RNA-editing-mediated exon evolution
- Galit Lev-Maor†1,
- Rotem Sorek†1, 2,
- Erez Y Levanon3, 4,
- Nurit Paz5,
- Eli Eisenberg6 and
- Gil Ast1Email author
© Lev-Maor et al.; licensee BioMed Central Ltd. 2007
Received: 25 September 2006
Accepted: 27 February 2007
Published: 27 February 2007
Alu retroelements are specific to primates and abundant in the human genome. Through mutations that create functional splice sites within intronic Alus, these elements can become new exons in a process denoted exonization. It was recently shown that Alu elements are also heavily changed by RNA editing in the human genome.
Here we show that the human nuclear prelamin A recognition factor contains a primate-specific Alu-exon that exclusively depends on RNA editing for its exonization. We demonstrate that RNA editing regulates the exonization in a tissue-dependent manner, through both the creation of a functional AG 3' splice site, and alteration of functional exonic splicing enhancers within the exon. Furthermore, a premature stop codon within the Alu-exon is eliminated by an exceptionally efficient RNA editing event. The sequence surrounding this editing site is important not only for editing of that site but also for editing in other neighboring sites as well.
Our results show that the abundant RNA editing of Alu sequences can be recruited as a mechanism supporting the birth of new exons in the human genome.
Analysis of the sequenced human genome has revealed that it contains about 200,000 exons . However, the exon content in mammalian genes is far from static. Rather, it is constantly changing through a dynamic evolutionary process in which exons are newly created and deleted. New exons can arise from gene duplication  and exon duplication , but perhaps the most intriguing process by which exons can be born is exonization by exaptation, where genomic sequences that did not originally function as exons are adopted into exonic sequences .
We have recently shown that Alu elements use this exonization mechanism to give rise to hundreds of novel internal exons in the human genome . Alu elements are unique primate-specific retrotransposons that occur in over one million copies in the human genome [2, 6, 7]. Their 300 bases-long consensus sequence contains motifs that resemble 5' and 3' potential splice sites (5' ss and 3' ss, respectively). Random mutations can turn these motifs into functional splice sites that can be recognized by the splicing machinery [5, 8, 9]. Alu-derived internal exons are almost always alternatively spliced, allowing the original isoform to coexist with the new one and preventing the deleterious effects of introducing a new protein at the expense of the original one [5, 8]. Thus, Alu elements can increase the coding capacity of human genes while maintaining the original protein repertoire.
Recently, Alus were reported to contribute to human transcriptome diversity by an additional mechanism, involving adenosine-to-inosine (A-to-I) RNA editing. A-to-I RNA editing refers to the deamination of selected adenosine residues, altering the nucleotide sequence of RNA transcripts from that encoded by genomic DNA. It is catalyzed by enzymes from the ADAR (adenosine deaminase acting on RNA) family. Editing targets are typically located within double stranded RNA (dsRNA), which is recognized by the ADAR enzymes . RNA editing can cause non-synonymous codon changes when occurring inside the coding sequence or occur in the non-coding parts of the pre-RNA molecule. It was lately reported that human transcripts contain excess editing over mouse, rat, chicken and fly transcripts [5, 11, 12]. The majority of editing sites in human (approximately 96%) were found to occur within Alu sequences. Due to the abundance of Alu elements in the human genome, two Alus in opposite orientation are frequently found near each other. When transcribed in the pre-mRNA, these two Alus can presumably fold to create a dsRNA; this substrate is recognized and edited by the ADAR enzymes. Edited Alus typically do not contribute to the protein repertoire, but rather reside in non-coding parts of the pre-RNA molecule - untranslated regions (UTRs) and introns [11, 13–18].
The observation that Alu elements are both extensively edited and can give rise to novel alternatively spliced exons in primate genomes raises the question of whether RNA editing can be involved in the birth of new Alu-exons. RNA editing was previously shown to regulate alternative splicing by creating a splice site . The most studied event is the auto-editing of the ADAR2 gene, in which intronic AA dinucleotide turns into a functional AG 3' ss following RNA editing . Indeed, it was recently suggested that such editing events may create functional splice sites in silent intronic Alu elements, thus promoting their exonization . In this study we detected a novel primate-specific Alu-exon that exclusively depends on RNA editing for its exonization. We show that RNA editing regulates the exonization in a tissue-dependent manner, both through creation of a functional AG 3' ss, elimination of a premature stop codon, and regulation of the inclusion/skipping level through alteration of exonic splicing enhancers and silencers within the exon. We also demonstrated that the sequence around an editing site is important not only for the editing in that site but also editing in neighboring sites located along this Alu-exon. Our results show that RNA editing can be recruited as a mechanism supporting the birth of new exons in the human genome.
