Methods xxx (2014) xxx–xxx
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Methods journal homepage: www.elsevier.com/locate/ymeth
Enrichment of cells with TALEN-induced mutations using surrogate reporters Young-Hoon Kim a,1, Suresh Ramakrishna a,1, Hyongbum Kim a,⇑, Jin-Soo Kim b,c,⇑ a
Graduate School of Biomedical Science and Engineering/College of Medicine, Hanyang University, Seoul, South Korea Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea c Department of Chemistry, Seoul National University, Seoul, South Korea b
a r t i c l e
i n f o
Article history: Received 11 November 2013 Revised 12 April 2014 Accepted 17 April 2014 Available online xxxx Keywords: Transcription activator-like effector nucleases Enrichment Mutant cells Flow cytometry Magnetic separation Hygromycin B
a b s t r a c t Targeted gene knockout using engineered nucleases such as transcription activator like-effector nucleases (TALENs) is a gold standard for investigating the functions of a gene of interest. Although most TALENs can cleave chromosomal DNA efficiently, the activities of designed TALENs are not always high enough to allow the efficient derivation of cells containing TALEN-driven mutations. Thus, simple methods to enrich cells containing TALEN-directed mutations would facilitate the use of TALENs. Here we describe the enrichment of such cells using surrogate episomal reporters coupled with flow cytometric sorting, magnetic separation, or hygromycin selection. Ó 2014 Published by Elsevier Inc.
1. Introduction Transcription activator like-effector (TALE) nucleases (TALENs) are promising tools for targeted genetic engineering [1–3]. TALENs are constructed of two modules: (i) a TALE, which serves as the sequence-recognition domain, and (ii) the catalytic domain of FokI nuclease, which cleaves DNA [4]. TALEs are proteins from Xanthomonas, a plant pathogenic bacterium, that activate transcription of endogenous plant genes [5]. A TALE comprises tandem arrays of 33- to 35-amino acid repeats, each of which recognizes a single base pair in the major groove of DNA [6,7]. The two amino acids at positions 12 and 13 of each repeat domain, the repeat variable diresidues (RVDs), determine base specificities for sequence recognition. For example, the bases guanine, adenine, cytosine, and thymidine are recognized by the RVD modules NN, NI, HD, and NG, respectively [4]. When two TALENs form a heterodimer through TALE-mediated sequence recognition, the catalytic domain make double strand breaks (DSBs) at the intervening sequence. ⇑ Corresponding authors addresses. Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea. Fax: +82 222202422 (H. Kim), Department of Chemistry, Seoul National University, Seoul, South Korea. fax: +82 28747455 (J.-S. Kim). E-mail addresses: [email protected] (H. Kim), [email protected] (J.-S. Kim). 1 These authors contributed equally to this work.
The gold standard for elucidating gene function is a comparison of the phenotypes of knockout cells or organisms with those of isogenic controls. Although knockout mice can be created via gene targeting, this conventional method requires substantial effort and time. In addition, it is difficult to achieve gene knockout in human and other higher eukaryotic cells without using programmable nucleases. The DSBs that these nuclease induce at specific genomic sites can be repaired through either nonhomologous end joining (NHEJ) or homology-directed repair (HDR) [8]. HDR requires homologous templates such as donor DNA or single strand oligonucleotides, whereas NHEJ does not. Because NHEJ is an errorprone process, the repair of DSBs through NHEJ often results in small insertions or deletions (collectively called ‘‘indels’’), which can lead to gene knockout. TALENs, like zinc finger nucleases (ZFNs) and RNA-guided endonucleases (RGENs), represent programmable nucleases [8]. TALENs can be designed to target almost any given sequence, whereas the design densities for RGENs and ZFNs are limited [8]. Originally, TALENs only required a 50 thymine at the end of the target sequence, a limitation that can be now overcome using TALENs with a modified N-terminal domain that recognizes all 50 bases [9]. In addition, almost all designed TALENs are functional unless the target sites are methylated [8,10]. These features make TALENs an attractive tool for creating knockout cells.
http://dx.doi.org/10.1016/j.ymeth.2014.04.012 1046-2023/Ó 2014 Published by Elsevier Inc.
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However, the efficiencies of designed TALENs are often low, hampering the generation of mutant cells created using these enzymes. The ability to enrich cells containing TALEN-induced mutations would greatly facilitate this process. Therefore, we previously developed three surrogate reporters that enable the efficient enrichment of cells containing programmable nucleaseinduced mutations [11,12]. Several methods, including flow cytometric sorting, magnetic separation [13,14], and antibiotics selection, have been developed for isolating specific populations of cells, and we have used each for mutant cell enrichment; each isolation method has pros and cons [12]. Flow cytometric sorting has been widely used to isolate cells expressing or labeled with fluorescent factors. Although this technique is efficient, it has disadvantages; the availability of the expensive flow cytometry machines is limited and some cells are damaged due to exposure to strong lasers and hydrostatic pressure during the isolation process. As an alternative, magnetic separation enables the isolation of cells that express specific antigens. For our reporter system, we used a truncated H-2Kk that lacks a cytoplasmic domain as the distinguishing specific antigen to avoid any effects generated by the expression of the native antigen [15,16]. H-2Kk is a mouse MHC class I molecule expressed only in some rare mouse strains such as AKR/J or CBA/J, but not in human or most other murine cells [17,18]. Another method for isolating specific populations of cells is the use of resistance factors against antibiotics. Hygromycin B phosphotransferase, encoded by the hygromycin-resistance gene, phosphorylates hygromycin B, leading to its inactivation [19]. This gene has been used as a selection marker for transformed prokaryotes [20] and transgenic eukaryotes [21,22] in the presence of hygromycin B, which kills both prokaryotes and eukaryotes by inhibiting protein synthesis [21,23,24]. In this article, we provide protocols for enriching TALEN-directed mutant cells using surrogate reporters coupled with flow cytometry, magnetic separation, or hygromycin selection. The step-by-step protocols described here will greatly facilitate the generation of knockout cells using TALENs, especially when low activity TALENs are used.
2. Materials 2.1. Plasmids encoding a pair of TALENs Plasmids encoding a pair of TALENs (e.g., Addgene, Cellectis Bioresearch, Life Technologies, Toolgen, Transposagen Biophamaceuticals) 2.2. Reporter plasmids 1. Reporter vectors (Fluorescent reporter, Magnetic reporter, Hygromycin reporter; previously described in Refs. [11,12,25]; commercially available from Toolgen (184, Gasan digital 2-ro, Geumcheon-gu, Seoul, Korea, 153-783, South Korea; http:// www.toolgen.com/)) 2. Restriction enzymes (EcoRI, BamHI (New England BioLabs, Inc.)) to prepare reporter plasmids for insertion and ligation of the target sequences 3. Oligonucleotides containing the TALEN target sequence (custom-ordered, e.g. Bioneer, South Korea) 4. Chemically competent cells (e.g. DH5a, Invitrogen) 5. Ligase (e.g. New England Biolabs) 6. LB broth 7. Kanamycin stock solution (100 mg/ml) 8. LB agar containing 100 lg/ml kanamycin
2.3. Cell culture 2.3.1. Cell culture medium for 293 cells 1. DMEM (Gibco/Invitrogen) 2. 10% fetal bovine serum (FBS, e.g. Gibco/Invitrogen) 3. 1% Penicillin/Streptomycin (e.g. Gibco/Invitrogen) 2.3.2. Cell culture reagents and plasticware 1. 0.25% trypsin solution (Gibco/Invitrogen) 2. Phosphate buffered saline (PBS) without magnesium and calcium (e.g. HyClone) 3. 35-mm culture dishes (e.g. BD biosciences) 4. 60-mm culture dishes (e.g. BD biosciences) 2.4. Transfection reagents Transfection reagents (e.g. Lipofectamine (Invitrogen) or polyethylenimine (PEI) (Polyscience)) 2.5. Enrichment of mutant cells 2.5.1. Flow cytometry 1. Flow cytometers (e.g. Aria (BD biosciences)) 2. Flow cytometry buffer (2% FBS in PBS) 2.5.2. Magnetic separation 1. PBE: PBS supplemented with 0.5% bovine serum albumin and 5 mM EDTA (e.g. Miltenyi Biotech, Germany) 2. Anti-H-2Kk antibody conjugated with magnetic beads (MACSelect Kk microbeads (120-000-450); Miltenyi Biotech, Germany) 3. MACS buffer (e.g. Miltenyi Biotech, Germany) 4. Separation column (MACS MS column (130-042-201) or LS column (130-042-401); Miltenyi Biotech, Germany) 5. MACS separator (130-090-976; Miltenyi Biotech, Germany) 6. MACS Multistand (130-042-303; Miltenyi Biotech, Germany) 2.5.3. Hygromycin selection 1. Hygromycin B (e.g. Invitrogen) 2.6. Determination of TALEN-induced mutations 2.6.1. PCR amplification of the target region 1. Genomic DNA Extraction Kit (Promega, USA) 2. RNase A (e.g. Invitrogen) 3. High-fidelity DNA polymerase (e.g. Pfu, Promega or Phusion polymerase, New England Biolabs) 4. Thermocycler (Biorad) 5. Water bath 2.6.2. T7E1 (T7 endonuclease I) assay 1. 2. 3. 4.
