

Translational and proteomic evidence for protein-coding Alu exons

To systematically assess the proteomic evidence for A/k exon derived peptides in human proteins, we queried the 262 putative coding A/k exons in Ensembl transcripts (Fig. 1a) against the PRoteomics IDEntifications Database (PRIDE) [25]. PRIDE is a comprehensive repository for proteomics data, containing protein and peptide sequences as well as their supporting spectral evidence from mass spectrometry experiments. We searched PRIDE peptide sequences against the putative open reading frames (ORFs) of A/k exon inclusion transcripts as well as the ORFs of all other human transcripts. We excluded peptide sequences mapped to multiple locations in human ORFs. Then we defined a putative protein-coding A/k exon as having a peptide

match in PRIDE if there was a peptide sequence uniquely mapped to the translated peptide sequence from the exon body or the splice junctions spanning the A/k exon and its upstream or downstream flanking exon. Of the 262 putative coding A/k exons, 85 had peptide evidence in the PRIDE database (Fig. 1a and Additional file 2: Table S2). Of note, 69 of these 85 (81 %) A/k exons had peptide sequences crossing the upstream or downstream splice junctions (Additional file 2: Table S2). Because the flanking exons of most A/k exons are not derived from repetitive elements, these splice junction spanning peptide sequences provide stronger evidence that these putative coding A/k exons are translated into protein sequences. Among the 52 putative protein-coding A/k exons with RNA-seq evidence for high splicing activities in human tissues, 18 had peptide matches in PRIDE (Fig. 1b and Table 1). A few examples are shown in Fig. 1c. In NEK4 (ENSG00000114904) we found six peptide sequences in PRIDE that mapped to the upstream or downstream splice junction of the A/k exon. In ALG8 (ENSG00000159063), the A/k exon was predicted to encode a different C-terminal peptide of the protein -this A/k exon peptide was supported by a peptide sequence in PRIDE. Another example was MCM3 (ENSG00000112118). In this gene, A/k exon inclusion caused a frameshift in the downstream 3' terminal exon, which resulted in a distinct C-terminal peptide by using a different reading frame within the same terminal exon. We found peptide sequences in PRIDE that mapped to either the A/k exon or the downstream splice junction. In addition to the PRIDE analysis, we also manually searched the 52 putative protein-coding A/k exons with high splicing activities against a second mass spectrometry database PeptideAtlas [26]. Different from PRIDE, PeptideAtlas reprocessed the original protein mass spectrometry data using stringent FDR criteria [26]. Therefore, PeptideAtlas has a very low false positive rate at the expense of a higher false negative rate. Our manual search against PeptideAtlas identified the peptide evidence for A/k exons in SUGT1 (ENSG00000165416) and DNMT1 (ENSG00000130816), both were also supported by PRIDE (Table 1). Overall, among the 52 putative coding A/k exons with high splicing activities, 18 (35 %) had peptide evidence in either PRIDE alone or both PRIDE and PeptideAtlas. It should be noted that this percentage is expected to be an underestimate, since peptide identification from prote-omics experiments is biased towards highly expressed proteins [27].

To obtain an independent line of evidence for the translation of these putative coding A/k exons into protein products, we analyzed the footprint of ribosomes on A/k exons using ribosome profiling (Ribo-seq) data. Ribo-seq has recently been developed as a powerful

approach for high-throughput analyses of protein translation [28]. Here we jointly analyzed the Ribo-seq and RNA-seq data of HeLa cells [29]. Specifically, we mapped the Ribo-seq and RNA-seq reads to the upstream, downstream, and exon-skipping splice junctions of Alu exons, and computed each Alu exon's transcript inclusion levels in the Ribo-seq and RNA-seq data, respectively (Materials and Methods). To ensure reliable estimation of transcript inclusion levels, we restricted this analysis to Alu exons with at least 10 reads mapped to one of three splice junctions in both Ribo-seq and RNA-seq data. As shown in Fig. 2a, among the 76 putative coding Alu exons that met this criterion, 38 exons had non-zero transcript inclusion levels in the Ribo-seq data, indicating ribosome footprints translating through the Alu exons. Seventeen exons had transcript inclusion levels of at least 15 % in the Ribo-seq data. Of note, 15 Alu exons had higher transcript inclusion levels in the Ribo-seq data than in the RNA-seq data (Fig. 2a and Additional file 3: Table S3), suggesting that the Alu exon inclusion mRNA isoform was translated at a comparable or even higher rate as compared to the ancestral mRNA isoform lacking the Alu exon. The Ribo-seq and RNA-seq signals of four Alu exons were shown in Fig. 2b-e. These include Alu exons with PRIDE or PeptideAtlas evidence (DNMT1 (ENSG00000130816), BIRC5 (ENSG00000089685)), as well as those without (SRP9 (ENSG00000143742), METTL10 (ENSG00000203791)). Of note, in both SRP9 and METTL10, the Alu exon was the penultimate exon, and the stop codon of the Alu exon inclusion mRNA isoform was located either within the Alu exon (SRP9) or in the immediate downstream terminal exon (METTL10). In both cases the Ribo-seq signal diminished beyond the stop codon (Fig. 2d, e). We note that nine Alu exons with PRIDE peptide sequences had no Ribo-seq reads mapped to the exon inclusion splice junctions, including three exons with RNA-seq transcript inclusion levels of over 50 % (Additional file 3: Table S3). This may be attributed to cell-type-specific differences in protein translation between the HeLa cells and other tissues and cell types.

We found that putative protein-coding Alu exons had a lower percentage of exons derived from the AluY subfamily, which was the youngest subfamily of Alu elements in the human genome [30]. In total, 4.2 % (11/262) putative protein-coding Alu exons were AluY derived, compared to 7.0 % (121/1734) for other Alu exons. Moreover, protein-coding Alu exons with PRIDE evidence had the lowest percentage of AluY (2.4 %, 2/85). These differences were not statistically significant (Fisher's exact test, P = approximately 0.1), which may be attributed to small sample size. However, the trend was interesting and consistent with the notion that it required time for Alu exons to

Table 1 Putative coding Alu exons with significant splicing activities and supporting peptide evidence in proteomics databases O

Gene symbol Gene ID Exon coordinate (hg19) Gene description MaxJC >10 ^ >0.33 MaxJC >10 |A^| >10% In PRIDE In PeptideAtlas

1 SUGT1 ENSG00000165416 chr13:53235609-53235705 SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae) Yes Yes Yes Yes

