WO2014033644A2

WO2014033644A2 - Methods of nuclease-based genetic engineering

Info

Publication number: WO2014033644A2
Application number: PCT/IB2013/058083
Authority: WO
Inventors: Yi Yang; Marcello Maresca
Original assignee: Novartis Ag
Priority date: 2012-08-28
Filing date: 2013-08-28
Publication date: 2014-03-06
Also published as: WO2014033644A3; US9567608B2; US20160032321A1

Abstract

The present invention relates to genetic techniques employing the direct Iigatation of an external DNA fragment generated in situ by the same ZFNs that target the genome. ObLiGaRe, i.e., the obligated ligation-gated recombination, is a new method for genetic engineering using custom designed nucleases, and a strategy of site-specific gene insertion utilizing the NHEJ pathway. It applies a similar logic to the one used in unidirectional loxP sites(Oberdoerffer et al., 2003) but maintains all the advantages and flexibility of CDNs.

Description

METHODS OF NUCLEASE-BASED GENETIC ENGINEERING

BACKGROUND OF THE INVENTION

[0001] The development of CDNs including ZFNs and TALENs has made it possible to perform precise genetic engineering in many cell types and species(Bibikova et al., 2003;Christian et al., 2010;Hockemeyer et al., 2009;Kim et al., 1996;Meyer et al., 2010;Moehle et al., 2007;Porteus and Baltimore, 2003;Urnov et al., 2010). These are hybrid endonucleases consist of a Fokl nuclease domain and a DNA binding domain assembled from optimized DNA binding modules that are specific for either single nucleotide (for TALENs) or trinucleotide motifs (for ZFNs). Once introduced in cells, these enzymes generate a DSB in the genome at or near the desired modification site. This event induces the natural DDR process to mend the breakage(Rouet et al., 1994). The primary pathway is NHEJ in which the two ends are processed and ligated together with nucleotide insertions and deletions. Though highly efficient, this mechanism can only produce functional knockout alleles that are often heterogeneous and difficult to isolate without clonal selection. Accurate gene modification relies on HR in which exogenous DNA fragments flanked by homology sequences around the DSB site can be copied faithfully from a template with defined boundaries (Rouet et al., 1994) .

[0002] Targeted gene modification has been almost exclusively mediated by homologous recombination. Though CDNs have made gene targeting feasible in cell lines that have low intrinsic HR efficiency, NHEJ is still the dominant DSB repair pathway. As a result, KO alleles generated by NHEJ are obtained at a much higher frequency than Kl alleles generated by HR. A deficiency in NHEJ can significantly promote HR as seen in E.coli in which NHEJ is neglectable(Liang et al., 1996; aresca et al., 2010) .

SUMMARY OF THE INVENTION

[0003] We have successfully applied ZFNs on generating knockout or knock-in alleles directly in mouse zygotes as reported in the literature(Cui et al., 201 1 ;Meyer et al.,

2010). While optimizing gene targeting conditions, we observed that a donor plasmid can be "ligated" into the genome if it contained the same ZFN recognition sites. It had been reported that short double strand DNAs with 5' overhangs could be ligated to the complementary ends generated after ZFN digestion(Orlando et al., 2010). This observation has not been further explored probably because it requires the knowledge of the overhangs generated by ZFNs and its application is limited to small

oligonucleotide insertions(Orlando ef al. , 2010). Furthermore, it had also been shown that sometimes donor molecules including single strand oligodeoxynucleotides

(ssODNs)(Chen et al., 2011 ;Radecke et al., 2010) and larger external linear sequences could be captured at DSB sites generated by ZFNs(Fung and Weinstock, 2011 ;Li et al., 2011 ;Mittelman et al., 2009). This feature has been harnessed to track "off-target" effects of the homing endonuclease l-Scel and ZFNs(Petek et al. , 2010). Based on these reports and our own observation in mouse embryos, we surmised that it should be possible to directly ligate an external DNA fragment generated in situ by the same ZFNs that target the genome.