T7E1 enzyme and NEB buffer 2 (NEB, USA) 6 DNA loading buffer (e.g. Elpis biotech, South Korea) Agarose for preparation of a 2% agarose gel (Sigma) 100 bp DNA ladder (Bioneer, South Korea)
2.6.3. DNA sequencing 1. T-vector (e.g. pGEM-T Easy vector, Promega) 2. Miniprep kits (e.g. Bioneer, South Korea)
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3. Sequencing primers (e.g. Solgent, South Korea) 3. Methods 3.1. Overview and the structure of reporters Phenotypic evaluation of cells or organisms after targeted selective gene knockout is the gold standard for determining gene functions. TALENs offer an attractive method for making knockout cells and organisms. However, gene knockout cell generation and recovery is sometimes hampered when the efficiency of the designed TALENs is low. Surrogate reporters can facilitate the recovery of TALEN-induced gene knockout cells by enabling the enrichment of cells containing TALEN-induced mutations [11,12]. Briefly, after the cotransfection of reporter plasmids and plasmids encoding TALENs, cells containing TALEN-induced mutations are enriched. The reporters for enrichment of TALEN-induced gene knockout cells using flow cytometry, magnetic separation, or hygromycin selection have several features in common. All encode mRFP, the expression of which is under the control of the constitutive CMV promoter (Figs. 1a, 2a and 3a), and all contain TALEN target sequences and a stop codon immediately after the mRFP gene. These elements are then followed by sequences encoding eGFPeGFP, eGFP-2A-H-2Kk, or 2A-HygroR-eGFP in the flow cytometry reporter, magnetic reporter, and hygromycin reporter, respectively. In the absence of TALEN activity on the target sequence
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of the reporter, the reporter-transfected cells will express mRFP but not eGFP, H-2Kk, or HygroR because of the presence of a double barrier: eGFP-eGFP, eGFP-2A-H-2Kk, and 2A-HygroR-eGFP are all out of frame relative to mRFP and the stop codon preceding these genes will terminate protein translation. The CMV promoter that drives the expression of mRFP is the only promoter in these reporters; there are no promoters downstream of the mRFP gene that can initiate the expression of eGFP, H-2Kk, or HygroR. If TALENs create DSBs in the reporter target sequence, the indels generated through error-prone NHEJ repair can lead to frame shifts, which in turn can lead to expression of the eGFP, H-2Kk, or HygroR genes. These three genes are each expressed as fusion proteins with mRFP. Subsequently, in the case of H-2Kk and HygroR, the H-2Kk protein and the HygroR-eGFP fusion protein are translated as separate proteins along with the mRFP protein because of the self-cleaving 2A peptide function [26]. However, if the number of inserted or deleted nucleotides is divisible by 3 (such as 3, 6, 9, 12, . . .), the reading frame will not be changed and thus the downstream genes will remain unexpressed. When random numbers of nucleotides are inserted or deleted, one out of three indels will make the GFP, H-2Kk, or HygroR genes in frame and expressed. In the case of the flow cytometry reporters, we have recently added an additional eGFP sequence so that eGFP is expressed in the presence of either 3n + 1 or 3n + 2 indels (Fig. 1a) as an mRFP-eGFP fusion protein. In the magnetic and hygromycin reporters, eGFP is expressed as well as H-2Kk or HygroR (Figs. 2a and 3a).
Fig. 1. Schematic representation of the enrichment of cells with TALEN-induced mutations using surrogate reporters coupled with flow cytometry. (A) Working mechanism of the fluorescent reporter. The reporter consists of the mRFP gene, the TALEN target sequence, and two eGFP genes. mRFP is constitutively expressed by the CMV promoter (PCMV), whereas functional eGFP is not expressed due to a double barrier: the two eGFP genes are out of frame relative to mRFP and a stop codon precedes them. If TALENs induce double strand breaks in the target sequence, the repair of the break through nonhomologous end joining (NHEJ) often induces frame shift mutations, which can make one of the eGFP genes in frame and expressed. (B) Flow cytometric sorting-mediated enrichment of cells with TALEN-induced mutations. Reporter plasmids and chromosomal target loci are illustrated. mRFP+ cells and mRFP+eGFP+ cells are shown in red and yellow, respectively. Black squares represent mutations.
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Fig. 2. Schematic representation of the enrichment of cells with TALEN-induced mutations using surrogate reporters coupled with magnetic separation. (A) Working mechanism of the magnetic reporter. The reporter consists of the mRFP gene, the TALEN target sequence, the eGFP gene, and the H-2Kk gene. mRFP is constitutively expressed by the CMV promoter (PCMV), whereas functional eGFP and H-2Kk are not expressed due to a double barrier: the two downstream genes are out of frame and a stop codon precedes them. If TALENs induce double strand breaks in the target sequence, the repair of the break through nonhomologous end joining (NHEJ) often induces frame shift mutations, which can make the eGFP and H-2Kk genes in frame and expressed. (B) Magnetic separation-mediated enrichment of cells with TALEN-induced mutations. Reporter plasmids, chromosomal target loci, and H-2Kk expression on the cell surface are illustrated. mRFP+ cells and mRFP+eGFP+ cells are shown in red and yellow, respectively. Black squares represent mutations.
To use these reporter plasmids to enrich for gene knockout cells, plasmids encoding TALENs and reporter plasmids are first co-transfected into cells of interest (here, 293 cells). After the plasmids enter the cell nuclei, TALENs are expressed from the TALENencoding plasmids and then have the opportunity to make DSBs at the target sequences in both the host chromosome and reporter plasmid. In the absence of donor DNA, the DSBs will be repaired through error-prone NHEJ, which often results in the generation of indels. If DSBs in the target sites of the host chromosome and reporter plasmids are repaired in a seamless manner without the formation of indels, the TALENs again have the opportunity to make DSBs at the target sites. If TALEN-induced mutations are generated in the target site of the reporter plasmid, there is a high probability that mutations will also be generated in the target site of the host chromosome in the same cell [11,12]. Thus, selection of GFP, H-2Kk, or HygroR-expressing cells results in the enrichment of cells containing TALEN-induced mutations in the host chromosome [11,12] (Figs. 1b, 2b and 3b).
Oligo 1: 50 -AATT[NX]-30 or 50 -AATT[(C)NX(G)]-30 Oligo 2: 30 -[NX]CTAG-50 or 30 -[(G)NX(C)]CTAG-50 (i) The NXG in oligo 1 and NXC in oligo 2 are complementary (Fig. 4); this complementary NX region includes the TALEN target sequence. (ii) The 50 ends of both oligonucleotides are noncomplementary and have EcoRI and BamHI restriction site overhangs (AATT and CTAG, respectively) which facilitate directional cloning into the reporter vectors. (iii) The GFP, H-2Kk, and HygroR genes must be out of frame relative to mRFP and the common stop codon. No other stop codons, especially in the TALEN target site, should precede this stop codon. To adjust these reading frames, additional nucleotides (usually one or two) can be added to the NX region. (iv) (Optional) To maintain the EcoRI and BamHI restriction sites after preparation of the reporter, add a C at the 30 end of 50 AATT-30 and a C at the 30 end of 30 -CTAG-50 . If the EcoRI and BamHI restriction sites are maintained, the modified plasmid can be used again to provide a digested backbone plasmid to generate reporter plasmids with different target sites.
3.2. Construction of reporters Two complementary oligonucleotides (oligo 1 and oligo 2) including target sequences should be custom-synthesized (e.g. Bioneer, South Korea) based on the following rules.
1. Prepare solutions of oligonucleotides at concentrations of approximately 100 lM each in TE (10 mM Tris, 1 mM EDTA, pH 8.0). Mix 1 ll of Oligo 1, 1 ll of Oligo 2, and 8 ll of distilled water (DW) in a PCR tube.