2 DNMT1 ENSG00000130816 chr19:10290862-10290910 DNA (cytosine-5-)-methyltransferase 1 Yes Yes Yes Yes

3 C21orf7 ENSG00000156265 chr21:30463988-30464082 Chromosome 21 open reading frame 7 Yes No Yes No

4 ADARB1 ENSG00000197381 chr21:46604388-46604508 Adenosine deaminase, RNA-specific, B1 Yes Yes Yes No

5 ALG8 ENSG00000159063 chr11:77813919-77813994 Asparagine-linked glycosylation 8, alpha-1, 3-glucosyltransferase homolog (S. cerevisiae) Yes No Yes No

6 NEK4 ENSG00000114904 chr3:52783707-52783845 NIMA (never in mitosis gene a)-related kinase 4 Yes No Yes No

7 ZNF415 ENSG00000170954 chr19:53618462-53618560 Zinc finger protein 415 Yes Yes Yes No

8 TPRKB ENSG00000144034 chr2:73959710-73959827 TP53RK binding protein Yes No Yes No

9 C21orf7 ENSG00000156265 chr21:30463821-30463897 Chromosome 21 open reading frame 7 Yes No Yes No

10 C11orf80 ENSG00000173715 chr11:66523823-66523976 Chromosome 11 open reading frame 80 Yes No Yes No

11 ZNF573 ENSG00000189144 chr19:38249115-38249236 Zinc finger protein 573 No Yes Yes No

12 MCM3 ENSG00000112118 chr6:52130032-52130183 Minichromosome maintenance complex component 3 No Yes Yes No

13 SLC3A2 ENSG00000168003 chr11:62639048-62639141 Solute carrier family 3 (activators of dibasic and neutralamino acid transport), member 2 Yes No Yes No

14 EIF4E ENSG00000151247 chr4:99807604-99807697 Eukaryotic translation initiation factor 4E Yes Yes Yes No

15 KCNRG ENSG00000198553 chr13:50592958-50593056 Potassium channel regulator Yes No Yes No

16 FAM124B ENSG00000124019 chr2:225265097-225265222 Family with sequence similarity 124B Yes Yes Yes No

17 B3GALNT2 ENSG00000162885 chr1:235659495-235659618 Beta-1,3-N-acetylgalactosaminyltransferase 2 Yes No Yes No

18 ZNF195 ENSG00000005801 chr11:3382972-3383119 Zinc finger protein 195 Yes Yes Yes No

| 0.8 £

.E 0.6

5) „ , 3 0.4

i 0.2-1

l With PRIDE peptide »Without PRIDE peptide

• METTL10 -DNMT1

• /MCM3 •

0 0 0.2 0.4 0.6 0.8 1.0 Exon inclusion in RNA-seq

Fig. 2 Ribo-seq data (HeLa cells) provide evidence for the translationalactivities of putative coding Alu exons. a Comparison of Alu exon inclusion levels in Ribo-seq and RNA-seq data of HeLa cells. Each dot represents an Alu exon. Seventy-six putative coding Alu exons with at least 10 reads mapped to one of the three splice junctions in both Ribo-seq and RNA-seq data are shown in the plot. Exons with PRIDE peptide sequences are indicated in red. b-e The UCSC genome browser view of the Ribo-seq and RNA-seq data of four representative Alu exons. The upstream junction read count (UJC), downstream junction read count (DJC), and skipping junction read count (SJC) are also indicated. The stop codon of each mRNA isoform is indicated by a STOP sign

strengthen splicing signals and develop protein-coding capabilities.

Assessment of transcriptomic and proteomic evidence for protein-coding Alu exons

We performed a series of analyses to further assess the transcriptomic and proteomic evidence for protein-coding A/k exons. First, to validate the splicing of these exons, we randomly selected 20 protein-coding A/k exons, and used fluorescently labeled RT-PCR to verify their exon inclusion patterns and quantify their splicing levels in a diverse panel of 21 human tissues (Additional file 4: Table S4). Nineteen out of the 20 exons were validated to be spliced into the human transcriptome (Additional file 5: Figure S1). This high validation rate (19 out of 20) was consistent with our previous RT-PCR and sequencing confirmation of UTR A/k exons identified by RNA-seq [9], confirming that our RNA-seq identification of A/k exon splicing had a very high accuracy. Second, we further assessed the Ribo-seq signal of protein-coding A/k exons in HeLa cells, using putative NMD-inducing A/k exons in protein-coding genes as the control. Seventeen out of 76 protein-coding A/k exons with sufficient Ribo-seq coverage had transcript inclusion levels of at least 15 % in the Ribo-seq data, as compared to 24 out of 180 for putative NMD-inducing A/k exons. We observed an increase in Ribo-seq signals of protein-coding A/k exons (22 % vs. 13 %), although the statistical significance was marginal (P = 0.056, one-sided Fisher's exact test), probably due to the small sample size and possibly the effect of the pioneering round of translation in NMD transcripts [31]. These data suggest that Ribo-seq provides a discriminative feature of protein-coding A/k exons but cannot be used alone as their sole evidence.

As the most central and direct evidence for protein-coding A/k exons in this work came from the analysis of PRIDE peptide data, we used multiple negative controls to assess the reliability of our PRIDE search. First, we used mouse peptides as a negative control and searched mouse peptides in PRIDE and in our own COPaKB database of cardiac proteins [32] against human A/k exons. We did not find any mouse peptide hit of longer than four amino acids in either database, which was below the length cutoff we required for human PRIDE peptide hits (>6 amino acids). Second, we used putative NMD-inducing A/k exons in protein-coding genes as another negative control to assess the FDR of our PRIDE analysis using human peptide data. Specifically, we performed PRIDE search on all NMD-inducing A/k exons and identified PRIDE hits for 47 out of 649 exons (7.2 %). This percentage is significantly lower than that of the putative protein-coding A/k exons (32.4 %, 85 out of 262; P = 1.8e-20, Fisher's exact test). Even if we take a very conservative estimate that all of these 649 NMD-inducing exons represent true negatives and none of them can be protein-coding via mRNA isoforms with alternative reading frames or A-to-I editing of the STOP codon (a possible scenario supported by the literature; see [33]), we would estimate that 19 of the 262 putative protein-coding A/k exons would generate false positive PRIDE hits (that is, 262 x 7.2 %), yielding a low upper-bound estimate of FDR of 22 % (that is, 19 out of 85). In summary, using putative NMD-inducing A/k exons as our negative control, we demonstrate that the FDR of our PRIDE search is low, and that the vast majority of the 85 PRIDE hits reflect bona fide proteomic evidence for protein-coding A/k exons.