[0004] We took advantage of the obligated herterodimeric property of the CDNs (Doyon et al., 201 1 jMiller et al. , 2007;Ramalingam et al, 2011 ;Szczepek et al, 2007) and designed a strategy to achieve efficient and precise gene targeting without homology in the donor plasmid. We named this method ObLiGaRe (Obligated Ligat ion-Gated Recombination) to reflect the etymologic meaning of the Latin verb obligare (to ligate head to head). It is broadly applicable in different cell lines and provides an additional approach for genetic engineering.

[0005] In this study we developed ObLiGaRe, a strategy of site-specific gene insertion utilizing the NHEJ pathway. It applies a similar logic to the one used in unidirectional loxP sites(Oberdoerffer et al, 2003) but maintains all the advantages and flexibility of CDNs. The alternate design of the ZFNs site that we insert in the vector is necessary and sufficient to achieve precise end joining of the vector in the genomic ZFN site. Though less frequent, we did observe that aberrant joining products involving small deletions or insertions at the junctions. We speculated that these might result from processing alternative overhang types generated by the same ZFNs that were mismatched (Hockemeyer er a/., 2009;Orlando et al. , 2010;Smith et al, 2000;Zeevi et al, 2008) . We never observed precise insertion of the vector at targeted genomic locus when a ZFNs site identical to the one present in the genome is introduced in the vector. In fact no integration of a surrogate reporter plasmid bringing a ZFNs site identical to the one in the genome was observed in a recent study(Kim et al, 201 1). ObLiGaRe eliminates cloning homology arms into the donor vector and does not require any previous knowledge of the overhangs generated by specific CDNs.

[0006] ObLiGaRe is applicable with both ZFNs and TALENs (Supplementary Fig. 1) and can be used as a high throughput method for screening potent CDNs replacing the current Cel-I assay (Reyon et al, 2012) It works in a wide variety of cell types including KBM7 and C2C12 cells in which precise gene insertion has not be demonstrated. We are currently testing whether it can be used in primary, non replicating cells in which NHEJ seems to be the predominant pathway to repair DSBs. We are also exploring whether it can work in embryos of mice and zebrafish. Finally we inserted the largest construct in the genome by ZFN to date (Fig. 3) and we predict that we can use it to deliver even larger construct such as BACs into a pre-defined genomic locus, which is very challenging, if not impossible, to achieve via HR.

[0007] Beyond the practical value of our method, it can be used as a new tool in the study of NHEJ and the crosstalk between NHEJ and HR. Although similar strategies were reported using the l-Scel homing endonuclease(Certo et al. , 201 1), our strategy allows us to track any endogenous locus that can be targeted by ZFNs. We are interested in using this reporter system to monitor differential utilizations of NHEJ and HR in cells before and after oncogenic transformation. We are also continuing to identify chemical and genetic modulators that influence the cells to choose NHEJ or HR.

BRIEF DESCRIPTION OF THE DRAWINGS

[0008] Figure 1 ObLiGaRe at AAVS1 locus.

[0009] (a) Schematic illustration of ObLiGaRe strategy. ZFN recognition sites are indicated as grey and blue circles with the corresponding sequences displayed in the same color scheme. The predicted joining sequences between the vector and the genome are shown. The insertion of the vector in the AAVS1 locus will cause a size shift from 6.7 kb (WT) to 14.2 kb (LP) of a Hindlll (H) digested fragment. AAVS1 internal probe (int) and vector specific probe (CM) are indicated in the map at the hybridization sites.

[00010] (b) Southern blot of 4 puro resistant colonies after ObLiGaRe at AAVS1 locus in HCT116 (upper), RKO (middle) and KBM-7 (lower) with int probe (left) and CM probe (right) with sequences at the 5' and 3' junctions corresponding to each clones listed on the right. Insertions are indicated in red, deletions are indicated as red dotted lines.

[00011 ] Figure 2 ObLiGaRe at PTEN locus.