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Fig. 3. Schematic representation of the enrichment of cells with TALEN-induced mutations using surrogate reporters coupled with hygromycin selection. (A) Working mechanism of the hygromycin reporter. The reporter consists of the mRFP gene, the TALEN target sequence, the eGFP gene, and the HygroR gene. mRFP is constitutively expressed by the CMV promoter (PCMV), whereas functional eGFP and HygroR are not expressed due to a double barrier: the two genes are out of frame and a stop codon precedes them. If TALENs induce double strand breaks in the target sequence, the repair of the break through nonhomologous end joining (NHEJ) often induces frame shift mutations, which can make the eGFP and HygroR genes in frame and expressed. (B) Hygromycin selection-mediated enrichment of cells with TALEN-induced mutations. Reporter plasmids and chromosomal target loci are illustrated. mRFP+ cells and mRFP+eGFP+ cells are shown in red and yellow, respectively. Black squares represent mutations.
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4.
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Fig. 4. Preparation of reporters. Two strands of complementary oligonucleotides including the TALEN target sequence are annealed and ligated to a reporter backbone vector digested with EcoRI and BamHI. The 50 four base overhangs in the annealed oligonucleotides and those in the digested vector are complementary, which facilitates the cloning reaction.
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2. Anneal the two oligonucleotides with a thermocycler using the following program. 95 °C for 5 min and then ramp down the temperature to 25 °C at 5 °C/minute.
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Alternatively, heat the oligo mixture to 95 °C for 5 min in a water bath and then turn off the water bath so that it can gradually cool down to room temperature. The annealed oligos can either be ligated into the destination vector immediately or stored at 20 °C until use. Dilute the annealed oligos 250-fold with nuclease-free water for ligation into the reporter vectors that have been digested with EcoRI and BamHI (Fig. 4). For ligation, mix 1 ll of destination vector (50 ng), 1 ll of diluted annealed oligos, 1 ll of 10 NEB ligation buffer, 1 ll of NEB T4 DNA ligase, and 6 ll of DW to reach a final total volume of 10 ll. Incubate the mixture at room temperature for 3–4 h or at 16 °C overnight. For transformation of the ligation product into competent cells, add 4–5 ll of ligation reaction to 100 ll of competent cells on ice and mix by gently flicking the tube. Excessive tapping or mixing the cells is not advisable, as the competent cells are quite fragile. After incubation on ice for 20–30 min, heat-shock the competent cells at 42 °C for 1 min, and immediately place the tubes back on ice for 5 min. Add 900 ll of LB broth to the competent cell mixture and incubate at 37 °C for 1–1.5 h while shaking (200 rpm). Collect the cells by centrifugation at 2000g for 3 min; resuspend the pellet in 200 ll of LB broth and then spread the cells on LB/kanamycin plates followed by overnight incubation at 37 °C.
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9. Screen for positive colonies using colony PCR. (a) Individually inoculate each single colony into 200 ll of LB broth supplemented with 50 lg/ml kanamycin and incubate the culture at 37 °C for 2 h while shaking (200 rpm). (b) Take 2 ll from each cell suspension and use for PCR screening. (The remaining cell suspensions should be individually stored at 4 °C until PCR screening is completed.) Add the 2 ll of cell suspension to a tube containing the following components (total 20 ll reaction) 4 ll of 5 PCR premix (HiPi PCR premix, ELPiS, South Korea) 1 ll (10 pmol) of forward primer (mRFP FP: 50 -GACGGCGGCGTGGTGACCGT-30 ) 1 ll (10 pmol) of reverse primer (Oligo 2) 12 ll of DW (c) Perform the PCR using the following conditions – Denaturation at 94 °C for 5 min – 30 cycles of 94 °C for 30 s, 58 °C for 30 s, and 72 °C for 30 s – 72 °C for 5 min (d) Run samples of the PCR products on a 2% agarose gel to determine which clones contain the desired inserts. 10. Expand the positive clones by culturing in LB broth supplemented with 50 lg/ml kanamycin overnight with shaking at 37 °C. 11. Isolate and sequence plasmid DNA from the positive clones to confirm that the reporter has been constructed properly. 3.3. Cotransfection of reporter plasmids and plasmids encoding TALENs The first step in the facilitated generation of TALEN-induced gene knockout cells is transient cotransfection of the reporter and TALEN-encoding plasmids into cells of interest. Any transient transfection method should work; we used PEI for the transfection of 293 cells in the current study. One day after cotransfection, RFP+ cells can be observed using fluorescent microscopy, which enables an estimation of transfection efficiency. The fraction of GFP+ cells should gradually increase over 3 days. GFP expression is usually stronger in the fluorescent reporter group than in the magnetic and hygromycin reporter groups. 3.4. Enrichment of mutant cells Enrichment of cells containing TALEN-induced mutations can be achieved using flow cytometric sorting, magnetic separation, or hygromycin selection depending on the reporter used. 3.4.1. Flow cytometric sorting Three days after cotransfection of fluorescent reporter and TALEN-encoding plasmids, the cells should be trypsinized to make single-cell suspensions, which are then subjected to flow cytometric sorting for GFP+RFP+ cells (Fig. 5). Before trypsinization, simple fluorescent microscopic evaluation of the cells can enable a quick estimation of the fraction of cells that are GFP+RFP+. 1. Three days after plasmid cotransfection, wash the adherent 293 cells using Ca2+Mg2+ free PBS (e.g. Invitrogen, USA). 2. Add 500 ll of trypsin–EDTA (0.25% trypsin, 1 mM EDTA, e.g. Invitrogen) to the 293 cells in a 60 mm dish. 3. Incubate the cells at 37 °C until the cells detach from the dish, then inactivate the trypsin by adding 4 ml DMEM supplemented with 10% FBS.
4. Centrifuge the cells at 300g for 5 min and discard the supernatant. 5. Resuspend the cells in 600 ll of PBS supplemented with 2% FBS and keep them on ice until flow cytometric sorting. 6. Sort the mRFP+eGFP+ cells using a flow cytometer (we used FACSAria II (BD biosciences)). To highly enrich for cells containing TALEN-induced mutations, cells with strong eGFP signals can be sorted. Untransfected cells and cells transfected with the reporter alone, the mRFP-expressing plasmid alone, or the eGFP-expressing plasmid alone are used as the sorting and analysis controls. 7. The sorted cells can be further cultured or subjected to analysis such as the T7E1 assay. 3.4.2. Magnetic separation Three days after cotransfection of magnetic reporter and TALEN-encoding plasmids, the cells should be trypsinized as above and then subjected to magnetic separation to select for H-2Kk+ cells (Fig. 6). Repeat steps 1–4 above (flow cytometric sorting). 5. Resuspend the cells in 320 ll of PBE per 1 107 cells. Add 80 ll of antibody conjugated with magnetic beads per 1 107 cells to label the H-2Kk+ cells. 6. Mix well and incubate for 20 min on ice. Every 5 min, mix the cells by gently flicking the tube. 7. Add PBE and adjust to a final volume of 2 ml per upto 108 cells. (For efficient enrichment, the single cell suspension should be prepared by careful pipetting of cells using 1 ml pipette tip. Simple microscopic evaluation is recommended to confirm the single cell suspension). 1. Place a column in the magnetic field of a suitable MACS separator. Use either an MS (for less than 107 cells) or an LS column (for less than 108 cells). 2. Rinse the column with PBE (MS, 0.5 ml; LS, 3 ml). 3. Apply the 2 ml of single cell suspension to the wet column. 4. Wash the column three times with PBE (MS, 0.5 ml; LS, 3 ml) to remove H-2Kk- cells. 5. Remove the column from the magnetic separator and flush out the H-2Kk+ cells with PBE. The isolated H-2Kk+ cells can be further cultured or subjected to analysis such as the T7E1 assay. 3.4.3. Hygromycin selection Two days after cotransfection of hygromycin reporter and TALEN-encoding plasmids, the cells should be cultured in the presence of an optimal concentration of hygromycin for an appropriate period of time. Specific conditions for each cell type should be determined using untransfected or empty vector-transfected cells as follows. (a) Plate the cells in two 6 well plates (or one 12 well plate) and incubate for 6–8 h (or overnight) to allow cells to attach to the surface. (b) Replace the medium with medium supplemented with 0, 30, 100, 300, 1000, or 2000 lg/ml hygromycin (in duplicate, i.e. two wells per each concentration) and incubate for 48 h with observation everyday. (c) Replace the medium with medium without hygromycin and continue to observe the cells everyday for two more days. The recommended hygromycin concentration to use is the lowest concentration that kills almost all the cells. If an optimal concentration is not identified initially, the hygromycin concentration can be varied further or the incubation time can be changed. In
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Fig. 5. Flow cytometric enrichment of cells containing TALEN-induced mutations. (A) Representative flow cytometry of cells (here 293 cells) 3 days after cotransfection with reporter and TALEN-encoding plasmids. mRFP+eGFP+ cells were flow cytometrically sorted. (B) T7E1 assay of the sorted and unsorted cells. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The mutation frequencies (Indel (%)) were calculated from the band intensities. Cells containing TALEN-induced mutations were enriched in the mRFP+eGFP+ cell population. (C) DNA sequences of the HPRT1 wild-type (WT) and mutant clones from unsorted and sorted cell populations. The TALEN recognition sites and spacer regions are underlined and in red, respectively, with deleted bases indicated by dashes. The number of occurrences is shown in parentheses. Mutation frequencies were calculated by dividing the number of mutant clones by the number of total clones.