RNA editing enables exonization of a nuclear prelamin A recognition factor Alu-exon
To check the possibility that Alu-derived exons were fixed into protein-coding genes through an RNA-editing-mediated process, we first used expressed sequence tags (ESTs) and cDNAs from GenBank version 136 aligned to the human genome (version hg16) to identify internal human exons that contain Alu elements, as described in . We looked for Alu-containing exons flanked by either AA at the 3' ss or AT at the 5'ss. These non-canonical splice sites will normally not be selected by the splicing machinery; however, each of these splice sites is theoretically capable of becoming a bona fide splice site through A-to-I RNA editing, because inosine is recognized by the splicing apparatus as a guanosine . We demanded that the Alu-exon will be supported by more than one EST/cDNA, and that it neither induced frame-shift nor contained a stop codon, as these parameters were shown to be indicative of functional alternatively spliced exons .
A-to-I RNA editing takes place in the context of dsRNA, to which the ADAR proteins bind through a dsRNA-binding domain (reviewed in [21, 22]). It was therefore shown that, for the vast majority of edited Alus in human exons, there is a nearby (up to 2,000 base-pairs apart) intronic Alu counterpart in the opposite orientation, which presumably serves as the template for dsRNA formation [13, 14]. Indeed, we were able to find an oppositely oriented Alu sequence 25 bases upstream of the exonized Alu. The antisense Alu has 81% identity when aligned to the exon-producing Alu, suggesting that these two Alus might form a stable intramolecular dsRNA formation following transcription (Figure 1b). This, in addition to the non-canonical AA splice site, implies that RNA editing participates in the exonization of that Alu.
Editing within Alu elements frequently occurs in more than one position, due to the long RNA duplex usually formed by two oppositely oriented nearby Alus [11, 13–15, 18, 23]. Indeed, by searching for A→G discrepancies in the alignments of cDNAs to the human genome we detected five additional potential editing sites in the Alu-exon (Figure 1b, E1-E5). The first of these, found in position 19 of the exon, is of particular interest, because it has the potential to change a TAG codon (termination of translation) to a TGG codon (coding for tryptophane). In the absence of RNA editing in the E1 position, the insertion of this Alu-exon would have caused a premature termination. It is important to note that the editing in the exonic E1-E5 sites is directly recognizable from the ESTs or cDNAs in comparison to human genomic DNA, whereas editing in the potential 3'ss is postulated based only on the genomic sequence.
Different levels of exonization among human tissues
We sequenced all of the exon inclusion PCR products and analyzed the editing frequencies at the five editing sites (named E1-E5, Figure 1b) using the Discovery Studio (DS) Gene 1.5 program (Accelrys Inc., San Diego, CA, USA). Importantly, the first exonic editing site, E1 (at position 19 of the exon), was edited at nearly 100% efficiency in all tested tissues and cell lines, whereas the editing levels of the other sites varied (E2 being edited in an average of 53.6% of RNAs, E3 in an average of 26.1%, E4 in an average of 7.9% and E5 in an average of 37.5%) (Figure 2b). Notably, editing sites E1, E3 and E5 are mistakenly annotated as single nucleotide polymorphisms (SNPs) in dbSNP  (rs17855348, rs17849311 and rs17855349, respectively) based on the variance in cDNA data. Many similar examples of RNA editing sites erroneously deposited in dbSNP have been recently reported .
Usually, editing efficiency is much lower than 100% per site, depending on the expression levels of the ADAR enzymes in the given tissue, the secondary structure of the substrate, or the surrounding sequence. As shown above, position E1 in the NARF Alu-exon is edited in nearly all RNA molecules containing this exon. Inactivation of the nonsense-mediated mRNA decay (NMD) by adding puromycine (see Materials and methods) to 293T cell line did not affect the >97% editing efficiency in site E1 (data not shown). This indicates that the high level of editing in site E1 is not due to elimination of unedited, stop-codon containing mRNAs, but rather is indicative of a high efficiency of editing in that site. Apart from the Q/R site of gluR-B , which is restricted to brain, this is the highest editing efficiency documented in human, though it has a much broader tissue expression spectrum. This result suggests that additional regulatory mechanisms have evolved to ensure that the stop codon is edited to a Trp codon in all mRNAs containing the Alu-exon. It further implies that the exonization of the NARF Alu-exon is functional in the human transcriptome.