Human-specific increase in the splicing activity of a protein-coding Alu exon in SUGT1

We studied an A/k exon derived peptide in SUGT1, which was supported by multiple lines of evidence from

proteomics (PRIDE and PeptideAtlas) and Ribo-seq data (Fig. 3a-c). SUGT1 is an assembly factor for the kineto-chore and is required for the G1/S and G2/M transitions [34]. The A/k exon encodes a peptide of 33 amino acids inserted at the end of the third tetratricopeptide repeat (TPR) in the SUGT1 protein product. We identified five peptide sequences in PRIDE that matched to the upstream or downstream splice junction of this A/k exon, and additional peptide evidence was found in the highly stringent PeptideAtlas (Fig. 3a). This exon had a significant splicing activity in HeLa cells with a transcript inclusion level of 49 % according to RNA-seq data, while its transcript inclusion level in the Ribo-seq data was even higher (66 %; see Figs. 2a and 3c), suggesting active translation of the A/k exon inclusion mRNA isoform. Given the strong evidence for this A/k exon derived peptide, we next asked whether the expression of this A/k exon inclusion protein isoform has been detected in previous studies. A literature search showed that the SUGT1 protein isoform containing the 33 amino acids encoded by exon 6 (that is, the A/k exon) was first identified as a doublet band in Hela cell extracts, as well as in human tissues including brain, liver, lung, and testis, and termed as SUGT1B, while the exon 6 skipping protein isoform was called SUGT1A [35]. The authors thought SUGT1B (that is, the exon inclusion isoform) was the ancestral full-length isoform while SUGT1A (that is, the exon skipping isoform) represented an alternative isoform of the gene. Later studies also detected SUGT1B protein in HeLa, THP-1, and 293T cell extracts [34, 36]. However, it was not recognized that

exon 6 was derived from a primate specific A/k retro-transposon [34-36].

The recent origin of A/k elements suggests that the A/k exon derived peptide in SUGT1 could contribute to the evolutionary divergence of the human and nonhuman primate protein products. To investigate the evolution of this A/k exon further, we designed RT-PCR primers for its flanking constitutive exons in human, chimpanzee, and rhesus macaque genomes and quantified the exon splicing levels in four tissues (brain, kidney, liver, and muscle) (Fig. 3d; also see Additional file 5: Figure S2 for the fluorescently labeled RT-PCR gel images). Our RT-PCR analyses showed this exon had the highest levels of splicing (12-35 %) in human tissues. By contrast, the orthologous exon region was completely absent from the rhesus macaque transcripts. Chimpanzee transcripts showed intermediate transcript inclusion levels (0-24 %).

Next we aligned the human, chimpanzee, and rhesus genomic sequences with the consensus sequence of the corresponding A/k subfamily (A/uSx) (Additional file 5: Figure S3). The resulting alignment suggested that this A/k exonization event occurred prior to the most recent common ancestor of humans and chimpanzees. Specifically, a C to T substitution created the 5' splice site GT dinucleotide, which, when combined with the preexisting 3' splice site AG dinucleotide in A/uSx, led to A/k exonization. Additionally, a G to A substitution at the +3 intronic position of the 5' splice site strengthened the splice site score from 5.29 to 9.46 as calculated by MAXENT [37], representing an over 16-fold increase in the likelihood of matching to the consensus MAXENT

SUGT1—

— PRIDE peptide

— PeptideAtlas peptide

D^qasa^czK

Alu exon

Alu exon

TSSDPPALDSQSAGITGADAN

¿■8

TEGQKLDlifflÄiOMiMliGADANFSVWIKR

40%-i 30%-20V 10%-0%

□ Hs □ Pt □ Rm i5i

Brain Kidney Liver Muscle

Fig. 3 A protein-coding Alu exon in SUGT1 supported by multiple lines of proteomics and Ribo-seq evidence. a The splicing pattern and deduced peptide sequence of a putative coding Alu exon in SUGT1 and its corresponding peptide evidence from PRIDE and PeptideAtlas. b Tandem mass spectrometry (MS/MS) spectrum of the peptide TSSDPPALDSQSAGITGADAN from PRIDE (experiment ID: 26855, spectrum ID: 7275). c The UCSC genome browser view of the Ribo-seq and RNA-seq data of the SUGT1 Alu exon. d RT-PCR analysis of the SUGT1 Alu exon in four different tissues in human (Hs), chimpanzee (Pt), and rhesus macaque (Rm). Error bars show standard error of the mean from at least three replicate experiments

5' splice site model. The rhesus sequence lacked the essential GT dinucleotide at the 5' splice site, consistent with the observation that the exon was completely skipped in rhesus transcripts. We did not observe any nucleotide difference between the human and chimpanzee sequences within the exon or the 5' and 3' splice site regions (Additional file 5: Figure S3). However, beyond the splice sites there were a number of nucleotide differences in the upstream and the downstream intronic regions, which may be responsible for the difference in splicing levels between the human and chimpanzee exons.

We carried out a comprehensive investigation of the genomic sequence changes that strengthened the SUGT1 A/k exon in the human lineage (Fig. 4). There was no obvious candidate for causal cis sequence change(s) based on sequence analysis of splicing regulatory elements. Between human and chimpanzee, no sequence divergence was found within the A/k exon or in the 9 bp 5' splice site and 23 bp 3' splice site regions.