[00012] (a) Strategy for targeting human PTEN (left) and PTENP1. PTEN ZFN recognition sites are indicated as orange and cyan circles with the corresponding sequences displayed in the same color scheme. The predicted joining sequences between the vector and the genome are indicated. The insertion of the vector will cause a size shift of a BsrGI (B) digested fragment from wild type of 2.4 kb (WT) to the ligation product of 7.8 kb (LP) at PTEN locus and 25.6 kb (WT) to 31 .0 kb (LP) at PTENP1 locus. AAVS1 internal probe (int) and vector specific probe (CM) are indicated in the map at the hybridization sites.

[00013] (b) Southern blots using probes specific for PTEN (PT, left), PTENP1 (P1 middle), and the vector (CM, right) for 4 G418 resistant colonies. The sequence of the 5' junction between PTEN or PTENP1 and mCherry are indicated in the table. Insertions are indicated in red where "ins" represents a 224bp insertion.

[00014] Figure 3 ObLiGaRe in C2C112 and MEF cells.

[00015] (a) Strategy for targeting Nras locus in MEF and C2C12 cells. Nras ZFN sites are indicated as violet and red circles with the corresponding sequences displayed in the same color scheme. The predicted joining sequences between the vector and the genome are shown. Primers for PCR detection of the junctions and probes (CM and NR) are indicated. The insertion of the vector will cause a size shift of an Ndel (N) digested fragment from wild type of 6.2 kb (WT) to the ligation product of 11.6 kb (LP) at Nras locus. AAVS1 internal probe (int) and vector specific probe (CM) are indicated in the map at the hybridization sites.

[00016] (b) Southern blot for 4 C2C12 clones expressing mCherry. LP indicates the expected ligation product band upon integration of the vector in the genome.

[00017] (c) Genomic PCR products amplified from pools of MEFs after transfection with ObLiGaRe donor alone (V) or co-transfection with ObLiGaRe donor and Nras ZFNs

(V+l). P1 -P2 primers amplify the 5' junction and P3-P4 primes amplify the 3'junction.

The table lists the sequences of 5' and 3' junctions from pooled MEF cells obtained by cloning the genomic PCR products into TOPO TA vectors followed by sequences.

Deletions are indicated as red dotted lines and insertion in red capital letters.

[00018] Figure 4 Introduce a 15 kb inducible gene expression cassette in AAVS1 locus by single step ObLiGaRe.

[00019] (a) Strategy to introduce an inducible gene expression cassette. ZFN cutting sites are the same as in Figure 1 . The expression of rtTA is controlled by the constitutive CAG promoter while GFP is under the doxycycline responsive promoter (tetO). The STOP sign indicates a transcription termination cassette. Int and CM represent the probe for Southern blot. P1 -P2 and P3-P4 are PCR primers used to amplify the 5' and 3' junctions. K: Kpnl.

[00020] (b) Southern blot of 8 positive clones is showed with both internal (int) and vector specific probe (CM). LP product indicates the expected ligation product upon vector integration. The sequence for 5' and 3' junction of the 8 clones are reported in the table on the right with dotted lines indicate deletions.

[00021 ] (c) GFP fluorescence is detected by fluorescence microscopy in cells from Clone No. 6 without (-) and with (+) 48 hr treatment of 1 g/ml doxycycline (dox).

[00022] Figure 5 ObLiGaRe is mediated via NHEJ.

[00023] (a) Illustration of the reporter DGF cassette in the AAVS1 locus. ZFN sites are the same as in Figure 3. A functional GFP is generated after HR using the HA plasmid as donor, while a functional mCherry is inserted upon ObLiGaRe using the ObLiGaRe donor. The two donors are about the same size.

[00024] (b) Determination of fluorescent cells number after co-transfection of Nras ZFN, ObLiGaRe and HA donors by FACS. Detection of GFP and mCherry cells were gated using parental cells (WT, left) which did not show any fluorescent cells upon co- transfection. When the reporter cell line was contrasfected with the 3 constructs, GFP and mCherry cells were shown in their corresponding gates (DGF, right).