the case of the 293 cells that we used, the optimal concentration of hygromycin was 2 mg/ml. 1. Two days after plasmid cotransfection, add 80 ll of hygromycin stock solution (50 mg/ml) to 2 ml of culture medium (working
concentration: 2 mg/ml) and culture the cells for 2 days. Cells should start to die 24 h after the addition of hygromycin. 2. Two days after the hygromycin addition, the remaining cells that are resistant to hygromycin can be further cultured or subjected to analysis such as the T7E1 assay (Fig. 7).
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Fig. 6. Magnetic separation-mediated enrichment of cells containing TALEN-induced mutations. (A) Schematic illustrating the process of magnetic separation. To separate H2Kk+ cells 3 days after cotransfection with reporter and TALEN-encoding plasmids, the cells were labeled with magnetic bead-conjugated antibody against H-2Kk. (B) T7E1 assay of the separated and unseparated cells. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The mutation frequencies (Indel (%)) were calculated from the band intensities. Cells containing TALEN-induced mutations were enriched in the magnetically separated H-2Kk+ cells.
3.5. Evaluation of mutant cells To determine the mutation frequency in a population of isolated cells, the genomic region containing the TALEN target site can be PCR amplified using high fidelity DNA polymerase and subjected to one of the following analyses. (a) Assay using mismatch-sensitive nucleases (Fig. 8): T7E1 assay [27] or Surveyor’s nuclease assay [28] (b) Sanger sequencing (c) Deep sequencing 3.6. Generation and evaluation of mutant clones by clonal culture The cells enriched for TALEN-induced mutations can be subjected to clonal culture by plating cells at a density of 0.25 cells/ well in 96-well plates or at low density (61000 cells) in a 100mm dish. Two or three weeks after the initiation of these dilute
Fig. 7. Hygromycin selection-mediated enrichment for cells containing TALENinduced mutations. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The mutation frequencies (Indel (%)) were calculated from the band intensities. The selection using hygromycin B enriched cells containing TALEN-directed mutations.
cultures, round colonies can be manually picked as clones. The DNA region containing the TALEN target site can be PCR amplified using high fidelity DNA polymerase and subjected to Sanger sequencing to determine what mutations are present.
4. Quality control Simple fluorescent microscopic observation can enable an estimation of the enrichment process before and after magnetic separation or hygromycin selection. The degree of enrichment of GFP+ cells can be analyzed by flow cytometry as well. Making a single cell suspension is critical for efficient enrichment through magnetic separation and flow cytometric sorting; simple microscopic evaluation of an aliquot of the cell suspension can enable a quick estimation the degree of cell separation. In the case of hygromycin selection, optimizing the concentrations and exposure times of hygromycin for the cell type of the interest is important for efficient enrichment. To use magnetic reporters, the untransfected cells should constitutively express beta2-microglobulin, which is required for the surface expression of H-2Kk, and be free of H-2Kk expression. Practically, almost all mammalian cell types are suitable for magnetic separation because (i) H-2Kk expression is restricted to certain rarely used mouse strains (e.g. AKR/J and CBA/Ca) and (ii) b2microglobulin is expressed in almost all mouse, rat, and human cell types [29–31]. When we evaluated the relationship between the mutation frequencies at the target site in the host chromosome and those in the reporter plasmids, a positive correlation was observed as expected (Fig. 9). The main underlying mechanism for this correlation would be that the reporter plasmid and host chromosome are within the same cell. The factors that affect the efficiency of TALEN-induced mutation in individual cells vary; these factors include nuclease
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Fig. 8. Schematic overview of the T7E1 or surveyor nuclease assay. DNA segments including the TALEN target site are PCR-amplified using genomic DNA isolated from cells transfected with TALEN-encoding plasmids. The amplicons are melted, annealed, and subjected to T7E1 or surveyor nuclease, which are mismatch-sensitive endonucleases. If an amplicon contains mutated as well as wild-type sequences, heteroduplexes can be formed, which can be digested with T7E1 or surveyor nuclease. Homoduplexes cannot be digested with either nuclease. The T7E1- or surveyor nuclease-treated samples are then subjected to agarose gel electrophoresis. A schematic gel result is illustrated. M, size marker.
Fig. 9. The relationship between mutation frequency at the host chromosomal target site and that in the transfected episomal surrogate reporter. Human or mouse cells were cotransfected with fluorescent reporter plasmids and plasmids encoding TALENs, zinc finger nucleases (ZFNs), or RNA-guided engineered nucleases (RGENs). The percentage of eGFP+ cells, which reflects the indel generation frequency in the episomal surrogate reporter, was determined by flow cytometry; the mutation frequencies at the host chromosomal target site were calculated by the T7E1 assay. The original raw data used to make this graph have been previously published in Refs. [11,12,25].
concentration [11], which is, at least partly, determined by the transfection efficiency. Within a given cell, the reporter plasmids and host chromosome share the same nuclease concentrations
and other extrinsic factors that may affect TALEN-induced mutagenesis. Thus, the mutation frequencies of the reporter plasmid and host chromosome have a high probability of being positively associated. The reporter plasmids have been tested when they are cotransfected with plasmids encoding programmable nucleases including TALENs [11,12,25]. When TALENs [32], ZFNs [33], and RGENs [34,35] are delivered without using plasmids, the reporter plasmids would facilitate the selection of cells containing nuclease-induced mutations as well [35]. Programmable nuclease-induced homology-directed repair (HDR) can lead to genome editing including gene correction, mutagenesis, and gene insertion [8]. For efficient HDR, high nuclease activity and a sufficient concentration of targeting vector are required. Because surrogate reporter-based selection enriches cells with high nuclease activity and highly transfected cells that contain high concentrations of targeting vectors, it is expected that this reporter-based selection can enrich TALEN-induced genomeedited cells created through HDR as well. However, this possibility awaits experimental evaluation. The enrichment efficiencies by flow cytometry, magnetic separation, or hygromycin selection are all comparable [12,25]. Thus, users can choose the appropriate enrichment methods based on their experimental purposes and conditions. The cost, time, labor, and enrichment efficiency of the three methods are compared in Table 1. Detailed advantages and disadvantages of each enrichment method have been previously described [12].
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Table 1 Comparison of the enrichment methods. Enrichment method Cost-generating items (except general cost for the cell culture) Times required for the selection process Labor Enrichment fold
Flow cytometry – Usage fee for flow cytometers – Flow cytometer Hours Comparable Comparable
The enrichment of cells containing TALEN-induced mutations has also been achieved by selecting the transfected cells through flow cytometric sorting or antibiotic selection using vectors expressing fluorescent proteins or antibiotic resistance factors [36–38]. However, the enrichment efficiency of this approach can be limited because nuclease-induced mutations occur in only a limited fraction of transfected cells [11,25]. Our surrogate reporter systems allow the selection of cells in which nuclease is active from the pool of transfected cells, enabling a more efficient enrichment of mutant cells than selection of transfected cells alone [11,25]. Acknowledgment
Magnetic separation
Hygromycin selection k
– Magnetic-bead conjugated antibody against the H-2K – Magnetic separation instrument Hours
[11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]
H.K. is supported in part by the National Research Foundation of Korea (2011-0013568, 2011-0019357, 2013M3A9B4076544, 20080062287) and the Health Technology R&D Project, Ministry of Health and Welfare of Korea (HI10C1740).
