Search tips
Search criteria 


Logo of bmcmbBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Molecular Biology
BMC Mol Biol. 2010; 11: 58.
Published online 2010 August 13. doi:  10.1186/1471-2199-11-58
PMCID: PMC2928235

Homologous illegitimate random integration of foreign DNA into the X chromosome of a transgenic mouse line



It is not clear how foreign DNA molecules insert into the host genome. Recently, we have produced transgenic mice to investigate the role of the fad2 gene in the conversion of oleic acid to linoleic acid. Here we describe an integration mechanism of fad2 transgene by homologous illegitimate random integration.


We confirmed that one fad2 line had a sole integration site on the X chromosome according to the inheritance patterns. Mapping of insertion sequences with thermal asymmetric interlaced and conventional PCR revealed that the foreign DNA was inserted into the XC1 region of the X chromosome by a homologous illegitimate replacement of an entire 45,556-bp endogenous genomic region, including the ovarian granulosa cell tumourigenesis-4 allele. For 5' and 3' junction sequences, there were very short (3-7 bp) common sequences in the AT-rich domains, which may mediate the recognition of the homologous arms between the transgene and the host genome. In addition, analysis of gene transcription indicated that the transgene was expressed in all tested fad2 tissues and that its transcription level in homozygous female tissues was about twice as high as in the heterozygous female (p < 0.05).


Taken together, the results indicated that the foreign fad2 behaved like an X-linked gene and that foreign DNA molecules were inserted into the eukaryotic genome through a homologous illegitimate random integration.


Direct microinjection of foreign DNA into the pronucleus of fertilised zygotes is a conventional method to generate transgenic animals, whereas the exact integration site and the number of copies of the transgene are random and unpredictable [1,2]. Previous studies involving animal transgenesis indicate that the linear DNA molecules injected into the pronucleus undergo rapid circularisation followed by random linearisation and concatemer formation by homologous recombination before integration into the host genome [3-5]. It was thought that the foreign DNA concatemers would be finally inserted into the host DNA randomly through imperfect sequence recognition via heterologous recombination followed by cellular DNA repair activity [2,6]. Until now, it was not clear how foreign DNA molecules insert into the host genome. A few studies have unravelled some of the mystery of random integration and indicated that the integration site of foreign DNA is not totally random [6,7]. More detailed analyses of the integration sites revealed some interesting trends. For instance, a review of 35 different insertion mutants generated in transgenic mouse lines revealed that some chromosomes, such as chromosome 10 and 6, are selected more often for illegitimate integration than others [8]. Intrinsic DNA structures such as bent DNA elements could be a major determinant in chromosomal illegitimate recombination because their structure can provide a preferential donor site for the integration [9,10]. In addition, short identical sequences of 1 to 3 nucleotides have been found at the genome-transgene junctions [11]. These integration sites are usually associated with the consensus sequence for topoisomerase-I cleavage sites [11,12].

Recently, we have successfully used standard pronuclear microinjection to produce transgenic mice integrated with the fad2 gene from the cotton plant, encoding fatty acid desaturase-2. Those transgenic mice were used to study the role of FAD2 in the conversion of oleic acid to linoleic acid. In the present study, using the transgene inheritance pattern of F1 progeny, we showed that one of the transgenic lines had only one integration site on the X chromosome. Thermal asymmetric interlaced PCR (TAIL-PCR) [13,14] was used to identify the transgene-chromosome junction in mice previously [15-17]. To investigate the exact insertion site on the X chromosome, this method was also employed to map the 3' chromosomal boundaries of the integration site in fad2 mice. We successfully defined the 3' integration site by TAIL-PCR and the 5' integration site by conventional PCR. Based on the sequence data of both junctions, the mechanism of the homologous illegitimate random integration of the foreign DNA in transgenic animals was also analysed. Finally, the transcription characteristics of the X-linked fad2 were investigated further.


Analysis of transgene inheritance

PCR (Figure (Figure1A)1A) and Southern blotting analysis (Figure (Figure1B)1B) demonstrated that a male mouse (mouse-1) integrated the foreign gene. PCR analysis of its F1 offspring produced by seven C57 females showed that all 23 heterogeneous males were nontransgenic, whereas all 27 heterogeneous females were transgenic (Figure (Figure1C).1C). The results indicated that the fad2 transgene integrated into the X chromosome.

Figure 1
Transgene analysis. (A) PCR and (B) Southern blot analysis of total DNA from wild-type C57 (wt), mouse-1 (lane 1) and mouse-2 (lane 2) shows that mouse-1 was fad2 transgenic, whereas mouse-2 was nontransgenic. P, the mixture of fad2 plasmid and wt genomic ...

Identity of the 3' integration site

To determine the integration site of the foreign DNA on the X chromosome, TAIL-PCR was used to define the 3' chromosomal boundaries of the transgene (Figure (Figure2A).2A). Each PCR fragment, amplified by the tertiary cycling from the samples of three mouse-1 progeny, was purified and sequenced directly (Figure (Figure2B).2B). Sequencing and BLAST search results in the Mus musculus (C57BL/6J) genome showed that the mouse-15 fragments were derived from the transgene itself, whereas PCR products of mouse-3 and mouse-5 contained both the foreign DNA and the X flanking sequences (Figure (Figure2C).2C). Homology analysis indicated that the foreign gene was integrated into the XC1 region and that the junction site was located at base 87,507,732.