[00025] (c) Representation of the percentage of GFP and mCherry positive cells out of total live cells in WT HCT116 cells, reporter HCT1 16 cells, without any treatment (DGF) or after treatment with 10 M Nu7026 or 4 mM Caffeine. Error bars: standard deviation; n=3.

[00026] Figure 6 ObLiGaRe using AAVS1 TALEN.

[00027] (a) Schematic illustration of ObLiGaRe strategy at PPP1 R12C (AAVS1) locus with TALENs. TALENs recognition sites are indicated as grey and blue circles connected with small arrows (cutting sites). The DNA sequence of AAVS1 specific

TALENs site (wt) and the ObLiGaRe TALENs site (iv) are shown. The predicted joining sequences after precise end joining between the vector and the genome are indicated.

[00028] (b) Southern blot of 6 puromycin resistant clones after ObLiGaRe. LP indicates the predicted ligation product. The probes are the same as used in Fig. 1. The 5' and 3' junction sequences of the 6 clones are in the tables on the right. S: Sphl.

[00029] Figure 7 Generate a reporter cell line for monitoring HR vs. ObLiGaRe.

[00030] (a) Strategy of inserting the DGF reporter at the AAVS1 locus. Primers used for PCR screening (P1 -P2) and probe for Southern blot (int) are reported in the map.

[00031 ] (b) Genomic PCR screening of 15 puromycin resistant colonies for the insertion of the puro cassette at PPP1 R12C locus.

[00032] (c) Southern blot of the seven clones identified after PCR screening. WT indicates the expected wild type band upon Hindlll (H) digestion. HRP indicates the expected homologous recombination product upon correct integration at PPP1 R12C locus. Clone#10 was used for the experiments described in Fig. 5.

DETAILED DESCRIPTION OF THE INVENTION

[00033] We have successfully applied ZFNs on generating knockout or knock-in alleles directly in mouse zygotes as reported in the literature(Cui et al., 2011 ;Meyer ef al., 2010) . While optimizing gene targeting conditions, we observed that a donor plasmid can be "ligated" into the genome if it contained the same ZFN recognition sites. It had been reported that short double strand DNAs with 5' overhangs could be ligated to the complementary ends generated after ZFN digestion(Orlando et al., 2010). This observation has not been further explored probably because it requires the knowledge of the overhangs generated by ZFNs and its application is limited to small

oligonucleotide insertions(Orlando et al. , 2010). Furthermore, it had also been shown that sometimes donor molecules including single strand oligodeoxynucleotides

[00034] We took advantage of the obligated herterodimeric property of the

CDNs(Doyon et al., 201 1 ;Miller et al., 2007;Ramalingam et al., 2011 ;Szczepek et al., 2007) and designed a strategy to achieve efficient and precise gene targeting without homology in the donor plasmid. We named this method ObLiGaRe (Obligated Ligation- Gated Recombination) to reflect the etymologic meaning of the Latin verb obligare (to ligate head to head). It is broadly applicable in different cell lines and provides an additional approach for genetic engineering.

[00035] In this study we developed ObLiGaRe, a strategy of site-specific gene insertion utilizing the NHEJ pathway. It applies a similar logic to the one used in unidirectional loxP sites(Oberdoerffer et al. , 2003) but maintains all the advantages and flexibility of CDNs. The alternate design of the ZFNs site that we insert in the vector is necessary and sufficient to achieve precise end joining of the vector in the genomic ZFN site. Though less frequent, we did observe that aberrant joining products involving small deletions or insertions at the junctions. We speculated that these might result from processing alternative overhang types generated by the same ZFNs that were mismatched (Hockemeyer et al,, 2009;Orlando et al, , 2010;Smith et al, 2000;Zeevi et al., 2008) . We never observed precise insertion of the vector at targeted genomic locus when a ZFNs site identical to the one present in the genome is introduced in the vector. In fact no integration of a surrogate reporter plasmid bringing a ZFNs site identical to the one in the genome was observed in a recent study(Kim et al., 201 1). ObLiGaRe eliminates cloning homology arms into the donor vector and does not require any previous knowledge of the overhangs generated by specific CDNs.

