Gene-targeted embryonic stem cells: real-time PCR assay for estimation of the number of neomycin selection cassettes
© Mancini et al; licensee BioMed Central Ltd. 2011
Received: 29 July 2011
Accepted: 28 October 2011
Published: 28 October 2011
In the preparation of transgenic murine ES cells it is important to verify the construct has a single insertion, because an ectopic neomycin phosphortransferase positive selection cassette (NEO) may cause a position effect. During a recent work, where a knockin SCA28 mouse was prepared, we developed two assays based on Real-Time PCR using both SYBR Green and specific minor groove binder (MGB) probes to evaluate the copies of NEO using the comparative delta-delta Ct method versus the Rpp30 reference gene.
We compared the results from Southern blot, routinely used to quantify NEO copies, with the two Real-Time PCR assays. Twenty-two clones containing the single NEO copy showed values of 0.98 ± 0.24 (mean ± 2 S.D.), and were clearly distinguishable from clones with two or more NEO copies.
This method was found to be useful, easy, sensitive and fast and could substitute for the widely used, but laborious Southern blot method.
Two methods are available for the introduction and modification of mouse genomic DNA sequences: (i) microinjection of one or more transgenes into the pronucleus of a fertilized mouse oocyte, which usually leads to random incorporation into the genome as head-to-tail concatamers of 1-1000 units, or (ii) the use of constructs that undergo a site-specific recombination in embryonic stem cells (ES) in order to disrupt the function of a target gene (knockout) or to mutate a gene (knockin). Modified ES cells are then injected into the blastocyst . In the latter case, the production of knockout or knockin ES cells is obtained through gene targeting by homologous recombination. In this work, ES cells were transfected by electroporation with a construct containing a specific genomic sequence harbouring the required mutation, along with the neomycin phophortransferase positive selection cassette (NEO) for selection of positive recombinants, flanked by two homology sequences ("arms") driving the recombination [2, 3]. Homologous recombination occurs in a small number of transfected cells, resulting in the introduction of the mutation present in the targeting construct into the gene of interest. However, despite the presence of the two "arms", there may be a variable number of random integrations that may cause a position effect [4–6]. To identify the mutant ES cell clones to be microinjected, two Southern blots are usually performed: one to detect ES clones in which homologous recombination has occurred, and the other to verify the number of NEO cassettes. Usually between two and three hundred clones are analysed: useful clones are routinely just 1 - 2% of the total. This low percentage is mainly due to the event of the vector being inserted in ectopic sites.
One member of our group is responsible for a facility within the Molecular Biotechnology Center in Torino, aimed at the preparation of transgenic mice using recombinant ES cells. In routine work, it became necessary to have a rapid test to exclude the presence of additional copies of the NEO cassette in ES clones in which homologous recombination was successfully obtained. Here we describe a screening method using a rapid semi-quantitative real-time PCR, which was validated on ES clones with different NEO copies (0, 1, 2, > 2 copies), previously assessed by Southern blot.
From one of the projects involving the preparation of recombinant mice, we selected 45 genomic DNA extracted from ES clones that then underwent Southern blot screening. DNA extraction was performed using standard phenol-chloroform method . Southern blot was performed using standard conditions for gel run, transfer and hybridisation. A NEO probe of 773 bp was used to evaluate the number of transgenic plasmid insertions.
In the MGB-assay we combined the two NEO and Rpp30 assays in a duplex PCR including two internal Taqman-MGB probes (5'-FAM labelled for NEO and 5'-VIC labelled for Rpp30) (Figure 1). Each sample was consistently run in triplicate with a blank well to check for contaminations.
In the SYBR-assay the two reactions were run in separate wells, using a Fast SYBR green mix (Applied Biosystems). The efficiency of each assay was verified with a standard curve starting from 100 ng of mouse DNA, using four serial dilutions from 1:1 to 1:8. The MGB-assay had 80% efficiency, whereas SYBR-assay gave 93% efficiency.
Gene copy-number was calculated using the comparative delta-delta Ct method . In each experiment, we normalized the ΔCt of the sample to the mean ΔCt of three ES clones with a single NEO copy verified using Southern blot; these values (named nNEO) were expected to be ~ "1" in the case of a single copy of NEO, ~ "2" in the case of two copies of NEO, and "n" for "n" copies of NEO.