Figure 2
TAIL-PCR analysis of the 3' integration site. (A) Schematic diagram of the transgenic construct indicating the positions of three transgene primers (tgp) used, along with an arbitrary degenerate primer. (B) Gel analysis of TAIL-PCR products amplified ...

Junction sequence analysis also showed that there was an additional 29-bp fragment (Figure (Figure2C,2C, from -22 to +7) between the 3' end of the transgene and the X flanking sequence. This 29-bp sequence was 100% identical to the initial 5'-end of the foreign DNA in which the last seven nucleotides (5'-ttaatag-3', Figure Figure2C,2C, from +1 to +7) were also shared by the X chromosome sequence. Additional PCR amplification using the specific primers that spanned the above junction sequence confirmed that the 3' integration site (data not shown) was successfully mapped. These results suggest that the transgene integration was mediated by the seven common nucleotides.

Identity of heterozygotes

Genotypes were determined by PCR amplification using transgene-specific (567-bp) and genome-specific primer (495-bp) sets concurrently. As shown in Figure Figure3,3, amplification of the heterozygous transgenic DNA in the X+X female sample resulted in two bands, 567 bp and 495 bp. C57 DNA yielded only a single 495-bp band, and homozygous transgenic DNA in the X+X+ female or the X+Y male yielded only a 567-bp band.

Figure 3
Identity of homozygous or heterozygous fad2 mice. (A) Schematic diagram of the primer positions indicating the fragments spanning the 3' integration site in wild-type C57 or transgene-specific fragments in fad2 mice. (B) Site-specific primers used to ...

Identity of the 5' integration site

Based on the 3' integration site at 87,507,732, several primer sets corresponding to its known upstream sequence (GenBank accession no. NT_039706.7) were designed to map the 5' integration position. Among them, the results of three amplifications are shown in Figure Figure4.4. P1 primers, corresponding to the -54,088 to -53,884 region, successfully amplified the 205-bp fragment in all of the X+X+, X+X, X+Y and C57 samples. P2 and P3 primers, corresponding to regions -29,872 to -29,553 and -44,562 to -44,144, respectively, only amplified the 320-bp and 419-bp fragments, respectively, in X+X and C57, but not in the X+X+ or X+Y samples (Figure (Figure4B).4B). These results indicate that the 5'-integration site was within the -53, 884 to -44,562 region.

Figure 4
PCR analysis of the 5' integration site. (A) Schematic diagram of the approximate positions of five primer sets used for PCR analysis of the 5' integration site. P1 (-54,088 to -53,884), P2 (-29,872 to -29,553), and P3 (-44,562 to -44,144) primer pairs ...

Further PCR analysis was performed using several additional primer sets consisting of the forward primers, corresponding to X loci from -53, 884 to -44,562, and the common reverse primer, corresponding to the CMV enhancer sequence included in the transgene construct. Among them, results of two amplifications are shown in Figure Figure4.4. P4, from -46,680, or P5, from -45,797, successfully produced the 1732-bp and 799-bp bands, respectively, in all fad2 samples, but not in the C57 samples. Sequencing and homology analysis of two fragments showed that the resulting sequence could be divided into three parts. The 3'-end sequence was 100% identical to the initial sequence of the transgenic molecules. The middle sequence, including 327 nucleotides (from -3 to +324 in Figure Figure4C),4C), showed 100% identity with the transgenic complementary sequence from 3580 to 3259 that linked the 3'-end sequence with five additional nucleotides. The 5'-end sequence was 100% identical to the XC1 upstream sequence at position 87,462,177, in which three common nucleotides from -3 to -1 (5'-TGT-3') were shared by the transgene and the X chromosome (Figure (Figure4C4C).

Based on the 5' and 3' junction mapping results, we concluded that the entire 45,556-bp genomic region (from 87,462,177 to 87,507,732, in the XC1 region of chromosome X) was successful replaced by the foreign DNA molecules during the process of random integration (Figure (Figure5).5). For each junction, a very short homologous arm (3-7 bp) in the AT-rich domain presumably mediated the recombination of the transgene and the host genome (Figure (Figure66).

Figure 5
Transgene mapping on the X chromosome. The map of mouse chromosome X shows that the entire 45,556-bp region from 87,462,177 to 87,507,732 of XC1 was replaced by the foreign DNA during the process of random integration.
Figure 6
Analysis of the sequences surrounding the junction sites. The junction sequences present in the fad2 mice are underlined. Identical nucleotides in fad2 and X chromosome are indicated (grey shading). Three or seven identical nucleotides (boxed with grey ...

Transcription analysis

PCR and sequencing analysis using primer pairs spanning the 5' and 3' transgenic sequences showed multiple copies of the transgene inserted into the same site of chromosome X (data not shown). To assess the transcriptional potential of fad2, total RNA from liver, kidney, brain, muscle, and heart tissues was analysed by RT-PCR. As shown in Figure Figure7,7, the amplification results from five primer sets corresponding to different regions revealed that no transcriptional signals were detected in the upstream region (-1123 to -977) of the 5' integration site or the distal downstream region (+859 to +3069) of the 3' integration site in the C57 samples, while fad2 was expressed in all of the transgenic tissues (Figure (Figure7B).7B). In addition, the transcriptional signals of the 3' flanking sequences in the fad2 mice, which extended at least 2299 but no more than 3069 nucleotides past the 3' integration site, were detected by RT-PCR (Figure 7D-F).