[00036] ObLiGaRe is applicable with both ZFNs and TALENs (Supplementary Fig. 1) and can be used as a high throughput method for screening potent CDNs replacing the current Cel-I assay (Reyon et al. , 2012) It works in a wide variety of cell types including KBM7 and C2C12 cells in which precise gene insertion has not be demonstrated. We are currently testing whether it can be used in primary, non replicating cells in which NHEJ seems to be the predominant pathway to repair DSBs. We are also exploring whether it can work in embryos of mice and zebrafish. Finally we inserted the largest construct in the genome by ZFN to date (Fig. 3) and we predict that we can use it to deliver even larger construct such as BACs into a pre-defined genomic locus, which is very challenging, if not impossible, to achieve via HR.

[00037] Beyond the practical value of our method, it can be used as a new tool in the study of NHEJ and the crosstalk between NHEJ and HR. Although similar strategies were reported using the l-Scel homing endonuclease(Certo et al. , 201 1), our strategy allows us to track any endogenous locus that can be targeted by ZFNs. We are interested in using this reporter system to monitor differential utilizations of NHEJ and HR in cells before and after oncogenic transformation. We are also continuing to identify chemical and genetic modulators that influence the cells to choose NHEJ or HR.

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Example 1 : Precise end-joining by ObLiGaRe.

[00078] In order to directly ligate an exogenous DNA fragment into the genome, we initially introduced ZFN binding sites in a donor plasmid with the same orientation as in the genome. However we found this strategy often yielded unpredictable products presumably because the same ZFN binding sites were produced after ligation which could then be repetitively digested, a process that could stimulate end recessing before joining (Pruett-Miller et al., 2008) . One essential requirement for ZFN-mediated site- specific digestion using obligated heterodimers is that a pair of ZFNs needs to form heterodimers through the modified Fokl nuclease domain after binding to their targeted DNA sequences on the opposite strands. We thought that if we altered the orientation of the genomic ZFN recognition sequences in the donor plasmid we could lock the ligation product in a palindrome of identical half ZFN recognition site which would be no longer sensitive to the same obligated heterodimeric ZFN pairs. We used the well- characterized AAVS1 ZFN binding sites (located in the second intron of

PPP1 R12C)(Hockemeyer et al., 2009) to illustrate this design principle (Fig. 1a). Here we inverted the two half AAVS1 ZFN binding sites in the vector without changing the orientation of the linker region (Fig. 1a, ObLiGaRe donor). The AAVS1 ZFNs cut both the genome and the donor plasmid to produce complementary overhangs. After ligation, the newly formed junctions are resistant to further digestion by AAVS1 ZFNs.

[00079] To test this hypothesis we constructed a vector containing the modified AAVS1 ZFN site followed by a promoterless T2A-puro cassette. Precise ligation of this cassette into the AAVS1 site in the genome would render the cells resistant to puromycin. We also included a constitutive GFP reporter driven by CAG promoter(Xu et al., 2001) in the vector to track the cells transfected with the plasmid. We transfected the donor plasmid into HCT116 cells either with or without the plasmids encoding AAVS1 ZFNs and observed an increase in the number of puromycin resistant colonies when the donor plasmid was co-transfected with the plasmids encoding AAVS1

ZFNs(data not shown) . We randomly isolated four puromycin resistant, GFP positive clones and examined the vector integration by Southern blot. All four clones were heterozygous insertions of the vector as indicated with an AAVS1 locus specific probe (int probe, Fig. 1 b). In addition, we did not observe random insertions of the vector in the genome when using a vector specific probe (CM probe, Fig. 1 b). We then amplified the integration junctions by PCR and sequenced the PCR products. We found that 3 out of 4 clones had perfectly ligated junctions as predicted and one of them had a two nucleotides insertion in the linker region at the 5' junction (Fig. 1 b). Similar results were obtained in RKO cells (Fig. 1 b). Interestingly, one of the RKO clones turned out to be homozygous for a single copy vector insertion (clone #2). One clone (clone #4) was homozygous for a bigger insertion which might contain more than 1 copy of the vector.

