Precise repair of mPing excision sites is facilitated by target site duplication derived microhomology
© Gilbert et al. 2015
Received: 29 June 2015
Accepted: 28 August 2015
Published: 7 September 2015
A key difference between the Tourist and Stowaway families of miniature inverted repeat transposable elements (MITEs) is the manner in which their excision alters the genome. Upon excision, Stowaway-like MITEs and the associated Mariner elements usually leave behind a small duplication and short sequences from the end of the element. These small insertions or deletions known as “footprints” can potentially disrupt coding or regulatory sequences. In contrast, Tourist-like MITEs and the associated PIF/Pong/Harbinger elements generally excise precisely, returning the genome to its original state. The purpose of this study was to determine the mechanisms underlying these excision differences, including the role of the host DNA repair mechanisms.
The transposition of the Tourist-like element, mPing, and the Stowaway-like element, 14T32, were evaluated using yeast transposition assays. Assays performed in yeast strains lacking non-homologous end joining (NHEJ) enzymes indicated that the excision sites of both elements were primarily repaired by NHEJ. Altering the target site duplication (TSD) sequences that flank these elements reduced the transposition frequency. Using yeast strains with the ability to repair the excision site by homologous repair showed that some TSD changes disrupt excision of the element. Changing the ends of mPing to produce non-matching TSDs drastically reduced repair of the excision site and resulted in increased generation of footprints.
Together these results indicate that the difference in Tourist and Stowaway excision sites results from transposition mechanism characteristics. The TSDs of both elements play a role in element excision, but only the mPing TSDs actively participate in excision site repair. Our data suggests that Tourist-like elements excise with staggered cleavage of the TSDs, which provides microhomology that facilitates precise repair. This slight modification in the transposition mechanism results in more efficient repair of the double stranded break, and thus, may be less harmful to host genomes by disrupting fewer genes.
KeywordsmPing Excision site repair Target site duplication
Type II DNA transposable elements (TE) are present in most, if not all, eukaryotic genomes, but are especially abundant in plants where they play a role in genome evolution . Plant DNA TEs have been classified into superfamilies including hAT, MuDR/MU, CACTA, Mariner, and Harbinger/Pong . Each of these superfamilies is composed of autonomous elements that encode the proteins required for mobilization and non-autonomous elements that can only be mobilized in trans [3, 4]. Of special interest are the small (<500 bp) non-autonomous miniature inverted repeat TEs (MITEs). These are the most abundant TEs in the genome, often reaching thousands of copies, due to their ability for rapid proliferation [5–7]. The two best characterized MITE families, Stowaway and Tourist, have unique characteristics stemming from differences in their transposition mechanisms. Stowaway-like MITEs are mobilized by transposase proteins encoded by autonomous Mariner-like elements, produce a 2 bp target site duplication (TSD) upon insertion, and commonly leave small insertions or deletions (footprints) at their excision site . Tourist-like MITEs are mobilized by transposase proteins encoded by the autonomous PIF/Pong-like elements, produce a 3 bp TSD, and generally excise precisely leaving no footprints at their excision site .
DNA TEs and their associated MITEs are mobilized by a “cut and paste” mechanism in which transposase proteins bind to the terminal inverted repeats (TIRs), effectively positioning the catalytic domain for the DNA cleavage that is required for both excision and insertion . Staggered cleavage of the genomic DNA at the insertion site results in either a 5′ or 3′ overhang, both of which create small TSDs that flank the inserted elements. Based on the fact that Mariner-like and Stowaway-like elements have 2 bp TSDs, the transposase proteins likely produce a 2 bp overhang upon cleavage of the DNA . The PIF/Pong-like and Tourist-like elements have 3 bp TSDs, indicating cleavage by their encoded transposases produce a 3 bp overhang . Analysis of the excision sites of the elements can elucidate differences in the catalytic mechanism of their specific transposases. For example, the excision sites of the Ac and Ds elements in both plants and yeast demonstrate that their footprints are palindromic sequences from the flanking DNA, as opposed to pieces of the TE itself [12–14]. This suggests that this transposase cleaves at the end of the element, causing hairpin formation at the ends of the double stranded break. In contrast, the excision sites of Mariner/Stowaway-like elements contain footprints that often include some of the sequences of the element in addition to retaining the TSDs . This indicates that that the Mariner-like transposase cleaves with a staggered cut at the end of the TIR for excision, leaving behind the TSD and a short region of single stranded TIR .