Figure 7
RT-PCR analysis of the transgene and the X-linked sequences. Total RNA from liver, kidney, brain, muscle, and heart tissues of the C57 or homozygous fad2 females was analysed using the different sets of primers. (A) The X-linked Hprt gene (normalisation ...

Transcription level of the X-linked transgene

To gauge the transcription level of the X-linked fad2 in females, we measured the expression of the foreign gene. Kidney, brain, and liver tissues from the X+X+, X+X, C57 females, or X+Y males were analysed concurrently for reference. The real-time RT-PCR analysis showed that the foreign gene was expressed in all transgenic samples from the fad2 females or males and that the transcription level in the X+X+ females or X+Y males was about twice as high as in the X+X females (p < 0.05, Figure Figure8).8). The results suggest that the foreign fad2 behaved like an X-linked gene.

Figure 8
Relative expression of the X-linked transgene. Sets of primers corresponding to fad2 or Gapdh were used for real-time RT-PCR analysis of the samples of transgenic or C57 kidney, brain, and liver. Expression data of fad2 were normalised to Gapdh expression ...


Approximately 5-10% of the random DNA insertion events in transgenic animals are associated with recessive mutations or viable phenotypic alterations [4,18]. Integrated DNA may affect the endogenous genetic locus and result in inactivation of a given gene [19,20]. In some cases, transgene integration has been associated with host genome rearrangements, including duplications [21], translocation [22], and deletions [23-25]. The length of the deleted genome segments might be from 2-3 kb [23] to 22 kb [25]. In the current study, we successfully identified a foreign gene homologous inserted into the XC1 region by deletion of the entire 45,556-bp region of the endogenous DNA. Although the DNA deletion took place, all fad2 mice appeared normal, without any apparent lesions, and exhibited normal physiological activities and fertility. Sequence analysis revealed that no putative genes were positioned in the deleted 45,556-bp region in which one Gct4 phenotype allele of ovarian granulosa cell tumourigenesis 4 was involved (MGI ID: 98356). Previous studies involving juvenile granulosa cell tumours indicate that its susceptibility is an inherited, polygenic trait and that the X-linked Gct4 allele in the SJL mouse strain cause high-frequency, juvenile-type granulosa cell tumour development in females [26,27]. The fad2 gene inserted into the mouse genome could serve both as a mutagen and as a molecular tag to study the role of the Gct4 allele in juvenile-type granulosa cell tumour.

It is thought that linear DNA molecules injected into the pronucleus undergo rapid circularisation followed by random linearisation and concatemers formation by homologous recombination (Figure (Figure9A,9A, steps 1-3). Moreover, the injected molecules could then reconstitute and, most frequently, integrate as a head-to-tail array [2,3,5,28,29], with a minor modification of nucleotide deletion or insertion at some ends [7,11,30]. In the present study, the multiple copies of the fad2 transgene molecules lost the 5' initial GC dinucleotide, which was subsequently integrated into the X chromosome in a head-to-tail manner (Figure (Figure2C).2C). In addition, a head-to-head fusion also occurred in the transgene, whereby one strand joined its partial complementary strand with five additional nucleotides at the same insertion site (Figure (Figure4C,4C, Figure Figure9B9B).

Figure 9
Random integration mechanism of foreign DNA by homologous illegitimate random integration and course of fad2 inserted into the X chromosome. (A) Identical foreign DNA injected into the nucleus of a eukaryotic cell is circularised and randomly cleaved ...

As far as we know, it is not clear exactly how the concatemers insert into the host genome. It was previously reported that the foreign histocompatibility class II Eα gene, injected into pronuclei, was homologous targeted into the transgenic mouse genome [31]. In most cases, it is predicted that the foreign DNA concatemers would finally integrate into the host genome randomly through imperfect sequence recognition via heterologous recombination [2,21]. In the current study, it is worth noting that the 3-bp common sequence at the 5' junction and the 7-bp common sequence at the 3' junction were shared by the X chromosome and foreign transgenic molecules. Furthermore, the homologous nucleotides in the 5' junction would facilitate the recognition of two DNAs besides the 3-bp common sequence (Figure (Figure6,6, Figure Figure9B).9B). Such small regions of identity (3-5 bp) have been observed in previous studies of non-homologous recombination involving mouse transgenesis [11,29]. This suggests that the successful insertion of the transgene is mediated by these common sequences on both sides, which serve as anchors for the homologous illegitimate random integration (HIRI) but not heterologous recombination (Figure (Figure9).9). Because the homologous arms are very short and consist only of several identical nucleotides, they can be easily positioned at various regions of the host genome. Therefore, it appears that the foreign DNA is randomly integrated into the host genome and the integration sites are unpredictable in transgenic animals [1,2]. After homologous recognition between the two DNA molecules, the insertion of a foreign DNA molecule into a genome is mediated by the DNA repair mechanisms of the cell [2,6].