Alu-AludsRNA directs exonization
When the wild-type minigene was transfected into 293T cells, 23% of the mature mRNAs derived from this minigene represented the exon-inclusion form (Figure 3b, lane 1). However, deletion of the antisense Alu element upstream of the exonized Alu resulted in total abrogation of exon inclusion (Figure 3b, lane 2), indicating that these two adjacent Alus probably pair to create the dsRNA that is required for RNA editing. Without this dsRNA, editing does not occur, and functional AG in the 3'ss cannot be created. The effect of the antisense Alu deletion was reversed when the AA splice site near the Alu-exon was mutated to AG, indicating that a single AA→AG change is sufficient for exonization of this Alu (Figure 3b, lane 3). Interestingly, the AA→AG mutation increased exon-inclusion two-fold over the wild type, suggesting that, in 293T cells, about one-third of the AA pairs in the 3'ss are edited into a functional AG 3' ss. Also, a single AA→AT mutation at the 3'ss, created on the wild-type plasmid, resulted in full exon skipping, indicating the importance of editing at that site for exonization. Whereas, a single AA→AG mutation resulted in approximately 30% exonization (Figure 3b, lanes 4 and 5). The higher level of exonization after a single AA→AG mutation at the 3'ss without and with the antisense Alu presumably suggests that although the antisense Alu is essential for exonization, it also reduces the level of maximum exonization by interfering with spliceosome accessibility to the Alu-exon due to dsRNA formation (compare lanes 3 and 5). Combined together, these results demonstrate that the exonization of the Alu-exon 8 in NARF is mediated by RNA editing, and that this mechanism also controls the level of inclusion of this exon in different tissues.
Editing in one site affects the level of editing in other sites and the surrounding sequence and the opposite nucleotide are important for editing
Exonic regulatory sequences predicted to be changed following editing in the five exonic sites
RNA editing regulates the inclusion level of the NARF Alu-exon
We have demonstrated that the NARF Alu-exon 8 is exonized via RNA editing and that RNA editing is also involved in its tissue-dependent regulation. Previously, RNA editing was implicated in both anti-viral protection and transcript diversity regulation; we now show that editing can also support evolutionary processes such as the birth of new exons. In a recent study, Athanasiadis et al.  presented computational predictions of several Alu exonization events (not including the NARF Alu-exon) that were hypothesized to be regulated by RNA editing; our results provide exemplary confirmation of the validity of these predictions.
It has been shown that a few hundred Alu elements become exonized through single base-pair mutations that create functional splice sites within their sequences. Yet in the case of the NARF Alu-exon, exonization strictly depends on RNA editing. This situation provides a simple, yet powerful, way to regulate the levels of exon inclusion in a tissue/developmental stage-specific manner. Since editing levels control the level of Alu-exon inclusion, exon inclusion rates would follow the varying editing levels in different tissues (Figure 2). Usually, many regulatory sequence elements are needed to regulate alternative splicing in a tissue-specific manner. These sequence elements presumably can extend up to 150 bases from each side of the regulated exon . It is unlikely that a recently retroposed Alu element will carry all needed splicing regulatory elements; however, the RNA-editing-dependent exonization does not rely on such extensive sequence elements, and mainly depends on the expression level of the editing enzymes (ADARs) in the specific tissue. Moreover, we show that editing of two out of the five exonic edited sites affects alternative splicing levels (Figure 5). This provides an additional layer of regulation of alternative splicing through RNA editing.
Interestingly, the E1 as well as the E5 editing sites in the rhesus macaque (but not in chimpanzee) genome encode 'G', thus presenting only the edited version of the gene in those sites. However, there are differences between the genomic sequence of human and chimpanzee and that of rhesus. The Alu-exon (AluSx) and the sequence upstream and downstream of it are highly conserved between human and chimpanzee. But in the rhesus macaque there was an insertion of AluY (in the sense orientation) immediately upstream of AluSx (the one that exonized in human), leading the antisense AluSg (the one that forms the dsRNA) to be located 344 nucleotides upstream of the sense AluSx (and not 25 nucleotides upstream as it is in human). In addition, there was an insertion of 8 nucleotides in the sense AluSx in the rhesus macaque as well as a deletion of 44 nucleotides that includes the site used in human as 3'ss (Additional data file 2). These differences raise the question of whether AluSx in the rhesus macaque exonized at all.