SUGT1 Alu exon minigene

| D |pA|—— pl-11 (-H3) PL

Human (Hs) Chimpanzee (Pt) Rhesus (Rm)

SUGT1 minigene construct:

| R»p—t AlnJb~| | Rap—t AluSx ~

786bp Exon 6

Hs-WT ^^^mcO^ ■

Pt-WT Rm-WTi

Uhs-Dr ■

Upt-Dm

Uiwpt-Dpt I

UHS/K-DHI I Upt/Hf-Dpt I

Upt/Hs-DHl I b

357bp 430bp

I AG i I CT I

IGT ■

Inclusion Level

70±3% 50±7% 0%

67±3%

50±3%

50±4%

50±4% 68±2%

67±2%

nil/////

Inclusion (%) 68 54 0 64 47 48 48 67 65 Fig. 4 Minigene splicing reporter analysis of the human-specific splicing change of SUGT1 protein-coding Alu exon (Exon 6). a Schematic diagrams of the pI-11-H3 minigene splicing reporter and the wild-type/ mutant minigene constructs of SUGT1 Alu exon. The nucleotide differences between human and chimpanzee are indicated by asterisks on the chimpanzee sequence. b Representative gelimage for fluorescently labeled RT-PCR analyses in Hela cells using the SUGT1 Alu exon wild-type and mutant minigene constructs

Therefore, the causal cis sequence change(s) must reside in the upstream or downstream intronic region further away from the splice sites. These intronic regions contained a fairly large number of sequence changes between human and chimpanzee. We cloned a large genomic fragment surrounding the SUGT1 A/k exon into a minigene splicing reporter (see Materials and Methods) and generated three splicing reporter constructs corresponding to the wild-type human, chimpanzee, and rhesus genomic sequence (Hs-WT, Pt-WT, and Rm-WT; see Fig. 4a). When expressed in Hela cells, the chimpanzee minigene construct had an exon inclusion level of 50 ± 7 %, while the human minigene construct had a higher exon inclusion level of 70 ± 3 %, and no exon inclusion was observed for the rhesus minigene construct. The splicing difference between the human and chimpanzee wild-type minigene constructs was consistent with the difference of endogenous splicing levels in human and chimpanzee tissues (12-35 % vs. 0-24 %). The overall higher baseline exon inclusion levels in the minigene constructs may indicate deeper intronic splicing silencers that were not cloned into the minigene reporter, but this should not affect our human vs chimpanzee comparative analysis. Then we used a sequence swapping strategy [38] to make six additional splicing reporter constructs in which gen-omic segments from different species were swapped in order to narrow down the genomic region responsible for the human-specific splicing pattern (Fig. 4a). The analysis of these minigene splicing reporters indicates that a proximal 430 bp upstream intronic region is responsible for the human-specific increase in splicing compared to chimpanzee. All minigene constructs containing the chimpanzee version of this 430 bp intronic region showed approximately 50 % exon inclusion, while all minigene constructs containing the human version of this region showed close to 70 % exon inclusion, despite being placed within different surrounding sequence context (Fig. 4a, b). We obtained similar results when transfecting these reporters to a chimpanzee fibroblast cell line (data not shown), further supporting our hypothesis that the splicing divergence of this SUGT1 A/k exon was driven by cis sequence changes. Within this 430 bp upstream intronic region, there were six individual nucleotide substitutions between human and chimpanzee. We were unable to successfully perform further point mutation analyses of this region, due to the sequence homology between this region (which was AluSx derived) with an adjacent upstream AluJb element (see Fig. 4a). Nonetheless, our minigene splicing reporter data have established the role of specific cis genomic sequences in shaping the evolution of this A/k exon in the human lineage.

Collectively, our data indicate a gradually strengthened splicing activity of the SUGT1 A/k exon during recent primate and human evolution. It is possible that the

acquisition and increased expression of this Alu-derived peptide in human tissues have certain adaptive benefits and are driven by positive selection.

The Alu exon inclusion isoform of ADARB1 encodes an active RNA editing enzyme with an altered editing activity

To investigate whether Alu-derived peptides can be part of functional proteins, we selected a protein coding Alu exon in the RNA editing enzyme ADARB1 (ENSG00000197381, also known as ADAR2) for detailed studies. The crystal structure of the catalytic domain of human ADARB1 has been solved [39]. The Alu exon encodes a 40 amino acid peptide inserted into the catalytic deaminase domain, which is supported by two peptide sequences in PRIDE (Fig. 5a). This exon displayed moderate to high levels of splicing (25-100 %) across human tissues according to the RNA-seq data, including eight out of 19 tissues with over 75 % exon inclusion levels. Our RT-PCR analyses of human, chimpanzee, and rhesus tissues showed that the Alu exon was consistently spliced into transcripts with comparable splicing levels in all three species, while there was variation in its splicing

levels across different tissues and individuals (Additional file 5: Figure S4). In previous in vitro studies where purified recombinant ADARB1 protein isoforms were incubated with an artificial dsRNA substrate, the A/k exon inclusion protein isoform showed a lower catalytic activity than the A/k exon skipping isoform [19, 40]. However, the functional activity of the A/k exon inclusion ADARB1 protein isoform on endogenous mRNA transcripts has not been examined on a genome-scale in a live cell setting.

To test the effect of the ADARB1 protein isoforms on RNA editing, we selected the HEK293 cell line which had a low endogenous ADARB1 level, and ectopically expressed either the A/k exon inclusion or skipping ADARB1 protein isoform. Real-time qRT-PCR and western blot analyses indicated that both isoforms were expressed at similar levels (Additional file 5: Figure S5). To characterize the transcriptome-wide effect on RNA editing, we then performed strand-specific RNA-seq of cells transfected with one of the two ADARB1 protein isoforms or an empty vector control (Materials and Methods). We collected annotated A-to-I editing sites in human genes from the RADAR database of RNA editing

pride peptide

dsRBM dsRBM

ADARB1-Short | | | | |

catalytic domain

ADARBI-Long | | | | |

Alu exon

ARIFSPHEPILE

f S RSYTQAGVQWCN HGS LQP RPPGLLS DPSTSTFQGAGTT

EPADRHP

P=4.7e-10 2.5-, |-1

11.5-1

O). „

c 1.0-¡Ñ

S 0.5-

Short-EV Long-EV

Ill ■

60 40 20 0 -20 -40 -60

o Common (144) o Long specific* (70) o Short specific* (126)

• Long specific'

• Short specific"

Low-confidence High-confidence

-60 -40 -20 0 20 40 60 ¿Editing level (Short-EV) (%)

Fig. 5 ADARB1 Alu exon inclusion isoform encodes an active RNA editing enzyme with altered editing activity. a The schematic diagram of the protein domain structure of ADARB1 isoforms and supporting peptide sequences from the PRIDE database. b The change in overallRNA editing levels of 7,618 RNA editing sites in HEK293 cells upon ectopic expression of the exon skipping (Short) or the exon inclusion (Long) ADARB1 isoform as compared to the empty vector (EV) control. Error bars show standard errors calculated based on the 7,618 known RNA editing sites used in this analysis. c Common and isoform-specific differentially edited sites upon ectopic expression of the Alu exon inclusion (Long) or skipping (Short) ADARB1 isoform. Isoform-specific differentially edited sites are further classified (low-confidence, high-confidence) based on the strength of the RNA-seq evidence

sites [41], and restricted our analysis to a set of 7,618 sites with sufficient sequencing coverage in our data set (Materials and Methods). We then compared the overall RNA editing levels in the cells across different experimental conditions. Both the A/k exon inclusion and skipping protein isoforms significantly enhanced the overall editing levels in the HEK293 cells as compared to the empty vector control (Wilcoxon test, Short vs. EV: P = 6.5e-68, Long vs. EV: P = 2.1e-50; Fig. 5b), indicating the A/k exon inclusion protein isoform is an active RNA editing enzyme with a global impact on RNA editing. We also noted that the overall RNA editing level was lower in cells expressing the A/k exon inclusion isoform as compared to cells expressing the A/k exon skipping isoform (Wilcoxon test, P = 4.7e-10; Fig. 5b), consistent with the in vitro assay results on the synthetic RNA editing substrate [19, 40].