[00080] We then tested ObLiGaRe in KBM7 cells. KB 7 is a close to haploid human myeloid leukemia cell line in which gene targeting has not been reported(Andersson et al., 1995;Carette et al., 2009). We co-transfected the donor plasmid with plasmids encoding AAVS1 ZFNs into KBM7 cells. Since the transfection efficiency was low we sorted GFP positive cells by FACS and subjected them for puromycin selection. We characterized 4 puromycin resistant clones and found 3 had correct insertions at the

AAVS1 locus with no detectable random insertions as judged by Southern blot (Fig. 1 b). Interestingly, the sequences of the junctions were very heterogeneous and often involved deletions probably between potential micro-homologies (Fig. 1 b). It's important to add that the KB 7 resistant clones might have be originated from different cells as indicated by the appearance of additional bands and junctions sequences in the same clone (Fig. 1 b).

[00081 ] To determine whether ObLiGaRe is restricted to the AAVS1 locus and/or AAVS1 ZFNs, we used PTEN specific ZFNs to insert a vector containing a promoterless T2A-mCherry cassette and a CAG-neo selection marker into the PTEN locus in HCT1 16 cells. Human genome contains a PTEN pseudogene, PTENP1 (Poliseno et al.,

2010)which is also targeted by the PTEN ZFNs. We isolated 4 G418 resistant clones and examined integration sites at both PTEN and PTENP1 loci by Southern blot. All clones had an insertion of the vector in PTEN locus, 2 are heterozygous (clones #1 & 3, Fig. 2b) for the insertion while 2 clones had an insertion on both alleles of PTEN (clones # 2 & 3, Fig. 2b). Clone #2 had an insertion of one copy of the vector in one allele and a larger insertion in the other allele as indicated by the presence of a higher band (Fig. 2b). It also contained an insertion in PTENP1 locus (Fig. 2b). Interestingly, clones #1 had extra inserts in the genome as detected by the vector specific probe (CM probe) which might have been the result of either random insertion or insertion in other unidentified locus cleaved by PTEN ZFNs. However all the clones showed the precise predicted sequences at the junction between PTEN and T2A-cherry while clone #2 presents additional insertions at the junctions of the second targeted allele of both PTEN and PTENP1 (Fig. 2b table).

[00082] In order to test whether ObLiGaRe does not rely on any specific mutations in HCT116 and RKO cells which are known to be defective in DNA mismatch

repairs(Brown et al., 2003), we decided to use a pair of ZFNs to target exon3 of Nras gene in mouse myoblast C2C12 cells (Fig. 3a). We co-transfected C2C12 cells with either Nras ZFNs alone or Nras ZFNs plus an ObLiGaRe vector containing a promoterless T2AmCherry cassette with a PGKneo selection marker and determined targeted integration in 4 randomly selected G418 resistant, mCherry fluorescent clones by Southern blot. All the clones showed targeted insertion of the vector at Nras locus as well as additional genomic insertion events except clone #4 (Fig. 3b). We sequenced the junctions between Nras and mCherry and confirmed that all 4 clones had precise end joining (data not shown). Finally, we applied the same strategy to target primary mouse embryonic fibroblast (MEF) cells. Since we could not perform clonal selection with MEFs, we pooled cells 3 days after transfection. We genotyped the pools by genomic PCR using primers that were specific for both 5' and 3' junction. We observed PCR products expected for correct integration only in cells transfected with ObLiGaRe vector and Nras ZFNs pair (Fig. 3c). We cloned the PCR products in a TOPO TA vector and sequenced 6 clones for each end. Majority of the sequences were the precise end joining sequence at both 5^' and 3' ends (Fig. 3c).

[00083] Insertion of a 15 kb inducible gene expression cassette by ObLiGaRe at the AAVS1 locus.