Excision of these DNA TEs produces double stranded breaks that are repaired by the host DNA repair mechanisms. This can be accomplished using a complementary template for homologous recombination (HR) or by the non-homologous end joining (NHEJ) pathway . In plants, excision site analysis indicates that many of the repaired sites include insertions or deletions consistent with NHEJ [17–19]. In addition, yeast transposition experiments with the Ac element superfamily showed that repair of the double stranded break after excision required NHEJ proteins . This study also showed that microhomology (<6 bp) exposed by end processing between the two strands flanking the element is often used to facilitate repair . Differences in the proteins required for the repair of these ends may hint at the nature of the DNA breaks produced by the different transposases.
The focus of this study was to further characterize the transposition mechanism of the best studied Tourist-like MITE, mPing. In contrast to the previously mentioned elements, mPing excision sites are repaired precisely (leaving no element or TSD sequences). Based on these unique excision sites, we hypothesize that the mPing transposase proteins may cut at the TSD sequences adjacent to the element instead of within the element as seen for Mariner-like elements. Because the TSD sequences are identical, staggered cleavage at this location produces compatible sticky ends, providing microhomology for NHEJ that would easily restore the genome back to its original state before insertion of the element. Based on this hypothesis, we predict that alteration of mPing’s TSDs would alter the microhomology and reduce the effectiveness of NHEJ repair. Using a previously developed yeast transposition assay [20, 21], we tested the result of changing the TSDs for a Tourist-like MITE (mPing) and Stowaway-like MITE (OsMar 14T32 or the hyperactive OsMar 14T32-T7). By performing these assays in yeast strains with a defective NHEJ DNA repair pathway, we were able to distinguish between impaired element excision and DNA repair.
Results and discussion
NHEJ is used for excision site repair
In order to allow separate analysis of element excision and repair, we developed a yeast strain (DG21B9) that was capable of performing HR at the excision site (contained the ADE2* template), but also had an impaired NHEJ pathway (ku70). In this strain, the number of ADE2 revertant colonies was drastically reduced for both mPing and 14T32-T7 (Fig. 2), but was still higher than observed in the absence of a homologous template (Fig. 1). This drop in activity in this NHEJ deficient strain was consistent with the finding that NHEJ is the dominant pathway for repair of the excision sites. This together with the results for CB101 suggest that HR repair of these breaks functions as a backup to NHEJ and only occurs at about 10–20 % of the rate of NHEJ repair. Analysis of the DG219B ADE2 revertant mPing excision sites by digestion and sequencing showed that 100 % were repaired by HR (Fig. 2). Most of these excision sites (18/19) contained the ADE2* specific HaeIII site and the remaining site showed that ADE2* was used in such a way as to only remove the HpaI site and not add the HaeIII site (Fig. 2).
The ability to perform transposition assays in this NHEJ deficient strain (DG21B9) makes it possible to exclude the effects that the quality (i.e. blunt, staggered cut, presence or absence of microhomology) of the DNA break has on repair efficiency. This is because HR is less dependent on the immediate sequence at the end of the double stranded break, instead using sequences farther away from the cleavage site. Thus, this strain provides a method to differentiate whether a mutation affects the rate of NHEJ repair or the rate of excision.