To investigate potential differences in the site selectivity of these two ADARB1 isoforms, we sought to identify differentially edited sites upon ectopic expression of the A/k exon inclusion (long) or skipping (short) isoform. Specifically, for each annotated RNA editing site in the RADAR database [41], we counted and compared their edited and unedited RNA-seq reads with those of the empty vector (EV) transfected cells. For each individual replicate, we used Fisher's exact test to calculate the P value, then combined the P values of three replicates using Fisher's method to generate a combined P value for differential editing, followed by correction of multiple testing to generate FDR. The editing sites with FDR < 10 % were called differential RNA editing sites. We then compared the identified differential RNA editing sites for the A/k exon inclusion (long) or skipping (short) ADARB1 isoform to identify common and isoform-specific differential RNA editing sites. To guard against potential spurious calls of isoform-specific differential editing sites due to RNA-seq noise and statistical fluctuation, we also generated a high-confidence list of isoform-specific differential RNA editing sites, defined as those with FDR < 10 % for one isoform and FDR > 90 % for the other isoform. We identified a total of 360 differential RNA editing sites in the RNA-seq data after ectopic expression of one of the two isoforms (Fig. 5c). As seen in Fig. 5c, most of them were either common to the two isoforms, or were classified as isoform-specific but the difference between the two isoforms was minor and could be attributed to random RNA-seq noise and statistical fluctuation (that is, those classified as 'low-confidence' isoform specific sites). We did identify six high-confidence long isoform specific and 14 high-confidence short isoform specific differential RNA editing sites, but they represented a fairly small percentage of all identified differential RNA editing sites (Fig. 5c). It is interesting to note that in general, we identified almost twice as many short

isoform specific sites than long isoform specific sites, at various confidence level cutoffs (Fig. 5c). Collectively, these data suggest that regulated alternative splicing of this A/k exon may fine tune the editing activities and in limited cases the target site selectivity of the ADARB1 protein products.

Discussion

The creation and establishment of new exons provide an important evolutionary strategy for generating genetic novelties in existing genes [42, 43]. A large body of work has investigated the exonization of A/k elements as a major source for new exons during primate and human evolution [5, 7-9, 44-47]. Recent studies have shown that a subset of A/k exons in human genes have acquired strong splicing activities [8, 9], and that they play a variety of regulatory roles at the RNA level such as the control of mRNA degradation and translation [8-10]. On the other hand, the contribution of A/k exonization to the human proteome has been considered to be minimal [13]. In 2006, a survey of protein sequence entries in the PDB did not identify any peptide segment derived from A/k or other young transposable elements (TEs), leading the authors to conclude that 'functional proteins are unlikely to contain TE cassettes derived from young TEs, the role of which is probably limited to regulatory functions' [13].

In this work, we revisited the role of A/k exonization in human proteome evolution and adopted a proteotran-scriptomics approach [48] to systematically evaluate the evidence for A/k exon derived peptides in human proteins. We identified 262 putative coding A/k exons in Ensembl human transcripts, among which 85 exons had proteomic evidence in the PRIDE peptide database. Using multiple negative controls, we demonstrated that our proteomic identification of protein-coding A/k exons based on the PRIDE search had a low FDR. We also performed detailed analyses of RNA-seq and Ribo-seq data of human tissues and cell lines to provide more fine-grained information on the splicing and transla-tional profiles of these protein-coding A/k exons. Using RNA-seq data of 19 human tissues, we identified 52 protein-coding A/k exons with high transcript inclusion levels and/or tissue-specific splicing profiles, significantly expanding the catalog of coding-region A/k exons with strong splicing activities in normal human tissues, which were considered rare in previous work [8, 9]. Collectively, our data challenge the conventional view on the proteomic impact of A/k exonization and suggest that an appreciable number of coding-region A/k exons are translated into stable protein products. Therefore, the contribution of A/k exons to the human proteome is significantly higher than previously suggested [13].

We studied a protein coding A/k exon in SUGT1, a gene encoding a cell cycle regulator [34]. The translation of this SUGT1 A/k exon is supported by multiple lines of evidence (Ribo-seq, PRIDE, PeptideAtlas) as well as previous literature [34-36]. Although the specific function of this SUGT1 A/k exon inclusion isoform remains to be elucidated, existing data suggest that the splicing of this A/k exon is under dynamic regulation in human cells. SUGT1 is reported to be a member of the pro-inflammatory complex 'inflammasome' and its protein level, especially the level of the A/k exon inclusion isoform (known as 'SUGT1B' in the literature), increases after heat shock [49]. SUGT1B also appears to be preferentially translocated to and accumulate in the nucleus under heat shock [50]. Additionally, there is anecdotal evidence showing SUGT1B is expressed at a much higher level than SUGT1A (that is, the A/k exon skipping isoform) in a human malignant glioblastoma cell line U-251 MG [51], as compared to the near or lower than 1:1 ratio in liver and tonsil tissues tested in the same experiment as well as various tissues and cell lines analyzed in other reports [34-36, 49]. Interestingly, our RT-PCR analyses indicate a significant gradient in the splicing levels of this SUGT1 A/k exon between human, chimpanzee, and rhesus macaque tissues, with the exon spliced at the highest levels in human tissues and completely skipped in rhesus macaque tissues (Fig. 3d). Therefore, this A/k exonization event has contributed to the acquisition and increased expression of a novel pep-tide segment during very recent human evolution. Of note, using a moderate-coverage six-tissue RNA-seq dataset of human, chimpanzee, and rhesus macaque [52], we identified two additional protein-coding A/k exons in SRP9 and ZNF468 (see Additional file 1: Table S1 for their annotations) with more than 15 % increase in splicing levels in at least one human tissue compared to the corresponding chimpanzee and rhesus tissue. Given the limited RNA-seq depth of this dataset, this list is expected to be quite incomplete.