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Enrichment of cells with TALEN-induced mutations using surrogate reporters Young-Hoon Kim a,1, Suresh Ramakrishna a,1, Hyongbum Kim a,⇑, Jin-Soo Kim b,c,⇑ a
Graduate School of Biomedical Science and Engineering/College of Medicine, Hanyang University, Seoul, South Korea Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea c Department of Chemistry, Seoul National University, Seoul, South Korea b
a r t i c l e
i n f o
Article history: Received 11 November 2013 Revised 12 April 2014 Accepted 17 April 2014 Available online xxxx Keywords: Transcription activator-like effector nucleases Enrichment Mutant cells Flow cytometry Magnetic separation Hygromycin B
a b s t r a c t Targeted gene knockout using engineered nucleases such as transcription activator like-effector nucleases (TALENs) is a gold standard for investigating the functions of a gene of interest. Although most TALENs can cleave chromosomal DNA efficiently, the activities of designed TALENs are not always high enough to allow the efficient derivation of cells containing TALEN-driven mutations. Thus, simple methods to enrich cells containing TALEN-directed mutations would facilitate the use of TALENs. Here we describe the enrichment of such cells using surrogate episomal reporters coupled with flow cytometric sorting, magnetic separation, or hygromycin selection. Ó 2014 Published by Elsevier Inc.
1. Introduction Transcription activator like-effector (TALE) nucleases (TALENs) are promising tools for targeted genetic engineering [1–3]. TALENs are constructed of two modules: (i) a TALE, which serves as the sequence-recognition domain, and (ii) the catalytic domain of FokI nuclease, which cleaves DNA [4]. TALEs are proteins from Xanthomonas, a plant pathogenic bacterium, that activate transcription of endogenous plant genes [5]. A TALE comprises tandem arrays of 33- to 35-amino acid repeats, each of which recognizes a single base pair in the major groove of DNA [6,7]. The two amino acids at positions 12 and 13 of each repeat domain, the repeat variable diresidues (RVDs), determine base specificities for sequence recognition. For example, the bases guanine, adenine, cytosine, and thymidine are recognized by the RVD modules NN, NI, HD, and NG, respectively [4]. When two TALENs form a heterodimer through TALE-mediated sequence recognition, the catalytic domain make double strand breaks (DSBs) at the intervening sequence. ⇑ Corresponding authors addresses. Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea. Fax: +82 222202422 (H. Kim), Department of Chemistry, Seoul National University, Seoul, South Korea. fax: +82 28747455 (J.-S. Kim). E-mail addresses: [email protected] (H. Kim), [email protected] (J.-S. Kim). 1 These authors contributed equally to this work.
The gold standard for elucidating gene function is a comparison of the phenotypes of knockout cells or organisms with those of isogenic controls. Although knockout mice can be created via gene targeting, this conventional method requires substantial effort and time. In addition, it is difficult to achieve gene knockout in human and other higher eukaryotic cells without using programmable nucleases. The DSBs that these nuclease induce at specific genomic sites can be repaired through either nonhomologous end joining (NHEJ) or homology-directed repair (HDR) [8]. HDR requires homologous templates such as donor DNA or single strand oligonucleotides, whereas NHEJ does not. Because NHEJ is an errorprone process, the repair of DSBs through NHEJ often results in small insertions or deletions (collectively called ‘‘indels’’), which can lead to gene knockout. TALENs, like zinc finger nucleases (ZFNs) and RNA-guided endonucleases (RGENs), represent programmable nucleases [8]. TALENs can be designed to target almost any given sequence, whereas the design densities for RGENs and ZFNs are limited [8]. Originally, TALENs only required a 50 thymine at the end of the target sequence, a limitation that can be now overcome using TALENs with a modified N-terminal domain that recognizes all 50 bases [9]. In addition, almost all designed TALENs are functional unless the target sites are methylated [8,10]. These features make TALENs an attractive tool for creating knockout cells.
http://dx.doi.org/10.1016/j.ymeth.2014.04.012 1046-2023/Ó 2014 Published by Elsevier Inc.
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However, the efficiencies of designed TALENs are often low, hampering the generation of mutant cells created using these enzymes. The ability to enrich cells containing TALEN-induced mutations would greatly facilitate this process. Therefore, we previously developed three surrogate reporters that enable the efficient enrichment of cells containing programmable nucleaseinduced mutations [11,12]. Several methods, including flow cytometric sorting, magnetic separation [13,14], and antibiotics selection, have been developed for isolating specific populations of cells, and we have used each for mutant cell enrichment; each isolation method has pros and cons [12]. Flow cytometric sorting has been widely used to isolate cells expressing or labeled with fluorescent factors. Although this technique is efficient, it has disadvantages; the availability of the expensive flow cytometry machines is limited and some cells are damaged due to exposure to strong lasers and hydrostatic pressure during the isolation process. As an alternative, magnetic separation enables the isolation of cells that express specific antigens. For our reporter system, we used a truncated H-2Kk that lacks a cytoplasmic domain as the distinguishing specific antigen to avoid any effects generated by the expression of the native antigen [15,16]. H-2Kk is a mouse MHC class I molecule expressed only in some rare mouse strains such as AKR/J or CBA/J, but not in human or most other murine cells [17,18]. Another method for isolating specific populations of cells is the use of resistance factors against antibiotics. Hygromycin B phosphotransferase, encoded by the hygromycin-resistance gene, phosphorylates hygromycin B, leading to its inactivation [19]. This gene has been used as a selection marker for transformed prokaryotes [20] and transgenic eukaryotes [21,22] in the presence of hygromycin B, which kills both prokaryotes and eukaryotes by inhibiting protein synthesis [21,23,24]. In this article, we provide protocols for enriching TALEN-directed mutant cells using surrogate reporters coupled with flow cytometry, magnetic separation, or hygromycin selection. The step-by-step protocols described here will greatly facilitate the generation of knockout cells using TALENs, especially when low activity TALENs are used.
2. Materials 2.1. Plasmids encoding a pair of TALENs Plasmids encoding a pair of TALENs (e.g., Addgene, Cellectis Bioresearch, Life Technologies, Toolgen, Transposagen Biophamaceuticals) 2.2. Reporter plasmids 1. Reporter vectors (Fluorescent reporter, Magnetic reporter, Hygromycin reporter; previously described in Refs. [11,12,25]; commercially available from Toolgen (184, Gasan digital 2-ro, Geumcheon-gu, Seoul, Korea, 153-783, South Korea; http:// www.toolgen.com/)) 2. Restriction enzymes (EcoRI, BamHI (New England BioLabs, Inc.)) to prepare reporter plasmids for insertion and ligation of the target sequences 3. Oligonucleotides containing the TALEN target sequence (custom-ordered, e.g. Bioneer, South Korea) 4. Chemically competent cells (e.g. DH5a, Invitrogen) 5. Ligase (e.g. New England Biolabs) 6. LB broth 7. Kanamycin stock solution (100 mg/ml) 8. LB agar containing 100 lg/ml kanamycin
2.3. Cell culture 2.3.1. Cell culture medium for 293 cells 1. DMEM (Gibco/Invitrogen) 2. 10% fetal bovine serum (FBS, e.g. Gibco/Invitrogen) 3. 1% Penicillin/Streptomycin (e.g. Gibco/Invitrogen) 2.3.2. Cell culture reagents and plasticware 1. 0.25% trypsin solution (Gibco/Invitrogen) 2. Phosphate buffered saline (PBS) without magnesium and calcium (e.g. HyClone) 3. 35-mm culture dishes (e.g. BD biosciences) 4. 60-mm culture dishes (e.g. BD biosciences) 2.4. Transfection reagents Transfection reagents (e.g. Lipofectamine (Invitrogen) or polyethylenimine (PEI) (Polyscience)) 2.5. Enrichment of mutant cells 2.5.1. Flow cytometry 1. Flow cytometers (e.g. Aria (BD biosciences)) 2. Flow cytometry buffer (2% FBS in PBS) 2.5.2. Magnetic separation 1. PBE: PBS supplemented with 0.5% bovine serum albumin and 5 mM EDTA (e.g. Miltenyi Biotech, Germany) 2. Anti-H-2Kk antibody conjugated with magnetic beads (MACSelect Kk microbeads (120-000-450); Miltenyi Biotech, Germany) 3. MACS buffer (e.g. Miltenyi Biotech, Germany) 4. Separation column (MACS MS column (130-042-201) or LS column (130-042-401); Miltenyi Biotech, Germany) 5. MACS separator (130-090-976; Miltenyi Biotech, Germany) 6. MACS Multistand (130-042-303; Miltenyi Biotech, Germany) 2.5.3. Hygromycin selection 1. Hygromycin B (e.g. Invitrogen) 2.6. Determination of TALEN-induced mutations 2.6.1. PCR amplification of the target region 1. Genomic DNA Extraction Kit (Promega, USA) 2. RNase A (e.g. Invitrogen) 3. High-fidelity DNA polymerase (e.g. Pfu, Promega or Phusion polymerase, New England Biolabs) 4. Thermocycler (Biorad) 5. Water bath 2.6.2. T7E1 (T7 endonuclease I) assay 1. 2. 3. 4.