In addition to the common sequence, a palindromic sequence of 5'-ATTAAT-3' in both 5' and 3' junctions was found in the fad2 sequence, but not in the X sequence (Figure (Figure6).6). This sequence motif is required to induce a localised conversion in Streptococcus pneumoniae transformation [32]. The Ase I restriction endonuclease can recognise and cleave the sequence between the TT dinucleotide [33]. At this moment, we are not sure if an endonuclease plays a role in the HIRI process.

In mechanistic studies of natural transformation in prokaryotes, de Vries & Wackernagel reported that short stretches of sequence identity (3-8 bp) between the kanamycin-resistant nptII+ gene and the recipient DNA of transformed Acinetobacter facilitated the integration efficiency of foreign DNA into the prokaryotic genome by homology-facilitated illegitimate recombination using homologous regions ranging in length from 1 kb to 183 bp [34]. Simultaneously, a consistent integration mechanism, mediated by one-side homologous substrates and containing identical 4-10 nucleotide sequences between the donor and recipient DNA, was also observed in the human pathogen Streptococcus pneumoniae transformed by recombinant lambda bacteriophage [35]. In addition, in Pseudomonas stutzeri a similar phenomenon was observed, in which part of the short anchor segments recombined into the host genome [36]. In eukaryotes, events of illegitimate integration whose homologous sequences are very short (≤5 bp) are also found in mammalian cells [7,37], transgenic embryos [11], and mice [29]. Taken together, our observations suggest that the HIRI process is present in all organisms undergoing transformation/transgenesis (Figure (Figure9A9A).

Interestingly, although the HIRI process in prokaryotes usually happens within segments of high GC content [34-36], our results reveal that it occurred in the AT-rich, not GC-rich, region between the two DNAs in eukaryotes (Figure (Figure6).6). Similar results have been found in the transgenic embryo [11]. A systematic analysis of multiple illegitimate integration sites in somatic cells has found that in 93% of cases, these sites are only 10 bp away from a potential topoisomerase I cleavage site. The association of topoisomerase I sites with runs of purines and AT-rich regions with the site of integration is also significant [12]. Purine tracts can adopt non-B-DNA conformations, which may be able to recombine; these sequences are found in the centromeres and may promote recombination of the satellite DNA [6]. These observations suggest that AT-rich regions might be involved in the HIRI process.

Although in murine transformed 3T6 cells the poly (A) signal of the rabbit β-globin can direct efficient termination of polyomavirus DNA transcription through RNA polymerase II [38], in HeLa cells, in some cases, transcription of the foreign gene does not terminate thoroughly by the terminal signal of the 537-bp poly (A) full sequences [39]. The nucleotide sequence of the 3' flanking region of the rabbit β-globin gene was transcribed 2447 bp past the poly (A) site. The transcription level in the M13 bacteriophage vector gradually declines, under control of its own enhancer and promoter [40]. In fad2 mice, the transgene was expressed efficiently under the driven of the CMV enhancer and β-actin promoter (Figure (Figure7,7, Figure Figure8)8) and its transcription had not been terminated thoroughly by the terminal signal of the rabbit β-globin gene poly (A) yet. RT-PCR results revealed that the 2.3 kb flanking regions post the 3' integration site was transcribed within all examined fad2 tissues whereas these genomic regions kept silence in wild type (Figure 7D, 7E). Consistent with the previous study [40], these transcription level might gradually declines and the transcripts of the 3.0-kb distal flanking regions of the 3' integration site had not been detected within all examined fad2 tissues (Figure (Figure7F7F).

In mammals, dosage compensation takes place by silencing one of the two X chromosomes in female cells to achieve transcriptional balance with the XY male [41,42]. Transgenes carried on the X chromosome occasionally either escape the normal X-inactivation process [43] or behave like an X-linked gene [44,45]. The cloning and characterisation of the host sequences flanking these inserts may contribute to our understanding of the molecular control mechanisms of chromosome pairing [46,47] and mammalian X-inactivation [44,45]. As an X-linked transgene, the relative expression of fad2 was also examined in transgenic somatic tissues. The transgene expression behaved in a fashion similar to silence one of the two X chromosomes in female cells, at least within the tested female tissues. That was, only 50% of X+X cells expressed the fad2 gene, whereas all X+X+ female cells or X+Y male cells expressed the transgene. Subsequently, the relative amount expression of fad2 gene in the X+X organs was lower and estimated an approximately 50% amount of the X+X+ female or X+Y male cells. These results suggest that the XC1 region (from 87,462,177 to 87,507,732) is a locus amenable to the normal X-linked expression of foreign genes and can be used as a molecular tag to study the mechanism of X inactivation.


An X-linked transgenic mouse line is identified firstly in the current study. The real-time RT-PCR analysis indicates that the foreign fad2 gene is expressed in all transgenic samples from the fad2 females and that the transcription level in the homozygous females is about twice as high as in the heterozygous females. That is, the transgene expression behaves in a fashion similar to silence one of the two X chromosomes in female cells, at least within the tested female tissues.

We successfully map the sequences of both sides of transgene-chromosome in fad2 transgenic mice and identify that the 5' and 3' integration sites are located at base 87,462,177 and 87,507,732, respectively. PCR analysis reveals that the entire 45,556-bp genome in the XC1 region of chromosome X is deleted by the foreign DNA molecules during the process of random integration. The deleted 45,556-bp endogenous genomic region includes the ovarian granulosa cell tumourigenesis-4 allele.