[00084] Previously inducible transgene expression from the AAVS1 locus was achieved by targeting a tetracycline controlled responder in the AAVS1 locus followed by delivery of the reverse tetracycline transcription activator (rtTA) by lentiviral transduction or by gene targeting in a second allele of AAVS1 (DeKelver et al.,

2010;Hockemeyer et al., 2009). We decided to determine whether ObLiGaRe could facilitate insertion of the entire 15kb transgenic cassette into the AAVS1 locus in a single step which has not been reported before. We inserted the modified AAVS1 ZFN site at the 5' of an inducible cassette that contains all the components for doxycycline- induced transgene expressions in mice (Yi Yang, unpublished data) and co-transfected it with AAVS1 ZFNs in HCT116 cells. We screened 18 puromycin resistant clones for correct integrations by PCR and identified 14 have expected PCR product (data not shown). We chose 8 positive clones for further analysis by Southern blot and showed all of them had correct integration (Fig. 4b). We observed precise end joining in the majority of 8 clones tested at both 5' and 3' junctions (Fig. 4b). Furthermore we could induce GFP expression by adding doxycycline in all 8 clones as shown with clone# 6 (Fig. 4c).

Example 2: Mechanism of ObLiGaRe

[00085] We speculated that ObLiGaRe might be mediated by NHEJ since it dose not require any homology between the donor and the target. To test this hypothesis, we inserted a defective GFP (DGF) harboring a mouse Nras ZFN recognition site at the AAVS1 locus by HR in HCT116 cells (Fig. 5a). We chose one of the correctly heterozygous targeted clones as a reporter (Clone#10 Supplementary Fig. 2) . We co- transfected Nras ZFNs with 2 plasmids to measure ObLiGaRe vs. HR simultaneously. One had 500bp homology arms to the DGF and could reconstitute functional GFP by HR; the other had a modified Nras ZFNs site 5' to a promoterless T2A-mCherry cassette which would lead to mCherry expression upon insertion by ObLiGaRe (Fig. 5a). We FACS sorted cells and detected 6 times more mCherry positive cells than GFP positive cells in the reporter line but not the parental line (Fig. 5b). All clones derived from the mCherry fluorescent cells presented precise end joining of the mCherry with the defective GFP (data not shown). Interestingly, when we added 10 M Nu7026(Hollick et al., 2003) to the medium, a potent inhibitor of DNA-PK, the number of mCherry fluorescent cells was significantly reduced whereas that of GFP fluorescent cells was increased (p<0.001 , Fig. 5c), suggesting ObLiGaRe requires DNA-PK, a key component of NHEJ. On the other hand the addition of 4 mM caffeine to the medium, a non specific inhibitor of the ATM and ATR kinases which are involved in HR pathway(Sarkaria et al., 1999),causes a significant increase of mCherry fluorescent cells with a decrease of GFP fluorescent cells (p<0.001 , Fig. 5c). We plan to use our reporter system to study the balance between homologous recombination and NHEJ. Example 3: Cell culture and transections

[00086] HCT1 16 and RKO (American Type Culture Collection, VA) were cultured in McCoy's 5A medium (Life Technologies, CA) supplemented with 10% fetal bovine serum (Life Technologies, CA). C2C12 (American Type Culture Collection, VA) were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum (Life Technologies, CA). KBM7 cells, were cultured in IMDM Glutamax (Life

Technologies, CA) supplemented with 10% fetal bovine serum. HCT116, RKO, C2C12 and MEFs cells were plated in 6-wells plates (50-80% confluence) and transfected with Lipofectamine LTX according to manufacture's instructions. Briefly, 2 g of ZFNs plasmid and 0.5 g of ObLiGaRe vector were mixed with 12 I of Lipofectamine LTX reagent and co-transfected into 5* 10⁵ cells. 2 days after transfection cells were transferred to 15cm plates and subject to either puromycin (Life Technologies, CA) selection (0.5 g/ml) or G418 (Life Technologies, CA) selection (100 g/ ml ) the following day. GFP positive, puromycin resistant clones were harvested after 15 days of selection. 10⁷ KBM7 cells were electroporated with 8 g of ZFN plasmids and 2 g of ObLiGaRe donor using Gene Pulserll electroporation system (Bio-Rad, Melville, NY) with electrical settings of 250 V and 950 pF. GFP positive cells were sorted by FACS (Y- Aria Becton Dickinson, NJ) two days after transfection and 100 GFP positives cells were seeded in 12 wells and selected with puromycin (1.0 g/mL); GFP positives, puromycin resistant clones (pools) were harvested after 10 days of selection.