Conclusions

Our study has revealed a large list of A/k exons that may be translated and incorporated into primate-specific or even human-specific protein isoforms. These A/k exons are created in genes involved in a wide range of biological functions and molecular processes (Table 1). We selected an A/k exon in a tran-scriptome regulator ADARB1 and performed RNA-seq experiments to read out the activity of the A/k exon inclusion protein isoform on transcriptome-wide control of A-to-I RNA editing. For other protein-coding A/k exons identified in this work, future experiments tailored towards their genes' specific cellular functions are needed to elucidate the evolutionary significance

of the novel protein isoforms arising from A/k exonization.

Materials and methods

RNA-seq analysis of putative coding Alu exons

The locations of A/k elements in the human genome (hg19) were downloaded from the UCSC Genome Browser database [53]. The locations of internal cassette or constitutive exons were taken from Ensembl gene annotations (release 57) [54]. We defined an exon as A/u-derived if the A/k element covered at least 25 bp of the exon and more than 50 % of the total exon length.

We downloaded the Human Body Map 2.0 (HBM2.0) paired-end RNA-seq data from Gene Expression Omnibus (GEO) (accession number GSE30611). HBM2.0 RNA-seq data have a read length of 50 bp. They cover 16 tissues: adipose, adrenal, brain, breast, colon, heart, kidney, liver, lung, lymph node, ovary, prostate, skeletal muscle, testes, thyroid, and white blood cells. We also used paired-end RNA-seq data of three anatomical compartments of the human placenta (amnion, chorion, and decidua) generated in our previous work [55]. We used only 50 bp of each end for mapping and analysis based on the sequencing error profile. We used the same RNA-seq mapping method as previously described [55] to obtain the splice junction read counts and calculate each exon's transcript inclusion level. We used MATS to identify differential alternative splicing events in pairwise tissue comparisons [24].

Search of the PRIDE database

We searched the PRIDE (PRoteomics IDEntifications) database [25] for peptide evidence for putative coding A/k exons. We downloaded the peptide sequences in June 2014 with more than 1.5 million unique peptide sequences in PRIDE. Of these 1.5 million peptide sequences, approximately 900,000 were uniquely mappable to the coding regions of the human Ensembl transcripts (release 57). With these uniquely mappable peptide sequences, we examined the ORFs (open reading frames) containing putative coding A/k exons and identified 85 A/k exons with PRIDE peptide evidence.

Ribo-seq analysis of putative coding Alu exons

Ribo-seq data and corresponding RNA-seq data of HeLa cells were downloaded from [29]. The sequencing reads are 36 bp in length. We used the first 30 bp of each read for mapping and analysis. Reads were mapped to all splice junctions in human genes (Ensembl genes, release 57). Each splice junction is 54 bp in length, containing the last 27 bp of the upstream exon and the first 27 bp of the downstream exon. We used Bowtie [56] to map reads, allowing up to two mismatches and also required that each read should be uniquely mapped. Exons'

transcript inclusion levels were estimated as described previously [55].

Construction of ADARB1 isoform expression vectors

The ORF for the human ADARB1 short isoform (without the A/k exon) in the pCMV6-AC vector was purchased from OriGene, Inc. (catalog no. SC321955; reference transcript NM_001112). Mutageneses using the QuikChange method (Stratagene) were carried out to convert the ORF to encode the ADARB1 reference protein sequence NP_001103. Six nucleotides in pCMV6-AC encoding two additional amino acids at the C-terminus were removed. A minor allele SNP (rs199697177) 'C' (allele frequency <1 %) was mutated back to the major allele 'T' in the ADARB1 ORF. Then the A/k exon was inserted using the same mutagenesis method. Final pCMV6-ADARB1-short (without the A/k exon) and pCMV6-ADARB1-long (with the A/k exon) constructs were confirmed by sequencing.

Ectopic expression of ADARB1 isoforms in HEK293 cells

HEK293 cell line was grown in DMEM with 10 % FBS. Cells were transiently transfected with Lipofectamine 2000 reagent according to the manufacturer's protocol. Forty-eight hours after transfection, cells were collected for RNA extraction using TRIzol reagent (Life Technologies) and protein lysates with RIPA buffer. Trans-fection experiments were replicated in three different cell passages.

Total RNA samples were treated with DNaseI (Fermentas) and reverse transcribed using the High-Capacity cDNA RT kit (Applied Biosystems). Quantitative real-time PCR (qRT-PCR) was performed using Fast SYBR green Master Mix (Applied Biosystems). Total gene expression level and isoform-specific expression level of ADARB1 were measured using GAPDH as the reference gene. Relative expression level was measured by the comparative Ct (2-AACt) method [57]. Primers used are:

GAPDH_F: 5 '-TGGTATCGTGGAAGGACTCA-3', GAPDH_R: 5 '-ACAGTCTTCTGGGTGGCAGT-3', AD ARB1_Gene_F: 5' -AGTCTCCG CCAGTCAAGAAA-3', ADARB1_Gene_R: 5 '-GTTGTCCAGATTGCGGTTTT-3', ADARB1_short_F: 5'-AGGCTGAAGGAGAATGTCCA-3', ADARB1_short_R: 5 '-TGTCTATCTGCTGGTTCTTC-3', ADARB1_long_F: 5 '-CTCAACCTTCCAAGGAGCTG-3', ADARB1_long_R: 5'-GTCCGTAGCTGTCCTCTTGC-3'.

Total protein extract in RIPA buffer was used to assay for protein level. ADARB1 (sc-10012, Santa Cruz Biotechnology) and ACTB (A5441, Sigma) antibodies were used for western blot following standard protocol. Signals were detected by ChemiDoc™ MP imaging system (Bio-Rad). RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) and sequenced on an Illumina

HiSeq 2000 (100 cycles, paired-end). RNA-seq data were deposited in the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE65999.