For each junction sequence, a very short homologous arm (3-7 bp) in the AT-rich domain, for instance, TGT within the 5' junction and TTAATAG within the 3' junction, exists in both foreign fad2 gene and the X chromosome and presumably mediates the illegitimate recombination of two DNAs as the homologous arms. Based on the 5' and 3' junction mapping results, we predict that the foreign DNA insert into the host genome through a homologous illegitimate random integration (HIRI), which depends on several identical nucleotide sequences in the AT-rich domains on both sides.



All animals were maintained in a light-controlled room at 22°C. All animal procedures were approved by the Committee for Experimental Animals of our university.

Transgene construct

An 1182-bp DNA sequence of the cotton fad2 open reading frame (GenBank accession No. X97016) was optimised and synthesised (Invitrogen) with a modification of codon usage for easier expression in mammals. The expression vector for microinjection contained the fad2 gene driven by the cytomegalovirus (CMV) enhancer and the chicken β-actin promoter, as well as the rabbit β-globin poly (A) sequence at the 3' end. Transgenic mice were produced by pronuclear microinjection with the linear 3.6-kb transgenic cassettes digested by Sal I and BamH I.

Transgene detection by nucleic acid analysis

Genomic DNA was extracted from the tails of pups (3-4 weeks old) utilising the standard phenol-chloroform method, as previously described [1], and dissolved in TE buffer for nucleic acid analysis. The presence of the transgene was assayed by PCR amplification using transgene-specific primers (F: 5'-tacatcagcgacacaggcatc-3'; R: 5'-gtatttgtgagccagggcatt-3'). The amplified product was 567 bp long and spanned the fad2 gene sequence. PCR reactions contained 0.5-1.0 μg of genomic DNA, 0.2 mM dNTPs, 0.4 μM of primers, and 1 unit of Taq polymerase (Invitrogen) in 25 μl of 1 × reaction buffer. The reactions were performed at 94°C for 5 min; 35 cycles of 94°C for 30 sec, 58°C for 30 sec, and 72°C for 40 sec; and 72°C for 8 min.

For Southern blotting analysis, 10 μg of the genomic DNA was digested with EcoR I + Sca I for 12-16 hours, separated on 0.7% agarose gels overnight and blotted to Hybond-N+ membranes (Amersham, UK). The 1036-bp fragments from the pFAD2 plasmid produced by EcoR I + Sca I digestion were labelled with α-32P-dCTP (FuRui, China) using the Rediprime™II labelling kit (Amersham). The membranes were subsequently hybridised with the labelled probe according to standard protocols and exposed to X-ray film (Fuji Photo Film, Japan) for 24-48 hours at -80°C with an intensifying screen to obtain an autoradiograph image.

TAIL-PCR analysis of the 3' integration site

Three transgene specific primers (tgp1: 5'-ccttgagcatctgacttct-3'; tgp2: 5'-aagccttgacttgaggttagat-3'; tgp3: 5'-gcttggcgtaatcatggtca-3') and an arbitrary degenerate primer (5'-ngtcgaswganawgaa-3') were used for TAIL-PCR amplification. The thermal cycling conditions are summarised in Table Table1.1. Briefly, the primary PCR reaction contained 0.5-1.0 μg genomic DNA, 1.5 mM dNTPs, 0.2 μM of tgp1 primer, 2 μM of the a.d. primer, and 1 unit of Taq polymerase in 20 μl of 1 × reaction buffer. In the secondary or tertiary amplification, 0.65 μl of the first or secondary products, respectively, were used as templates and supplemented in the reaction. The products of tertiary TAIL-PCR reaction were separated on a 1.5% agarose gel. A single band in each mouse sample was gel purified with the TIANgel Midi Purification Kit (Tiangen, China) and sequenced directly. The resultant sequences were analysed using online BLAST from the database of Mus musculus genomic DNA

Table 1
Cycle Conditions used for TAIL-PCR

PCR analysis of transgene homozygotes and heterozygotes

Genomic DNA from the tails of C57 females (wild type), fad2 males (X+Y), or homozygous (X+X+) or heterozygous (X+X) fad2 females was used to determine their homozygosity or heterozygosity. In brief, genome-specific primers for 495-bp fragments (F: 5'-agtctgcaattttagatcctc-3'; R: 5'-gaagtttcagcagcaacac-3') and transgene-specific primers for 567-bp fragments were added to the same PCR reaction and amplified together. The PCR cycling parameters were as follows: 95°C for 5 min; 35 cycles of 94°C for 30 sec, 56°C for 30 sec, and 72°C for 60 sec; and 72°C for 10 min.