T7E1 enzyme and NEB buffer 2 (NEB, USA) 6 DNA loading buffer (e.g. Elpis biotech, South Korea) Agarose for preparation of a 2% agarose gel (Sigma) 100 bp DNA ladder (Bioneer, South Korea)
2.6.3. DNA sequencing 1. T-vector (e.g. pGEM-T Easy vector, Promega) 2. Miniprep kits (e.g. Bioneer, South Korea)
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3. Sequencing primers (e.g. Solgent, South Korea) 3. Methods 3.1. Overview and the structure of reporters Phenotypic evaluation of cells or organisms after targeted selective gene knockout is the gold standard for determining gene functions. TALENs offer an attractive method for making knockout cells and organisms. However, gene knockout cell generation and recovery is sometimes hampered when the efficiency of the designed TALENs is low. Surrogate reporters can facilitate the recovery of TALEN-induced gene knockout cells by enabling the enrichment of cells containing TALEN-induced mutations [11,12]. Briefly, after the cotransfection of reporter plasmids and plasmids encoding TALENs, cells containing TALEN-induced mutations are enriched. The reporters for enrichment of TALEN-induced gene knockout cells using flow cytometry, magnetic separation, or hygromycin selection have several features in common. All encode mRFP, the expression of which is under the control of the constitutive CMV promoter (Figs. 1a, 2a and 3a), and all contain TALEN target sequences and a stop codon immediately after the mRFP gene. These elements are then followed by sequences encoding eGFPeGFP, eGFP-2A-H-2Kk, or 2A-HygroR-eGFP in the flow cytometry reporter, magnetic reporter, and hygromycin reporter, respectively. In the absence of TALEN activity on the target sequence
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of the reporter, the reporter-transfected cells will express mRFP but not eGFP, H-2Kk, or HygroR because of the presence of a double barrier: eGFP-eGFP, eGFP-2A-H-2Kk, and 2A-HygroR-eGFP are all out of frame relative to mRFP and the stop codon preceding these genes will terminate protein translation. The CMV promoter that drives the expression of mRFP is the only promoter in these reporters; there are no promoters downstream of the mRFP gene that can initiate the expression of eGFP, H-2Kk, or HygroR. If TALENs create DSBs in the reporter target sequence, the indels generated through error-prone NHEJ repair can lead to frame shifts, which in turn can lead to expression of the eGFP, H-2Kk, or HygroR genes. These three genes are each expressed as fusion proteins with mRFP. Subsequently, in the case of H-2Kk and HygroR, the H-2Kk protein and the HygroR-eGFP fusion protein are translated as separate proteins along with the mRFP protein because of the self-cleaving 2A peptide function [26]. However, if the number of inserted or deleted nucleotides is divisible by 3 (such as 3, 6, 9, 12, . . .), the reading frame will not be changed and thus the downstream genes will remain unexpressed. When random numbers of nucleotides are inserted or deleted, one out of three indels will make the GFP, H-2Kk, or HygroR genes in frame and expressed. In the case of the flow cytometry reporters, we have recently added an additional eGFP sequence so that eGFP is expressed in the presence of either 3n + 1 or 3n + 2 indels (Fig. 1a) as an mRFP-eGFP fusion protein. In the magnetic and hygromycin reporters, eGFP is expressed as well as H-2Kk or HygroR (Figs. 2a and 3a).
Fig. 1. Schematic representation of the enrichment of cells with TALEN-induced mutations using surrogate reporters coupled with flow cytometry. (A) Working mechanism of the fluorescent reporter. The reporter consists of the mRFP gene, the TALEN target sequence, and two eGFP genes. mRFP is constitutively expressed by the CMV promoter (PCMV), whereas functional eGFP is not expressed due to a double barrier: the two eGFP genes are out of frame relative to mRFP and a stop codon precedes them. If TALENs induce double strand breaks in the target sequence, the repair of the break through nonhomologous end joining (NHEJ) often induces frame shift mutations, which can make one of the eGFP genes in frame and expressed. (B) Flow cytometric sorting-mediated enrichment of cells with TALEN-induced mutations. Reporter plasmids and chromosomal target loci are illustrated. mRFP+ cells and mRFP+eGFP+ cells are shown in red and yellow, respectively. Black squares represent mutations.
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Fig. 2. Schematic representation of the enrichment of cells with TALEN-induced mutations using surrogate reporters coupled with magnetic separation. (A) Working mechanism of the magnetic reporter. The reporter consists of the mRFP gene, the TALEN target sequence, the eGFP gene, and the H-2Kk gene. mRFP is constitutively expressed by the CMV promoter (PCMV), whereas functional eGFP and H-2Kk are not expressed due to a double barrier: the two downstream genes are out of frame and a stop codon precedes them. If TALENs induce double strand breaks in the target sequence, the repair of the break through nonhomologous end joining (NHEJ) often induces frame shift mutations, which can make the eGFP and H-2Kk genes in frame and expressed. (B) Magnetic separation-mediated enrichment of cells with TALEN-induced mutations. Reporter plasmids, chromosomal target loci, and H-2Kk expression on the cell surface are illustrated. mRFP+ cells and mRFP+eGFP+ cells are shown in red and yellow, respectively. Black squares represent mutations.
To use these reporter plasmids to enrich for gene knockout cells, plasmids encoding TALENs and reporter plasmids are first co-transfected into cells of interest (here, 293 cells). After the plasmids enter the cell nuclei, TALENs are expressed from the TALENencoding plasmids and then have the opportunity to make DSBs at the target sequences in both the host chromosome and reporter plasmid. In the absence of donor DNA, the DSBs will be repaired through error-prone NHEJ, which often results in the generation of indels. If DSBs in the target sites of the host chromosome and reporter plasmids are repaired in a seamless manner without the formation of indels, the TALENs again have the opportunity to make DSBs at the target sites. If TALEN-induced mutations are generated in the target site of the reporter plasmid, there is a high probability that mutations will also be generated in the target site of the host chromosome in the same cell [11,12]. Thus, selection of GFP, H-2Kk, or HygroR-expressing cells results in the enrichment of cells containing TALEN-induced mutations in the host chromosome [11,12] (Figs. 1b, 2b and 3b).
Oligo 1: 50 -AATT[NX]-30 or 50 -AATT[(C)NX(G)]-30 Oligo 2: 30 -[NX]CTAG-50 or 30 -[(G)NX(C)]CTAG-50 (i) The NXG in oligo 1 and NXC in oligo 2 are complementary (Fig. 4); this complementary NX region includes the TALEN target sequence. (ii) The 50 ends of both oligonucleotides are noncomplementary and have EcoRI and BamHI restriction site overhangs (AATT and CTAG, respectively) which facilitate directional cloning into the reporter vectors. (iii) The GFP, H-2Kk, and HygroR genes must be out of frame relative to mRFP and the common stop codon. No other stop codons, especially in the TALEN target site, should precede this stop codon. To adjust these reading frames, additional nucleotides (usually one or two) can be added to the NX region. (iv) (Optional) To maintain the EcoRI and BamHI restriction sites after preparation of the reporter, add a C at the 30 end of 50 AATT-30 and a C at the 30 end of 30 -CTAG-50 . If the EcoRI and BamHI restriction sites are maintained, the modified plasmid can be used again to provide a digested backbone plasmid to generate reporter plasmids with different target sites.
3.2. Construction of reporters Two complementary oligonucleotides (oligo 1 and oligo 2) including target sequences should be custom-synthesized (e.g. Bioneer, South Korea) based on the following rules.
1. Prepare solutions of oligonucleotides at concentrations of approximately 100 lM each in TE (10 mM Tris, 1 mM EDTA, pH 8.0). Mix 1 ll of Oligo 1, 1 ll of Oligo 2, and 8 ll of distilled water (DW) in a PCR tube.