The observed exonization of the NARF Alu-exon in all tested tissues and cell lines indicates that this exon is a bona fide, fixed functional exon in the human genome that originated from an exapted Alu (that is, an Alu that adopted a new function that was not its original function) . An additional example for such exaptation is exon 8 of the ADAR2 gene, which is an Alu-exon of 120 nucleotides (inserts 40 amino acids). The Alu-exon inclusion isoform does not change the specificity of ADAR2 activity compared to the original isoform (exon skipping) but rather changes the rate of the enzymatic activity .
Few mammalian ADAR substrates in which editing causes amino acid substitutions have been found so far; the first (and most studied ones) encode receptors that are all expressed in the central nervous system, including subunits of the glutamate receptor superfamily , the serotonin 5-HT2C-receptor  and the potassium channel KCNA1 . In all these examples, the amino acid substitutions due to editing have been shown to have a major impact on protein properties, and altered editing patterns in the genes encoding them have been found to be associated with several diseases, such as epilepsy , depression , ALS (Amyotrophic Lateral Sclerosis) , and malignant gliomas . Lately, additional evolutionarily conserved RNA editing sites that lead to a codon exchange have been discovered in another four genes [15, 40] - the functional importance of these sites was deduced by their extreme evolutionary conservation. The editing in the NARF Alu-exon is the only experimentally verified editing site in the coding region that is primate-specific. It would be interesting, therefore, to understand the function of the Alu-containing NARF isoform in the human transcriptome (as it might be responsible for a primate-specific trait); however, as the function of NARF itself is currently not clear, this must await future studies. A Pfam analysis indicates that the Alu-exon is inserted in NARF within a domain defined as 'Iron only hydrogenase large subunit, carboxy-terminal domain', and hence can presumably affect the substrate binding affinity/specificity, or the catalytic activity, of this domain.
It is worth noting that several other editing targets that cause predicted amino acid changes were detected in a genome-wide search for editing in Alu [13, 15], but most of them were located in predicted genes or in aberrantly spliced RNAs. Thus, the actual expression of proteins from these transcripts and the possible functional implications of these sites remain to be verified.
Our study provides additional verification for the close relationship between splicing and editing, which was demonstrated when physical association between spliceosomal components and ADAR proteins was reported . The actual mechanism that controls the interconnection of splicing and editing is still largely unknown, but it was shown that additional nuclear machineries are involved, such as the carboxy-terminal domain of RNA polymerase II in the auto-editing of ADAR2 [42, 43]. This auto-editing is so far the most studied demonstration of the feedback loop between editing and splicing, where editing-mediated inclusion of an exon fragment in the rat ADAR2 gene changes, in turn, the editing capacitates of the ADAR protein itself . Editing-mediated selection of splice sites has also been observed in other genes [39, 44]. ADAR2 knockout mice provide another example of the tight connection between editing and splicing, since the absence of editing in the Q/R site prevents proper splicing of the nearby intron . Our results show that this splicing-editing interconnection can also have evolutionary significance.
Although several thousand Alu sequences have the potential to undergo exonization , we were able to detect only one reliable event of a coding Alu-exon that seemed to be exonized through RNA editing, indicating that such a combination of evolutionary events is relatively rare in the human genome. However, this evolutionary mechanism for the birth of new exons might recur in other genomes. Moreover, this mechanism might allow additional Alu exonizations in the evolutionary future of Homo sapiens and other primate species. As some Alus are still active in the human genome (at a rate of 1 transposition every 200 births ), a novel Alu retroposition in the opposite orientation from a nearby preexisting Alu might lead to dsRNA formation and Alu-exonization even if this Alu does not contain a canonical splice site.
We have shown that RNA editing can lead to the creation of a new exon in the human genome. Similarly to Alu retroposition and alternative splicing, RNA editing was not originally 'designed' to serve evolutionary purposes; it was rather recruited for this, probably serendipitously. This demonstrates that the creation of genomic novelty can be assisted by numerous molecular biological mechanisms, most of which were originally designed to function in other processes. The dynamism of our genome can, therefore, arise through surprising paths.