PCR analysis of the 5' integration site

Based on the results of the 3' integration analysis, each DNA sample of X+Y, X+X+, X+X or C57 mice was amplified by the following primer sets: P1 (F: 5'-cgctcagtcagtcaccag-3'; R: 5'-ggacttcgattaccgttt-3'), P2 (F: 5'-catcagtgctcccattct-3'; R: 5'-aacaggcttgtggtcatt-3'), and P3 (F: 5'-aactcaagggacaccaca-3'; R: 5'-aatccgcatgaataccag-3'). The three primer pairs corresponded to the upstream 3' integration regions from -54,088 to -53,884, -29,872 to -29,553, and -44,562 to -44,144, respectively. PCR amplification was performed as follows: 95°C for 5 min; 30 cycles of 94°C for 30 sec, 57.6°C for 30 sec, and 72°C for 60 sec; and a final extension at 72°C for 10 min. P4 forward primer at -46,680 (5'-agcctagtggtacatcat-3') or P5 forward primer at -45,797 (5'-ggtatcttgttccctattc-3') of the 3' integration upstream region was used along with the common reverse primer (5'-gccaagtgggcagttta-3'), corresponding to the CMV molecules needed to amplify the relevant junction sequences. P4 amplification was performed as follows: 95°C for 5 min; 40 cycles of 94°C for 30 sec, 56.4°C for 30 sec, and 72°C for 2 min; and a final extension at 72°C for 8 min. P5 conditions were: 40 cycles of 94°C for 30 sec, 58°C for 30 sec, and 72°C for 60 sec. P4 and P5 products were sequenced directly.


Total RNA was extracted from the fresh tissues (liver, kidney, brain, muscle and heart) of fad2 or C57 females with TRIzol Reagent (Tiangen) and treated with RNase-free DNase I (TaKaRa) to remove the remaining genomic DNA prior to RT-PCR. Purified RNA (0.5 μg) was used for first-strand cDNA synthesis. Reverse transcription was performed using M-MLV reverse transcriptase (Promega) with oligo-dT primers according to the manufacturer's instructions. Reactions in the absence of reverse transcriptase were also included for each RNA sample to check for DNA contamination. The resultant cDNA was used in PCR amplification to investigate the level of gene transcription. Besides the transcriptional amplification of the fad2 gene using transgene-specific primers (F: 5'-tacatcagcgacacaggcatc-3'; R: 5'-gtatttgtgagccagggcatt-3'), RT-PCR was also used to investigate the expression of the 5' integration upstream region from -1123 to -977 (F: 5'-agcctagtggtacatcat-3'; R: 5'-ttggcctacattagacat-3') and the 3' integration downstream region from +859 to +1166 (F: 5'-attaggtcccctcagtgtc-3'; R: 5'-ctcatctcagaaatcattaccc-3'), +1952 to +2299 (F: 5'-tgacagagcgtctaagga-3'; R: 5'-gaggtaacccaatcacaaa-3'), and +1952 to +3069 (F: 5'- tgacagagcgtctaagga-3'; R: 5'-cagaacaccaatggcttg-3'). The annealing temperature was 55°C, 55°C, 56°C, or 57.6°C, respectively. Concurrently, the 352-bp control fragments of the Hprt gene (F: 5'-cctgctggattacattaaagcactg-3'; R: 5'-gtcaagggcatatccaacaacaaac-3') were amplified as follows: 95°C for 5 min; 35 cycles of 94°C for 30 sec, 55°C for 30 sec, and 72°C for 60 sec; and final extension at 72°C for 8 min.

Real-time RT-PCR

Real-time RT-PCR was used to determine the relative expression of the fad2 transgene (F: 5'-ttccacaacatcaccgacac-3'; R: 5'-ctccacgtacaggcactcc-3') in transgenic kidney, brain and liver tissues. Gapdh (F: 5'-gaacatcatccctgcatcc-3'; R: 5'-ccagtgagcttcccgttca-3') was amplified concurrently as an endogenous control. Each sample from X+X+, X+X, C57 females or X+Y males was amplified in triplicate. Real-time PCR reactions were performed on an ABI Prism 7500 sequence detection system (Applied Biosystems) using SYBR® Premix Ex Taq™ II kits (TaKaRa), following the manufacturer's protocol. The thermocycling protocol was as follows: 95°C for 30 sec, 40 cycles of 95°C for 5 sec and 60°C for 34 sec. Expression of the fad2 gene was examined relative to the internal control gene using the 2(-ΔΔC(T)) method.

Statistical analysis

RNAs from two mice of each genotype were processed and amplified by real-time RT-PCR, with at least three measurements per animal. All values are presented as means ± SEM. A ratio was considered significant if the mean t-test P value was less than or equal to 0.05 for each of the samples. Prism 4 for Windows (GraphPad) was used for all calculations.

Authors' contributions

BY carried out the molecular studies and data analysis. DL participated in the design of the study and assisted in writing the manuscript. KG conceived of the study, and participated in its design and coordination and wrote the manuscript. All authors read and approved the final manuscript.


The work was supported by Natural Sciences of Foundation in China (30571332), and 973 Project of China (2004CB117500). We thank Professor Sheng Cui for real-time RT-PCR and Professor Yaofeng Zhao for critic discussion.