RNA-seq analysis of A-to-I editing

Strand-specific paired-end RNA-seq reads were first mapped to Ensembl transcripts and the unmapped reads were then mapped to the human genome (hg19) using Tophat (version 1.4.1) [58]. We used REDItools [59] to calculate the edited and unedited read counts on the corresponding strand of each known RNA editing site collected in the RADAR database [41]. We removed the editing sites that had less than five edited counts in all the nine RNA-seq libraries to avoid using unreliable editing sites or sites not edited in the samples of interest. The sites that had no read coverage (edited counts and unedited counts) for all three replicates of either empty vector (EV), ADARB1 long form, or ADARB1 short form transfected cells were also removed from further analyses because they were uninformative for comparisons. In the end, 7,618 known editing sites were used in the analyses.

To compare the global editing levels between the three sample groups, we merged the RNA-seq reads of three replicates in each group, and the editing levels of each editing site were calculated as the fraction of edited counts over the total counts in the merged data. To avoid using sites with unreliable editing levels due to low read coverage, we used only the editing sites that had total read coverage >50. Then we calculated the significance for the editing level differences between two groups using two-tailed Wilcoxon test.

Total RNA preparation

Postmortem tissue samples of three adult chimpanzees and three adult rhesus macaques were generously provided by the Southwest National Primate Research Center (San Antonio, TX, USA). Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Total RNAs from various human tissues were purchased from Clontech (Mountain View, CA, USA), BioChain (Newark, CA, USA), and Ambion (now part of Thermo Fisher, Grand Island, NY, USA), or prepared as previously described [55].

Fluorescently labeled RT-PCR analysis of exon splicing

Single-pass cDNA was synthesized using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA, USA) according to manufacturer's instructions. Two micrograms of total RNA were used for each 20 ^L cDNA synthesis reaction. Fluorescently labeled RT-PCR was carried out as described previously [60]. PCR primer sequences

are listed in Additional file 4: Table S4. Each gel picture shown was a representation of at least three replicates.

Minigene analysis of SUGT1 protein-coding Alu exon splicing

A/k exon (Exon 6) of SUGT1 and its adjacent flanking intronic regions were amplified from the human, chimpanzee and rhesus genomic DNAs using KAPA HiFi HotStart ReadyMix PCR Kit (Kapa Biosystems, Inc., Wilmington, MA, USA). PCR products were subcloned into the NotI site of the pI-11-H3 minigene vector [61] (kindly provided by Dr. Russ P. Carstens, University of Pennsylvania, Philadelphia, PA, USA) using the In-Fusion Advantage PCR Cloning Kit (Clontech, Mountain View, CA, USA). Sequence swapping mutagenesis [38] was done using KAPA HiFi HotStart ReadyMix PCR Kit. All sequences and mutations were verified by DNA sequencing.

In vitro minigene splicing reporter assay

HeLa cells and chimpanzee fibroblast cells (S008861, Coriell Institute, Camden, NJ, USA) were grown in DMEM (Invitrogen, Thermo Fisher, Grand Island, NY, USA) with 10 % FBS (Invitrogen). Cells were plated in 12-well plates and transfected using Lipofectamine LTX and Lipofectamine 2000 (Invitrogen), respectively, according to the manufacturer's protocol. RNA was purified 16 h after transfection and reverse-transcribed into single-pass cDNA. Fluorescently labeled RT-PCR was performed as described above. The pI-11-H3 minigene-specific primer sequences were pI11-F: 5-GCTGTCT GCGAGGTACCCTA-3pI11-R: 5-CGTCGCCGTCCA GCTCGACCAGCGTTCGGAGGATGCATAGAG-3'.

Ethics statement

This work used post-mortem tissues obtained from the Southwest National Primate Research Center. The primate tissue repository was approved by the Institutional Animal Care and Use Committee at the Southwest National Primate Research Center at the Texas Biomedical Research Institute (Animal Welfare Assurance Number A3082-01; IACUC protocol number 525 PT for chimpanzees, and 525 MM for rhesus macaques).

Additional files

Additional file 1: Table S1. Fifty-two putative coding Alu exons with moderate-to-high levels of exon splicing or differential splicing activities among human tissues. (XLSX 16 kb)

Additional file 2: Table S2. Eighty-five putative coding Alu exons with peptide evidence from the PRIDE database. (XLSX 18 kb)

Additional file 3: Table S3. Seventy-six putative coding Alu exons with at least 10 reads mapped to one of the three splice junctions in both Ribo-seq and RNA-seq data from HeLa cells. (XLSX 18 kb)

Additional file 4: Table S4. List of RT-PCR primers. (XLSX 10 kb)

Additional file 5: Supplementary figures S1-5. (DOCX 2892 kb)

Abbreviations

cDNA: complementary DNA; CDS: coding DNA sequence; DJC: downstream junction read count; EST: expressed sequence tags; FDR: false discovery rate; GEO: Gene Expression Omnibus; mRNA: messenger RNA; NMD: nonsensemediated decay; PDB: Protein Databank; PRIDE: PRoteomics IDEntifications Database; PSI (Y): percent-spliced-in; PTC: premature termination codon; qRT-PCR: quantitative real-time PCR; Ribo-seq: ribosome profiling; RNA-seq: RNA sequencing; SJC: skipping junction read count; TE: transposable element; TPR: tetratricopeptide repeat; UJC: upstream junction read count; UTR: untranslated region.

Competing interests

The authors declare that they have no competing interests. Authors' contributions

LL, PJ, and YX conceived the study; LL and ZXL carried out the molecular biology experiments; PJ, JWP, JW, MPYL, and PP carried out the bioinformatics analyses; LL, PJ, and YX wrote the manuscript. All authors have read and approved the final manuscript.

Acknowledgements

We wish to thank Peter Stoilov for discussions and comments on this work, and Jerilyn Pecotte for assistance.

Funding

This work is supported by National Institutes of Health grants R01GM088342 and R01GM105431 (YX). YX is supported by an Alfred Sloan Research Fellowship. This work used biological materials obtained from the Southwest National Primate Research Center, which was supported by NIH-NCRR grant P51RR013986.

Author details

1Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA. 2Regenerative Biology, Morgridge Institute for Research, Madison, WI 53707, USA. 3Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA. 4KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA. 5Department of Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA. 6Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Received: 9 November 2015 Accepted: 8 January 2016 Published online: 28 January 2016

References

1. Feschotte C. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 2008;9:397-405.

2. Hasler J, Strub K. Alu elements as regulators of gene expression. Nucleic Acids Res. 2006;34:5491-7.

3. Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet. 2009;10:691-703.