TSD alteration disrupts element excision
To determine what role the TSDs play in mPing transposition, we performed yeast assays with mPing elements with altered TSDs. These experiments indicate that alteration of mPing’s TSDs also inhibits its transposition (Fig. 3b, Additional file 2a). Based on insertion site analysis, it was already known that T or A was acceptable at the middle position of the TSD . Changing the middle base to C or G (i.e. from TAA/TAA (5′/3′) to TCA/TCA) had a small effect with TGA/TGA TSDs producing more colonies than TCA/TCA TSDs (Additional file 2a). Changing the first base (i.e. GAA/GAA) or third base (i.e. TAC/TAC) caused a more severe drop in the number of ADE2 revertants. Changing all three bases completely disrupted the transposition of the element (Fig. 3b, Additional file 3a). To determine if this decrease in ADE2 revertants was caused by a drop in excision or from a decreased rate of repair, a subset of these altered elements were tested in the DG21B9 strain (HR only). If altering the TSDs to this extent only affects repair of the excision site and not excision itself, all of these altered TSDs would have the same ADE2 revertant rate as the control in DG21B9. However, almost no ADE2 revertant colonies were detected in the TAC/TAC or GCC/GCC TSD (5′/3′) combinations (Fig. 3b), indicating that these base changes inhibit the ability of the transposase proteins to catalyze excision. It is not clear if this is due to altered enzyme binding or if these bases are directly involved in the catalytic mechanism.
In addition to reducing the number of ADE2 revertant colonies by decreasing excision, sequencing the excision sites indicated that altering the TSDs can result in imprecise repair (Additional file 3b). The production of footprints was especially pronounced for the TAC/TAC TSDs, with 10 of 16 excision sites having indels. The inefficient excision of these altered elements may have resulted in strand cleavage in a non-standard position, creating double stranded breaks that were not as easily repaired.
mPing excision site repair is facilitated by TSD homology
Base pairing that results after 5′ or 3′ staggered cleavage of the mPing TSDs
Proposed middle base pairing
mPing target site duplications
Based on this model, we should see that some TSD combinations are more detrimental to excision site repair than others. In fact, analysis of additional combinations of mPing TSDs (TCA and TGA) showed that non-matching TSDs, that according to our model would result in T:C (pyrimidine:pyrimidine) or A:G (purine:purine) mismatches, produced fewer ADE2 revertants than TSD combinations that produce C:A (pyrimidine:purine) and T:G mismatches (pyrimidine:purine) (Additional file 4). Sequence analysis of the excision sites produced by selected TCA and TGA mismatched TSDs (Supplemental 4c) indicates that, for the most part, only one of the TSD sequences is left behind, as is expected of precise repair. However, about 14 % of the time both of the TSDs remained, leaving a footprint. This is in stark contrast to mPing elements with matching TSDs, which have never been observed to leave behind both TSDs upon excision (Fig. 2b) [20, 27].
It is not clear how common the excision site creation and repair mechanisms observed for mPing are present in other transposon superfamilies. Interestingly, alteration of the P-element TSDs from Drosophila showed a reduction in transposition activity . Also, a recent study with the Os3378 element (Mutator superfamily from rice) that also excises precisely, indicated that alteration of its TSDs reduces the rate of precise excision in yeast . Analysis of these elements in the CB101 and DG21B9 yeast strains would be able to determine if this is due to disruption of excision or excision site repair.
mPing TSDs do not influence target site insertion
Previous research has shown that mPing exhibits a strong preference for insertion into TAA or TTA sequences in the genome [20, 27, 30]. This is consistent with the findings of this study indicating that these sequences are required for efficient excision of the element. However, it was not known if the TSD sequences might play a role in the insertion preference of the element. To address this, 46 insertions of an mPing element with TCA/TCA TSDs were analyzed by sequencing transposon display PCR products . We observed that 45 of the insertions were in TTA or TAA, and only one was in TCA. This is consistent with the results observed for the wild type mPing element , suggesting that the TSDs do not play a large role in target site selection.