Example 4: Comparing Homologous Recombination to ObLiGaRe:

[00087] 2* 10⁵ reporter cells were transfected with 0.2 g ZFN plasmid, 0.3 g ObLiGaRe donor (Ob) and 0.5 g HA donor plasm ids (HA), using 4 L

Lipofectamine LTX in 12 wells.

[00088] The percentage of GFP and mCherry positive cells was measured using FACS cantoll flow cytometer (Becton Dickinson, NJ) 4 days after transfection.

[00089] Treatment with Nu7026 (Sigma Aldrich, MO) was started one day before transfection with a final concentration of 10 M Nu7026 (from a 10 mM stock solution in DMSO) and was continued for 2 days after transfection.

[00090] ANOVA and Tukey's HSD tests were adopted to perform statistical analysis using R statistics software.

[00091 ] ZFN expression plasmids

[00092] ZFNs against the human PTEN and Nras loci were designed and

manufactured by Sigma-Aldrich. ZFNs and TALENs used in this work carried obligate heterodimer forms of the Fokl endonuclease. AAVS1 ZFNs and TALENs were made according to (Hockemeyer et al , 2009;Hockemeyer et al., 201 1). The ZFN expression constructs were obtained by Sigma-Aldrich but modified to insert both ZFNs in one plasmids using ad h.o.c. recombination (Maresca ef al. unpublished).

[00093] PCR primers:

Southern blot internal probe for 5 '-tttctgtctgcagcttgtgg ⁵ '-gggtggaggggacagataaa

AA VS1

AA VS1 5' ObLiGaRe 5 '-cccetatgtccacttcagga ' - tgaggaagagttcttgcagct

AA VS1 3' ObLiGaRe '- tggctcattaggg atgctt 5 '- acaggaggtgggggttagac

Southern blot probe for CM 5'- tcactggatataccaccgttg 5 ' - tggtctgacagttattacgcc

Southern blot probe for PTEN 5'- gctgcagtccattgagcata 5 ' - gctgtggtgggttatggtct

Southern blot probe for hPTENPl 5'- attcgtcttctccccattcc 5 ' - gtgaattgctgcaacatga hPTEN 5' ObLiGaRe 5'- aagaccataacccaccacagc 5 ' - ttggtcaccttcagcttggc hPTENPl 5' ObLiGaRe 5'- aaagacattatgacaccgcc 5 '- ttggtcaccttcagcttggc

Southern blot probe for Nras 5'- gttccagtgccctgttcaat 5 '- cacaaccacttcccgaaact

Nras 5' ObLiGaRe 5'- ctgttagcgggttgagggta 5 '- aagcgcatgaactccttgat

Nras 3' ObLiGaRe 5'- attaatgcagctggcacgac 5 ' - tggcaaatacacagaggaacc

Southern blot probe for neo 5'- gatcggccattgaacaagat 5 '- gcgataccgtaaagcacgag

Claims

1. A method for providing site-specific gene insertion, said method employing obligated ligation-gated recombination.

2. The method of claim 1 whereby zinc finger nucleases (ZFNs) are used as enzymes for gene insertion.

3. The method of claim 1 whereby transcription activator-like effector nucleases (TALENs) are used as enzymes for gene insertion.

4. A method for engineering DNA damage repair (DDR) caused by a DNA double-strand break (DSB) in a target genome, said method employing obligated ligation-gated recombination.

5. The method of claim 4 whereby zinc finger nucleases (ZFNs) are used as enzymes for gene insertion.

6. The method of claim 4 whereby transcription activator-like effector nucleases (TALENs) are used as enzymes for gene insertion.