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Fig. 3. Schematic representation of the enrichment of cells with TALEN-induced mutations using surrogate reporters coupled with hygromycin selection. (A) Working mechanism of the hygromycin reporter. The reporter consists of the mRFP gene, the TALEN target sequence, the eGFP gene, and the HygroR gene. mRFP is constitutively expressed by the CMV promoter (PCMV), whereas functional eGFP and HygroR are not expressed due to a double barrier: the two genes are out of frame and a stop codon precedes them. If TALENs induce double strand breaks in the target sequence, the repair of the break through nonhomologous end joining (NHEJ) often induces frame shift mutations, which can make the eGFP and HygroR genes in frame and expressed. (B) Hygromycin selection-mediated enrichment of cells with TALEN-induced mutations. Reporter plasmids and chromosomal target loci are illustrated. mRFP+ cells and mRFP+eGFP+ cells are shown in red and yellow, respectively. Black squares represent mutations.
3.
4.
5.
Fig. 4. Preparation of reporters. Two strands of complementary oligonucleotides including the TALEN target sequence are annealed and ligated to a reporter backbone vector digested with EcoRI and BamHI. The 50 four base overhangs in the annealed oligonucleotides and those in the digested vector are complementary, which facilitates the cloning reaction.
6.
2. Anneal the two oligonucleotides with a thermocycler using the following program. 95 °C for 5 min and then ramp down the temperature to 25 °C at 5 °C/minute.
8.
7.
Alternatively, heat the oligo mixture to 95 °C for 5 min in a water bath and then turn off the water bath so that it can gradually cool down to room temperature. The annealed oligos can either be ligated into the destination vector immediately or stored at 20 °C until use. Dilute the annealed oligos 250-fold with nuclease-free water for ligation into the reporter vectors that have been digested with EcoRI and BamHI (Fig. 4). For ligation, mix 1 ll of destination vector (50 ng), 1 ll of diluted annealed oligos, 1 ll of 10 NEB ligation buffer, 1 ll of NEB T4 DNA ligase, and 6 ll of DW to reach a final total volume of 10 ll. Incubate the mixture at room temperature for 3–4 h or at 16 °C overnight. For transformation of the ligation product into competent cells, add 4–5 ll of ligation reaction to 100 ll of competent cells on ice and mix by gently flicking the tube. Excessive tapping or mixing the cells is not advisable, as the competent cells are quite fragile. After incubation on ice for 20–30 min, heat-shock the competent cells at 42 °C for 1 min, and immediately place the tubes back on ice for 5 min. Add 900 ll of LB broth to the competent cell mixture and incubate at 37 °C for 1–1.5 h while shaking (200 rpm). Collect the cells by centrifugation at 2000g for 3 min; resuspend the pellet in 200 ll of LB broth and then spread the cells on LB/kanamycin plates followed by overnight incubation at 37 °C.
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9. Screen for positive colonies using colony PCR. (a) Individually inoculate each single colony into 200 ll of LB broth supplemented with 50 lg/ml kanamycin and incubate the culture at 37 °C for 2 h while shaking (200 rpm). (b) Take 2 ll from each cell suspension and use for PCR screening. (The remaining cell suspensions should be individually stored at 4 °C until PCR screening is completed.) Add the 2 ll of cell suspension to a tube containing the following components (total 20 ll reaction) 4 ll of 5 PCR premix (HiPi PCR premix, ELPiS, South Korea) 1 ll (10 pmol) of forward primer (mRFP FP: 50 -GACGGCGGCGTGGTGACCGT-30 ) 1 ll (10 pmol) of reverse primer (Oligo 2) 12 ll of DW (c) Perform the PCR using the following conditions – Denaturation at 94 °C for 5 min – 30 cycles of 94 °C for 30 s, 58 °C for 30 s, and 72 °C for 30 s – 72 °C for 5 min (d) Run samples of the PCR products on a 2% agarose gel to determine which clones contain the desired inserts. 10. Expand the positive clones by culturing in LB broth supplemented with 50 lg/ml kanamycin overnight with shaking at 37 °C. 11. Isolate and sequence plasmid DNA from the positive clones to confirm that the reporter has been constructed properly. 3.3. Cotransfection of reporter plasmids and plasmids encoding TALENs The first step in the facilitated generation of TALEN-induced gene knockout cells is transient cotransfection of the reporter and TALEN-encoding plasmids into cells of interest. Any transient transfection method should work; we used PEI for the transfection of 293 cells in the current study. One day after cotransfection, RFP+ cells can be observed using fluorescent microscopy, which enables an estimation of transfection efficiency. The fraction of GFP+ cells should gradually increase over 3 days. GFP expression is usually stronger in the fluorescent reporter group than in the magnetic and hygromycin reporter groups. 3.4. Enrichment of mutant cells Enrichment of cells containing TALEN-induced mutations can be achieved using flow cytometric sorting, magnetic separation, or hygromycin selection depending on the reporter used. 3.4.1. Flow cytometric sorting Three days after cotransfection of fluorescent reporter and TALEN-encoding plasmids, the cells should be trypsinized to make single-cell suspensions, which are then subjected to flow cytometric sorting for GFP+RFP+ cells (Fig. 5). Before trypsinization, simple fluorescent microscopic evaluation of the cells can enable a quick estimation of the fraction of cells that are GFP+RFP+. 1. Three days after plasmid cotransfection, wash the adherent 293 cells using Ca2+Mg2+ free PBS (e.g. Invitrogen, USA). 2. Add 500 ll of trypsin–EDTA (0.25% trypsin, 1 mM EDTA, e.g. Invitrogen) to the 293 cells in a 60 mm dish. 3. Incubate the cells at 37 °C until the cells detach from the dish, then inactivate the trypsin by adding 4 ml DMEM supplemented with 10% FBS.
4. Centrifuge the cells at 300g for 5 min and discard the supernatant. 5. Resuspend the cells in 600 ll of PBS supplemented with 2% FBS and keep them on ice until flow cytometric sorting. 6. Sort the mRFP+eGFP+ cells using a flow cytometer (we used FACSAria II (BD biosciences)). To highly enrich for cells containing TALEN-induced mutations, cells with strong eGFP signals can be sorted. Untransfected cells and cells transfected with the reporter alone, the mRFP-expressing plasmid alone, or the eGFP-expressing plasmid alone are used as the sorting and analysis controls. 7. The sorted cells can be further cultured or subjected to analysis such as the T7E1 assay. 3.4.2. Magnetic separation Three days after cotransfection of magnetic reporter and TALEN-encoding plasmids, the cells should be trypsinized as above and then subjected to magnetic separation to select for H-2Kk+ cells (Fig. 6). Repeat steps 1–4 above (flow cytometric sorting). 5. Resuspend the cells in 320 ll of PBE per 1 107 cells. Add 80 ll of antibody conjugated with magnetic beads per 1 107 cells to label the H-2Kk+ cells. 6. Mix well and incubate for 20 min on ice. Every 5 min, mix the cells by gently flicking the tube. 7. Add PBE and adjust to a final volume of 2 ml per upto 108 cells. (For efficient enrichment, the single cell suspension should be prepared by careful pipetting of cells using 1 ml pipette tip. Simple microscopic evaluation is recommended to confirm the single cell suspension). 1. Place a column in the magnetic field of a suitable MACS separator. Use either an MS (for less than 107 cells) or an LS column (for less than 108 cells). 2. Rinse the column with PBE (MS, 0.5 ml; LS, 3 ml). 3. Apply the 2 ml of single cell suspension to the wet column. 4. Wash the column three times with PBE (MS, 0.5 ml; LS, 3 ml) to remove H-2Kk- cells. 5. Remove the column from the magnetic separator and flush out the H-2Kk+ cells with PBE. The isolated H-2Kk+ cells can be further cultured or subjected to analysis such as the T7E1 assay. 3.4.3. Hygromycin selection Two days after cotransfection of hygromycin reporter and TALEN-encoding plasmids, the cells should be cultured in the presence of an optimal concentration of hygromycin for an appropriate period of time. Specific conditions for each cell type should be determined using untransfected or empty vector-transfected cells as follows. (a) Plate the cells in two 6 well plates (or one 12 well plate) and incubate for 6–8 h (or overnight) to allow cells to attach to the surface. (b) Replace the medium with medium supplemented with 0, 30, 100, 300, 1000, or 2000 lg/ml hygromycin (in duplicate, i.e. two wells per each concentration) and incubate for 48 h with observation everyday. (c) Replace the medium with medium without hygromycin and continue to observe the cells everyday for two more days. The recommended hygromycin concentration to use is the lowest concentration that kills almost all the cells. If an optimal concentration is not identified initially, the hygromycin concentration can be varied further or the incubation time can be changed. In
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Fig. 5. Flow cytometric enrichment of cells containing TALEN-induced mutations. (A) Representative flow cytometry of cells (here 293 cells) 3 days after cotransfection with reporter and TALEN-encoding plasmids. mRFP+eGFP+ cells were flow cytometrically sorted. (B) T7E1 assay of the sorted and unsorted cells. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The mutation frequencies (Indel (%)) were calculated from the band intensities. Cells containing TALEN-induced mutations were enriched in the mRFP+eGFP+ cell population. (C) DNA sequences of the HPRT1 wild-type (WT) and mutant clones from unsorted and sorted cell populations. The TALEN recognition sites and spacer regions are underlined and in red, respectively, with deleted bases indicated by dashes. The number of occurrences is shown in parentheses. Mutation frequencies were calculated by dividing the number of mutant clones by the number of total clones.