4. Sorek R. The birth of new exons: mechanisms and evolutionary consequences. RNA. 2007;13:1603-8.

5. Lev-Maor G, Sorek R, Shomron N, Ast G. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science. 2003;300:1288-91.

6. Zhang XH, Chasin LA. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc Natl Acad Sci USA. 2006;103:13427-32.

7. Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G. Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol. 2007;8:R127.

8. Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, et al. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet. 2008;4:e1000225.

9. Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, et al. Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci USA. 2011;108:2837-42.

10. Zarnack K, Konig J, Tajnik M, Martincorena I, Eustermann S, Stevant I, et al. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell. 2013;152:453-66.

11. Makalowski W, Mitchell GA, Labuda D. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 1994;10:188-93.

12. Nekrutenko A, Li WH. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001;17:619-21.

13. Gotea V, Makalowski W. Do transposable elements really contribute to proteomes? Trends Genet. 2006;22:260-7.

14. Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK. Evaluating the protein coding potential of exonized transposable element sequences. Biol Direct. 2007;2:31.

15. Goodier JL, Kazazian Jr HH. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell. 2008;135:23-35.

16. Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res. 2002;12:1060-7.

17. Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 2007;41:331-68.

18. Birzele F, Csaba G, Zimmer R. Alternative splicing and protein structure evolution. Nucleic Acids Res. 2008;36:550-8.

19. Gerber A, O'Connell MA, Keller W. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. RNA. 1997;3:453-63.

20. Hsu DW, Lin MJ, Lee TL, Wen SC, Chen X, Shen CK. Two major forms of DNA (cytosine-5) methyltransferase in human somatic tissues. Proc Natl Acad Sci U S A. 1999;96:9751 -6.

21. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57-63.

22. Hillman RT, Green RE, Brenner SE. An unappreciated role for RNA surveillance. Genome Biol. 2004;5:R8.

23. Katz Y, Wang ET, Airoldi EM, Burge CB. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods. 2010;7:1009-15.

24. Shen S, Park JW, Huang J, Dittmar KA, Lu ZX, Zhou Q, et al. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res. 2012;40:e61.

25. Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013;41:D1063-9.

26. Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, et al. State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.

J Proteome Res. 2014;13:60-75.

27. Fonslow BR, Stein BD, Webb KJ, Xu T, Choi J, Park SK, et al. Digestion and depletion of abundant proteins improves proteomic coverage. Nat Methods. 2013;10:54-6.

28. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324:218-23.

29. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 2010;466:835-40.

30. Price AL, Eskin E, Pevzner PA. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 2004;14:2245-52.

31. Isken O, Maquat LE. Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev. 2007;21:1833-56.

32. Zong NC, Li H, Li H, Lam MP, Jimenez RC, Kim CS, et al. Integration of cardiac proteome biology and medicine by a specialized knowledgebase. Circ Res. 2013;113:1043-53.

33. Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E, Ast G. RNA-editing-mediated exon evolution. Genome Biol. 2007;8:R29.

34. Steensgaard P, Garre M, Muradore I, Transidico P, Nigg EA, Kitagawa K, et al. Sgt1 is required for human kinetochore assembly. EMBO Rep. 2004;5:626-31.

35. Niikura Y, Kitagawa K. Identification of a novel splice variant: human SGT1B (SUGT1B). DNA Seq. 2003;14:436-41.

36. Mayor A, Martinon F, De Smedt T, Petrilli V, Tschopp J. A crucial function of SGT1 and HSP90 in inflammasome activity links mammalian and plant innate immune responses. Nat Immunol. 2007;8:497-503.

37. Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol. 2004;11:377-94.

38. Kirsch RD, Joly E. An improved PCR-mutagenesis strategy for two-site mutagenesis or sequence swapping between related genes. Nucleic Acids Res. 1998;26:1848-50.

39. Macbeth MR, Schubert HL, Vandemark AP, Lingam AT, Hill CP, Bass BL. Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science. 2005;309:1534-9.

40. O'Connell MA, Keller W. Purification and properties of double-stranded RNA-specific adenosine deaminase from calf thymus. Proc Natl Acad Sci U S A. 1994;91:10596-600.

41. Ramaswami G, Li JB. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 2014;42:D109-13.

42. Boue S, Letunic I, Bork P. Alternative splicing and evolution. Bioessays. 2003;25:1031-4.

43. Xing Y, Lee C. Alternative splicing and RNA selection pressure-evolutionary consequences for eukaryotic genomes. Nat Rev Genet. 2006;7:499-509.

44. Gal-Mark N, Schwartz S, Ast G. Alternative splicing of Alu exons-two arms are better than one. Nucleic Acids Res. 2008;36:2012-23.

45. Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, Ast G. Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol. 2009;5:e1000300.

46. Sorek R, Lev-Maor G, Reznik M, Dagan T, Belinky F, Graur D, et al. Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. Mol Cell. 2004;14:221-31.

47. Corvelo A, Eyras E. Exon creation and establishment in human genes. Genome Biol. 2008;9:R141.

48. Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nat Methods. 2014;11:1114-25.

49. Zabka M, Lesniak W, Prus W, Kuznicki J, Filipek A. Sgt1 has co-chaperone properties and is up-regulated by heat shock. Biochem Biophys Res Commun. 2008;370:1 79-83.

50. Prus W, Zabka M, Bieganowski P, Filipek A. Nuclear translocation of Sgt1 depends on its phosphorylation state. Int J Biochem Cell Biol. 2011;43:1747-53.

51. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, et al. Towards a knowledge-based Human Protein Atlas. Nat Biotechnol. 2010;28:1248-50.

52. Brawand D, Soumillon M, Necsulea A, Julien P, Csardi G, Harrigan P, et al. The evolution of gene expression levels in mammalian organs. Nature. 2011;478:343-8.

53. Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2015;43:D670-81.

54. Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2015. Nucleic Acids Res. 2015;43:D662-9.

55. Kim J, Zhao K, Jiang P, Lu ZX, Wang J, Murray JC, et al. Transcriptome landscape of the human placenta. BMC Genomics. 2012;13:115.

56. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.

57. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25:402-8.

58. Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-11.

59. Picardi E, Pesole G. REDItools: high-throughput RNA editing detection made easy. Bioinformatics. 2013;29:1813-4.

60. Zhao K, Lu Z-x, Park JW, Zhou Q, Xing Y. GLiMMPS: Robust statistical model for regulatory variation of alternative splicing using RNA-Seq data. Genome Biol. 2013;14:R74.

61. Warzecha CC, Sato TK, Nabet B, Hogenesch JB, Carstens RP. ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol Cell. 2009;33:591-601.