These results demonstrate a key difference in the transposition mechanisms used by the Tourist-like and Stowaway-like MITEs. While the excision sites of both mPing and 14T32 elements are primarily repaired by the NHEJ pathway in yeast, the 14T32 element appears to be more sensitive to alteration of NHEJ pathway genes. Our study suggests that the TSDs flanking both elements are required for their efficient excision. On the other hand, complementarity of the two TSDs was found only to be critical to the efficiency and precision of mPing’s excision site repair. Based on this finding, we conclude that the transposases that excise mPing, and presumably other Tourist-like MITEs, produce a staggered cut at the TSDs that provides microhomology that facilitates precise repair of the excision site.
Yeast strains and vectors
MATa ade2∆::hphMX4 his3∆1 leu2∆0 met15∆0 ura3∆0
MATa ade2∆::hphMX4 his3∆1 leu2∆0 met15∆0 ura3∆0 lys2∆::ADE2*
MATa rad50∆::kanMX4 ade2∆::hphMX4 his3∆1 leu2∆0 met15∆0 ura3∆0
MATa mre11∆::kanMX4 ade2∆::hphMX4 his3∆1 leu2∆0 met15∆0 ura3∆0
MATa ku70∆::kanMX4 ade2∆::hphMX4 his3∆1 leu2∆0 met15∆0 ura3∆0
MATa ku70∆::kanMX4 ade2∆::hphMX4 his3∆1 leu2∆0 met15∆0 ura3∆0 lys2∆::ADE2*
Saccharomyces cerevisiae strains, BY4741 (JIM17) or Yeast Deletion Project strains [32, 33] in the BY4741 background (JIM16, JIM22, JIM21), were adapted for the study by deleting the ADE2 gene using the hphMX4 (pAG32) cassette replacement technique  using the following primers: ADE2hphMX For-CAATCAAGAAAAACAAGAAAATCGGACAAAACAATCAAGTCCTTGACAGTCTTGACGTGC, ADE2hphMX Rev-ATAATTATTTGCTGTACAAGTATATCAATAAACTTATATACGCACTTAACTTCGCATCTG.
The partial ADE2 template (ADE2*) was synthesized with the following sequence 5′-TTTGGCATACGATGGAAGAGGTAACTTCGTTGTAAAGAATAAGGAAATGATTCCGGAAGCTTTGGAAGTACTGAAGGATCGTCCTTTGTACGCCGAAAAATGGGCACCATTTACTAAAGAATTAGCAGTCATGATTGTGAGATCTGTGAATGGCCTAGTGTTTTCTTACCCAATTGTAGAGACTATCCACAAGGACAATATTTGTGACTTATGTTATGCGCCTGCTAGAGTTCCGGACTCCGTTCAACTTAAGGCGAAGTTGTTGGCAGAAAATGCAATCAAATCTTTT-3′ and cloned between the BglII and HindIII sites of the pIS 385 disintegrator plasmid . To make the CB101 and DG21B9 yeast strains, this plasmid was then linearized with NruI (New England Biolabs, Massachusetts, USA) and transformed into the LYS2 locus of JIM17 and JIM21, respectively. Selection and screening were performed as described  to remove the URA3 selectable marker and identify transformants that maintained the genomic copy of the ADE2* template.