  • Nagy A, Gertsenstein M, Vintersten K, Behringer R. Manipulating the Mouse Embryo: A Laboratory Manual. 3. New York: Cold Spring Harbor Laboratory Press; 2003.
  • Houdebine L-M. Animal Transgenesis and Cloning. 1. John Wiley & Sons Ltd; 2003. full_text.
  • Brinster RL, Chen HY, Trumbauer M, Senear AW, Warren R, Palmiter RD. Somatic expression of herpes thymidine kinase in mice following injection of a fusion gene into eggs. Cell. 1981;27:223–231. doi: 10.1016/0092-8674(81)90376-7. [PubMed] [Cross Ref]
  • Jaenisch R. Transgenic animals. Science. 1988;240:1468–1474. doi: 10.1126/science.3287623. [PubMed] [Cross Ref]
  • Bishop JO, Smith P. Mechanism of chromosomal integration of microinjected DNA. Mol Biol Med. 1989;6:283–298. [PubMed]
  • Wurtele H, Little KC, Chartrand P. Illegitimate DNA integration in mammalian cells. Gene Ther. 2003;10:1791–1799. doi: 10.1038/ [PubMed] [Cross Ref]
  • Merrihew RV, Marburger K, Pennington SL, Roth DB, Wilson JH. High-frequency illegitimate integration of transfected DNA at preintegrated target sites in a mammalian genome. Mol Cell Biol. 1996;16:10–18. [PMC free article] [PubMed]
  • Rijkers T, Peetz A, Ruther U. Insertional mutagenesis in transgenic mice. Transgenic Res. 1994;3:203–215. doi: 10.1007/BF02336773. [PubMed] [Cross Ref]
  • Milot E, Belmaaza A, Wallenburg JC, Gusew N, Bradley WE, Chartrand P. Chromosomal illegitimate recombination in mammalian cells is associated with intrinsically bent DNA elements. EMBO J. 1992;11:5063–5070. [PubMed]
  • Kusakabe T, Sugimoto Y, Maeda T, Nakajima Y, Miyano M, Nishikawa J. et al. Linearization and integration of DNA into cells preferentially occurs at intrinsically curved regions from human LINE-1 repetitive element. Gene. 2001;274:271–281. doi: 10.1016/S0378-1119(01)00631-X. [PubMed] [Cross Ref]
  • Hamada T, Sasaki H, Seki R, Sakaki Y. Mechanism of chromosomal integration of transgenes in microinjected mouse eggs: sequence analysis of genome-transgene and transgene-transgene junctions at two loci. Gene. 1993;128:197–202. doi: 10.1016/0378-1119(93)90563-I. [PubMed] [Cross Ref]
  • Konopka AK. Compilation of DNA strand exchange sites for non-homologous recombination in somatic cells. Nucl Acids Res. 1988;16:1739–1758. doi: 10.1093/nar/16.5.1739. [PMC free article] [PubMed] [Cross Ref]
  • Liu YG, Whittier RF. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics. 1995;25:674–681. doi: 10.1016/0888-7543(95)80010-J. [PubMed] [Cross Ref]
  • Liu YG, Mitsukawa N, Oosumi T, Whittier RF. Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J. 1995;8:457–463. doi: 10.1046/j.1365-313X.1995.08030457.x. [PubMed] [Cross Ref]
  • Yanaka N, Kobayashi K, Wakimoto K, Yamada E, Imahie H, Imai Y. et al. Insertional Mutation of the Murine Kisimo Locus Caused a Defect in Spermatogenesis. Journal of Biological Chemistry. 2000;275:14791–14794. doi: 10.1074/jbc.C901047199. [PubMed] [Cross Ref]
  • Babushok DV, Ostertag EM, Courtney CE, Choi JM, Kazazian HH Jr. L1 integration in a transgenic mouse model. Genome Res. 2006;16:240–250. doi: 10.1101/gr.4571606. [PubMed] [Cross Ref]
  • Pillai MM, Venkataraman GM, Kosak S, Torok-Storb B. Integration site analysis in transgenic mice by thermal asymmetric interlaced (TAIL)-PCR: segregating multiple-integrant founder lines and determining zygosity. Transgenic Res. 2008;17:749–754. doi: 10.1007/s11248-007-9161-4. [PubMed] [Cross Ref]
  • Palmiter RD, Brinster RL. Germ-line transformation of mice. Annu Rev Genet. 1986;20:465–499. doi: 10.1146/ [PubMed] [Cross Ref]
  • Woychik RP, Stewart TA, Davis LG, D'Eustachio P, Leder P. An inherited limb deformity created by insertional mutagenesis in a transgenic mouse. Nature. 1985;318:36–40. doi: 10.1038/318036a0. [PubMed] [Cross Ref]
  • Weiher H, Noda T, Gray DA, Sharpe AH, Jaenisch R. Transgenic mouse model of kidney disease: insertional inactivation of ubiquitously expressed gene leads to nephrotic syndrome. Cell. 1990;62:425–434. doi: 10.1016/0092-8674(90)90008-3. [PubMed] [Cross Ref]
  • Wilkie TM, Palmiter RD. Analysis of the integrant in MyK-103 transgenic mice in which males fail to transmit the integrant. Mol Cell Biol. 1987;7:1646–1655. [PMC free article] [PubMed]
  • Mahon KA, Overbeek PA, Westphal H. Prenatal Lethality in a Transgenic Mouse Line is the Result of a Chromosomal Translocation. PNAS. 1988;85:1165–1168. doi: 10.1073/pnas.85.4.1165. [PubMed] [Cross Ref]