the case of the 293 cells that we used, the optimal concentration of hygromycin was 2 mg/ml. 1. Two days after plasmid cotransfection, add 80 ll of hygromycin stock solution (50 mg/ml) to 2 ml of culture medium (working
concentration: 2 mg/ml) and culture the cells for 2 days. Cells should start to die 24 h after the addition of hygromycin. 2. Two days after the hygromycin addition, the remaining cells that are resistant to hygromycin can be further cultured or subjected to analysis such as the T7E1 assay (Fig. 7).
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Fig. 6. Magnetic separation-mediated enrichment of cells containing TALEN-induced mutations. (A) Schematic illustrating the process of magnetic separation. To separate H2Kk+ cells 3 days after cotransfection with reporter and TALEN-encoding plasmids, the cells were labeled with magnetic bead-conjugated antibody against H-2Kk. (B) T7E1 assay of the separated and unseparated cells. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The mutation frequencies (Indel (%)) were calculated from the band intensities. Cells containing TALEN-induced mutations were enriched in the magnetically separated H-2Kk+ cells.
3.5. Evaluation of mutant cells To determine the mutation frequency in a population of isolated cells, the genomic region containing the TALEN target site can be PCR amplified using high fidelity DNA polymerase and subjected to one of the following analyses. (a) Assay using mismatch-sensitive nucleases (Fig. 8): T7E1 assay [27] or Surveyor’s nuclease assay [28] (b) Sanger sequencing (c) Deep sequencing 3.6. Generation and evaluation of mutant clones by clonal culture The cells enriched for TALEN-induced mutations can be subjected to clonal culture by plating cells at a density of 0.25 cells/ well in 96-well plates or at low density (61000 cells) in a 100mm dish. Two or three weeks after the initiation of these dilute
Fig. 7. Hygromycin selection-mediated enrichment for cells containing TALENinduced mutations. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The mutation frequencies (Indel (%)) were calculated from the band intensities. The selection using hygromycin B enriched cells containing TALEN-directed mutations.
cultures, round colonies can be manually picked as clones. The DNA region containing the TALEN target site can be PCR amplified using high fidelity DNA polymerase and subjected to Sanger sequencing to determine what mutations are present.
4. Quality control Simple fluorescent microscopic observation can enable an estimation of the enrichment process before and after magnetic separation or hygromycin selection. The degree of enrichment of GFP+ cells can be analyzed by flow cytometry as well. Making a single cell suspension is critical for efficient enrichment through magnetic separation and flow cytometric sorting; simple microscopic evaluation of an aliquot of the cell suspension can enable a quick estimation the degree of cell separation. In the case of hygromycin selection, optimizing the concentrations and exposure times of hygromycin for the cell type of the interest is important for efficient enrichment. To use magnetic reporters, the untransfected cells should constitutively express beta2-microglobulin, which is required for the surface expression of H-2Kk, and be free of H-2Kk expression. Practically, almost all mammalian cell types are suitable for magnetic separation because (i) H-2Kk expression is restricted to certain rarely used mouse strains (e.g. AKR/J and CBA/Ca) and (ii) b2microglobulin is expressed in almost all mouse, rat, and human cell types [29–31]. When we evaluated the relationship between the mutation frequencies at the target site in the host chromosome and those in the reporter plasmids, a positive correlation was observed as expected (Fig. 9). The main underlying mechanism for this correlation would be that the reporter plasmid and host chromosome are within the same cell. The factors that affect the efficiency of TALEN-induced mutation in individual cells vary; these factors include nuclease
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Fig. 8. Schematic overview of the T7E1 or surveyor nuclease assay. DNA segments including the TALEN target site are PCR-amplified using genomic DNA isolated from cells transfected with TALEN-encoding plasmids. The amplicons are melted, annealed, and subjected to T7E1 or surveyor nuclease, which are mismatch-sensitive endonucleases. If an amplicon contains mutated as well as wild-type sequences, heteroduplexes can be formed, which can be digested with T7E1 or surveyor nuclease. Homoduplexes cannot be digested with either nuclease. The T7E1- or surveyor nuclease-treated samples are then subjected to agarose gel electrophoresis. A schematic gel result is illustrated. M, size marker.
Fig. 9. The relationship between mutation frequency at the host chromosomal target site and that in the transfected episomal surrogate reporter. Human or mouse cells were cotransfected with fluorescent reporter plasmids and plasmids encoding TALENs, zinc finger nucleases (ZFNs), or RNA-guided engineered nucleases (RGENs). The percentage of eGFP+ cells, which reflects the indel generation frequency in the episomal surrogate reporter, was determined by flow cytometry; the mutation frequencies at the host chromosomal target site were calculated by the T7E1 assay. The original raw data used to make this graph have been previously published in Refs. [11,12,25].
concentration [11], which is, at least partly, determined by the transfection efficiency. Within a given cell, the reporter plasmids and host chromosome share the same nuclease concentrations
and other extrinsic factors that may affect TALEN-induced mutagenesis. Thus, the mutation frequencies of the reporter plasmid and host chromosome have a high probability of being positively associated. The reporter plasmids have been tested when they are cotransfected with plasmids encoding programmable nucleases including TALENs [11,12,25]. When TALENs [32], ZFNs [33], and RGENs [34,35] are delivered without using plasmids, the reporter plasmids would facilitate the selection of cells containing nuclease-induced mutations as well [35]. Programmable nuclease-induced homology-directed repair (HDR) can lead to genome editing including gene correction, mutagenesis, and gene insertion [8]. For efficient HDR, high nuclease activity and a sufficient concentration of targeting vector are required. Because surrogate reporter-based selection enriches cells with high nuclease activity and highly transfected cells that contain high concentrations of targeting vectors, it is expected that this reporter-based selection can enrich TALEN-induced genomeedited cells created through HDR as well. However, this possibility awaits experimental evaluation. The enrichment efficiencies by flow cytometry, magnetic separation, or hygromycin selection are all comparable [12,25]. Thus, users can choose the appropriate enrichment methods based on their experimental purposes and conditions. The cost, time, labor, and enrichment efficiency of the three methods are compared in Table 1. Detailed advantages and disadvantages of each enrichment method have been previously described [12].
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Table 1 Comparison of the enrichment methods. Enrichment method Cost-generating items (except general cost for the cell culture) Times required for the selection process Labor Enrichment fold
Flow cytometry – Usage fee for flow cytometers – Flow cytometer Hours Comparable Comparable
The enrichment of cells containing TALEN-induced mutations has also been achieved by selecting the transfected cells through flow cytometric sorting or antibiotic selection using vectors expressing fluorescent proteins or antibiotic resistance factors [36–38]. However, the enrichment efficiency of this approach can be limited because nuclease-induced mutations occur in only a limited fraction of transfected cells [11,25]. Our surrogate reporter systems allow the selection of cells in which nuclease is active from the pool of transfected cells, enabling a more efficient enrichment of mutant cells than selection of transfected cells alone [11,25]. Acknowledgment
Magnetic separation
Hygromycin selection k
– Magnetic-bead conjugated antibody against the H-2K – Magnetic separation instrument Hours
[11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24]
H.K. is supported in part by the National Research Foundation of Korea (2011-0013568, 2011-0019357, 2013M3A9B4076544, 20080062287) and the Health Technology R&D Project, Ministry of Health and Welfare of Korea (HI10C1740).
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