The pAG413 Pong ORF1, pAG415 Pong transposase L418A, L420A and pWL89A mPing plasmids were described previously . The pAG415 Osmar14 transposase was made by PCR amplification of the open reading frame from a previously described Osmar14 transposase plasmid  with the following primers Osmar 14 For – GGGGACAAGTTTGTACAAAAAAGCAGGCTTCATGCAAGAGTACGGCGTGTATGC, Osmar 14 Rev- GGGGACCACTTTGTACAAGAAAGCTGGGTCTTAAACTGCACTTGGTTGGCTAATGCT. The PCR product was inserted into the Gateway® pDONR™/Zeo vector using a BP clonase reaction (Life Technologies, Carlsbad, CA), then transferred into pAG415 GAL ccdb using an LR clonase Reaction (Life Technologies, Carlsbad, CA). The reporter plasmids pwL89A 14T32 and 14T32-T7 were described previously [14, 21]. TSD mutations were made to the MITEs mPing and Osmar 14T32-T7 by PCR amplification using primers altered at the TSD (underlined positions indicate TSD), for example:
mPing TGA For – AGTCTCTACAATTGGGTAAGAAAACACTAAACCGTTGA GGCCAGTCACAATGGGGGTTTC
mPing TGA Rev – ACTAAAGAATTAGCAGTCATGATTGTGAGGTCTGTCA GGCCAGTCACAATGGCTAGTGTC
14T32 AT For –CTAAAGAATTAGCAGTCATGATTGTGAGGTCTGTTAT CTCCCTCCGTCCCAGAAAGAAGG, and
14T32 AT Rev – GTCTCTACAATTGGGTAAGAAAACACTAAACCGTTAT CTCCCTCCGTCCCAGAAAGAAGC
The resulting PCR products were purified using a clean and concentrate kit (Zymo Research, Irvine, CA) and then transformed together with HpaI digested pWL89A using the LiAc method . Mutations were verified by sequencing PCR products or purified plasmids with following primers that flank the ADE2 HpaI site: ADE2-CF-GGGTTTTCCATTCGTCTTGAAGTCGAGGAC and ADE2-CR-CATTTCCACACCAAATATACCACAACCGGGA.
Yeast transposition assay
Transposition assays were performed using two techniques depending on the relative transposition rates. For low activity combinations (i.e. Figs. 1, 3 and 4b, and Additional files 3 and 4) transformed yeast were grown in 5 ml of selective media (2 % dextrose) at 30 °C for 48 h, centrifuged to concentrate the culture, plated on selective 2 % galactose plates (150 mm) lacking adenine, and incubated at 30 °C for 15 days as described . For experiments with higher rates of transposition (i.e. Fig. 2, 5a and Additional file 1), a 3 ml liquid (2 % dextrose) culture was grown for 24 h at 30 °C and 100 μl was plated on selective 2 % galactose plates (100 mm) and incubated at 30 °C for 10 days. A time course of this procedure showed that the number of ADE2 revertant colonies had a linear rate of appearance (Additional file 1). Dilution series of the liquid cultures plated on complete YPD media were used to determine the total number of cells plated. Transposition rate was calculated by dividing the number of ADE2 revertant colonies by the total number of yeast plated.
Excision site analysis
ADE2 revertant colonies were suspended in 20 μl of 1 unit/μl Zymolyase (Zymo Research, Irvine, CA) and incubated for 15 min at 37 °C to lyse the yeast cells. PCR amplification of the excision site was performed using the ADE2-CF and ADE2-CR primers in a 20 μl reaction with 2 μl of lysed yeast as the template. PCR products were diluted and digested with HpaI or HaeIII (New England Biolabs, Massachusetts, USA) and then analyzed by agarose gel electrophoresis. PCR products were treated with ExoSAP-IT (USB Corporation, Ohio, USA) per instruction of the manufacturer prior to sequencing.
Insertion site analysis
Transposon display analysis of mPing insertion sites were performed as described previously [20, 30, 31]. Individual bands were sequenced after cutting them from the gel and performing PCR amplification with the transposon display primers.
Miniature inverted repeat transposable element
Target site duplication
Terminal inverted repeat
Non-homologous end joining
We thank Dr. Guojun Yang for providing the 14T32 and 14T32-T7 constructs. We also thank Dr. Clifford Weil for advice and Christie Bradshaw for technical assistance. We also thank the many undergraduates including Tyler Shealy, Wesley Tindal, Lee B. Sharpe, Lucy Fu, and the spring 2009 HHMI Dynamic Genome class (Justin Brown, Charles B. Allen Jr., Krelin Naidu, Ashley Turner) that helped with aspects of the project. Portions of this research were funded by a grant from the Howard Hughes Medical Institute to Susan R. Wessler. David Gilbert was funded by USCA Connections and USC Magellan grant.
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