The remaining 23 ES clones (≥ 2 NEO copies) showed a variable number of nNEO from ~2 to > 60 (Figure 2B). Comparing results of the two qPCR assays for the same sample, we saw that the values of nNEO had a minimal variability. Although the nNEO number probably reflects the amount of cassettes, calculating their exact number was beyond our scope. Curiously, we found high copy-number insertions that reached up to 60; this could be explained by the presence of concatamers of the vector, rather than multiple insertions in the mouse genome.
Southern blot analysis has long been the reference method for the detection of NEO copy number in ES clones. However, this method requires large amounts of DNA samples, as well as being laborious, time-consuming, and sometimes difficult to interpret. Our experience in transgenic mouse model preparation has led to the conclusion that having an alternative method is highly favourable. We propose a semi-quantitative real-time PCR method, that only requires small amounts of DNA, and much less time to be performed (the Fast, SYBR-assay format takes under one hour). This method appears to be sensitive enough even for identification of single NEO insertions. Of the two assays tested, the MGB-assay is the least convenient, as it requires two specific and expensive fluorescently-labelled probes, and does not show any practical advantage over the SYBR-assay.
Approaches based on real-time PCR to validate ES positive clones have been previously described, using absolute quantification of NEO, or a relative quantification to detect deletion of the target gene [9, 10]. Our method, based on a relative PCR quantification, can be easily reproduced in other laboratories using different technical platforms, and does not need the preparation of standards.
One possible drawback may be the genomic DNA quality/degradation that needs to be checked in case of non-reproducible data.
In conclusion, our real-time PCR assay to quantify NEO copy number is a valid alternative tool to Southern blot for the rapid screening of large numbers of ES cell clones during the production of knockout or knockin mouse models.
This work was supported by Telethon research grant GGP07110 to AB.
- Thomas KR, Deng C, Capecchi MR: High-fidelity gene targeting in embryonic stem cells by using sequence replacement vectors. Mol Cell Biol. 1992, 12: 2919-2923.PubMed CentralView ArticlePubMed
- Meier ID, Bernreuther C, Tilling T, Neidhardt J, Wong YW, Schulze C, Streichert T, Schachner M: Short DNA sequences inserted for gene targeting can accidentally interfere with off-target gene expression. FASEB J. 2010, 24: 1714-1724. 10.1096/fj.09-140749.View ArticlePubMed
- Joyner A: Gene targeting a practical approach. 2000, New York: Oxford University Press
- Olson EN, Arnold HH, Rigby PW, Wold BJ: Know your neighbors: three phenotypes in null mutants of the myogenic bHLH gene MRF4. Cell. 1996, 85: 1-4. 10.1016/S0092-8674(00)81073-9.View ArticlePubMed
- Rijli FM, Dolle P, Fraulob V, LeMeur M, Chambon P: Insertion of a targeting construct in a Hoxd-10 allele can influence the control of Hoxd-9 expression. Dev Dyn. 1994, 201: 366-377. 10.1002/aja.1002010408.View ArticlePubMed
- Pham CT, MacIvor DM, Hug BA, Heusel JW, Ley TJ: Long-range disruption of gene expression by a selectable marker cassette. Proc Natl Acad Sci USA. 1996, 93: 13090-13095. 10.1073/pnas.93.23.13090.PubMed CentralView ArticlePubMed
- Sambrook J, Russell D: Molecular Cloning: A Laboratory Manual. 2001, Cold Spring Harbor Laboratory Press
- Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25: 402-408. 10.1006/meth.2001.1262.View ArticlePubMed
- Valenzuela DM, Murphy AJ, Frendewey D, Gale NW, Economides AN, Auerbach W, Poueymirou WT, Adams NC, Rojas J, Yasenchak J: High-throughput engineering of the mouse genome coupled with high-resolution expression analysis. Nat Biotechnol. 2003, 21: 652-659. 10.1038/nbt822.View ArticlePubMed
- Coumoul X, Shukla V, Li C, Wang RH, Deng CX: Conditional knockdown of Fgfr2 in mice using Cre-LoxP induced RNA interference. Nucleic Acids Res. 2005, 33: e102-10.1093/nar/gni100.PubMed CentralView ArticlePubMed
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