Materials and methods
Computational search for candidate edited Alus
ESTs and cDNAs from GenBank version 136 were aligned to the human genome (version hg16) to identify internal human exons that contain Alu elements, as described in Alu-containing exons were identified using blastn analysis against the Alu consensus with a threshold of 1E-10. Alus having AA/GT or AG/AT 3' ss/5' ss, which flank exons in the protein-coding region of the genes, were taken for further analysis. Only Alu-exons supported by multiple cDNAs and not containing stop codons (in the ESTs and cDNA) were further considered. Exons were manually screened to remove false computational predictions.
Oligonucleotide primers were designed to amplify (from human genomic DNA) a minigene that contains exons 7, 8, and 9 (and the introns in between) of NARF (GenBank: NM_012336). Each primer contained an additional extension encoding a restriction enzyme sequence. The PCR product of NARF (2.8 kb) was restriction digested and inserted between the KpnI/XhoI sites in the pEGFP-C3 vector, which contains green fluorescent protein (GFP; Clontech, Palo Alto, CA, USA).
Site directed mutagenesis
Overlapping oligonucleotide primers containing the desired mutations were used to amplify a mutation-containing replica of the wild-type minigene plasmid, using PfuTurbo DNA polymerase (Stratagene, La Jolla, CA, USA) (Additional data file 3). After PCR amplification the reaction was digested with DpnI restriction enzyme (New England Biolabs, Ipswich, MA, USA) for 1 h at 37°C, 1-3 μl of the reaction was transformed into the Escherichia coli XL-1 strain, and colonies were picked for Mini-prep extraction (Qiagen, Valencia, CA, USA). All plasmids were confirmed by sequencing.
Transfection, RNA isolation and RT-PCR amplification
293T cells were cultured in Dulbecco's modified Eagle's medium, supplemented with 4.5 g/ml glucose (Biological Industries, Bait-Haemek, Israel), 10% fetal calf serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 1 U/ml nystatin (Biological Industries, Bait-Haemek, Israel). Cells were grown on 6-well plates under standard conditions at 37°C with 5% CO2. Cells were grown to 60% confluence, and transfection was performed using FuGENE6 (Roche Diagnostics, Basel, Switzerland) with 1 μg of plasmid DNA. Cells were harvested after 48 h. Total RNA was extracted using TRIzol Reagent (Sigma-Aldrich, St. Louis, MO, USA), followed by treatment with 1 U of RNase-free DNase (Ambion, Austin, TX, USA). Reverse transcription (RT) was preformed on 2 μg total RNA for 1 h at 42°C using Oligo-dT reverse primer and 2 U of reverse transcriptase avian myeloblastosis virus (A-AMV; Roche Diagnostics, Basel, Switzerland).
The spliced cDNA products derived from the expressed minigenes were detected by PCR using the pEGFP-C3-specific reverse primer and an exon 7 forward primer (Additional data file 3). Amplification was performed for 30 cycles, consisting of 1 minute at 94°C, 45 s at 61°C, and 1.5 minutes at 72°C. The products were resolved on 1.5% agarose gel and confirmed by sequencing. Band quantification was performed by densitometry scanning of ethidium bromide stained gels, using ImageJ software .
For the NMD treatment, cells 48 h post-transfection were subjected to 100 μg/ml puromycin (Sigma-Aldrich, St. Louis, MO, USA) for 4 h before RNA extraction.
Analysis of RNA editing
Products from RT-PCR or from PCR obtained from commercial cDNAs (BioChain, Hayward, CA, USA) were separated by electrophoresis on 1.5% agarose gels. The appropriate PCR product was excised and the DNA was extracted and purified (Promega, Madison, WI, USA). Direct sequencing from both ends was done using the ABI PRISM (Applied Biosystems, Foster-City, CA, USA). The editing percentage from direct sequencing was calculated as for the forward primer and for the reverse primer; the presented percentages represent an average of three separated experiments or three independent amplifications. The nucleotides were quantified by the Discovery Studio (DS) Gene 1.5 program (Accelrys Inc., San Diego, CA, USA).
Additional data files
The following additional data are available with the online version of this paper. Additional data file 1 contains two figures showing semi-quantitative PCR analysis. Additional data file 2 contains alignment of AluSx between human, chimpanzee and rhesus macaque, and also the rhesus macaque sequence of AluSx and its upstream surrounding AluY sequence. Additional data file 3 is a table listing the primer sequences used in this research.
We thank Sergey Nemzer for his dedicated assistance. This work was supported by a grant from the Israel Science Foundation (1449/04 and 40/05), MOP Germany-Israel, GIF, DIP, and EURASNET. EE was supported by an Alon Fellowship at Tel Aviv University.
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