  • Radice G, Lee JJ, Costantini F. H beta 58, an insertional mutation affecting early postimplantation development of the mouse embryo. Development. 1991;111:801–811. [PubMed]
  • Covarrubias L, Nishida Y, Mintz B. Early Postimplantation Embryo Lethality due to DNA Rearrangements in a Transgenic Mouse Strain. PNAS. 1986;83:6020–6024. doi: 10.1073/pnas.83.16.6020. [PubMed] [Cross Ref]
  • Mark WH, Signorelli K, Blum M, Kwee L, Lacy E. Genomic structure of the locus associated with an insertional mutation in line 4 transgenic mice. Genomics. 1992;13:159–166. doi: 10.1016/0888-7543(92)90216-F. [PubMed] [Cross Ref]
  • Beamer WG, Shultz KL, Tennent BJ, Nadeau JH, Churchill GA, Eicher EM. Multigenic and Imprinting Control of Ovarian Granulosa Cell Tumorigenesis in Mice. Cancer Res. 1998;58:3694–3699. [PubMed]
  • Dorward AM, Shultz KL, Ackert-Bicknell CL, Eicher EM, Beamer WG. High-Resolution Genetic Map of X-Linked Juvenile-Type Granulosa Cell Tumor Susceptibility Genes in Mouse. Cancer Res. 2003;63:8197–8202. [PubMed]
  • Costantini F, Lacy E. Introduction of a rabbit beta-globin gene into the mouse germ line. Nature. 1981;294:92–94. doi: 10.1038/294092a0. [PubMed] [Cross Ref]
  • Allen MJ, Jeffreys AJ, Surani MA, Barton S, LNorris M, Collick A. Tandemly repeated transgenes of the human minisatellite MS32 (D1S8), with novel mouse gamma satellite integration. Nucl Acids Res. 1994;22:2976–2981. doi: 10.1093/nar/22.15.2976. [PMC free article] [PubMed] [Cross Ref]
  • Rohan RM, King D, Frels WI. Direct sequencing of PCR-amplified junction fragments from tandemly repeated transgenes. Nucl Acids Res. 1990;18:6089–6095. doi: 10.1093/nar/18.20.6089. [PMC free article] [PubMed] [Cross Ref]
  • Brinster RL, Braun RE, Lo D, Avarbock MR, Oram F, Palmiter RD. Targeted Correction of a Major Histocompatibility Class II Ealpha Gene by DNA Microinjected into Mouse Eggs. PNAS. 1989;86:7087–7091. doi: 10.1073/pnas.86.18.7087. [PubMed] [Cross Ref]
  • Garcia P, Gasc AM, Kyriakidis X, Baty D, Sicard M. DNA sequences required to induce localized conversion in Streptococcus pneumoniae transformation. Mol Gen Genet. 1988;214:509–513. doi: 10.1007/BF00330488. [PubMed] [Cross Ref]
  • Polisson C, Morgan RD. Asel, a restriction endonuclease from Aquaspirillum serpens which recognizes 5'AT TAAT3'. Nucl Acids Res. 1988;16:10365. doi: 10.1093/nar/16.21.10365. [PMC free article] [PubMed] [Cross Ref]
  • de Vries J, Wackernagel W. Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proceedings of the National Academy of Sciences of the United States of America. 2002;99:2094–2099. doi: 10.1073/pnas.042263399. [PubMed] [Cross Ref]
  • Prudhomme M, Libante V, Claverys JP. Homologous recombination at the border: Insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae. Proceedings of the National Academy of Sciences of the United States of America. 2002;99:2100–2105. doi: 10.1073/pnas.032262999. [PubMed] [Cross Ref]
  • Meier P, Wackernagel W. Mechanisms of homology-facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri. Mol Microbiol. 2003;48:1107–1118. doi: 10.1046/j.1365-2958.2003.03498.x. [PubMed] [Cross Ref]
  • Sakagami K, Tokinaga Y, Yoshikura H, Kobayashi I. Homology-associated nonhomologous recombination in mammalian gene targeting. Proceedings of the National Academy of Sciences of the United States of America. 1994;91:8527–8531. doi: 10.1073/pnas.91.18.8527. [PubMed] [Cross Ref]
  • Lanoix J, Acheson NH. A rabbit beta-globin polyadenylation signal directs efficient termination of transcription of polyomavirus DNA. EMBO J. 1988;7:2515–2522. [PubMed]
  • Levitt N, Briggs D, Gil A, Proudfoot NJ. Definition of An Efficient Synthetic Poly(A) Site. Genes & Development. 1989;3:1019–1025. [PubMed]
  • Rohrbaugh ML, Johnson JE, James MD, Hardison RC. Transcription unit of the rabbit beta 1 globin gene. Mol Cell Biol. 1985;5:147–160. [PMC free article] [PubMed]
  • Lyon MF. Gene action in the X-chromosome of the mouse (Mus musculus L.) Nature. 1961;190:372–373. doi: 10.1038/190372a0. [PubMed] [Cross Ref]
  • Chow J, Heard E. X inactivation and the complexities of silencing a sex chromosome. Curr Opin Cell Biol. 2009;21:359–366. doi: 10.1016/ [PubMed] [Cross Ref]
  • Goldman MA, Stokes KR, Idzerda RL, McKnight GS, Hammer RE, Brinster RL. et al. A chicken transferrin gene in transgenic mice escapes X-chromosome inactivation. Science. 1987;236:593–595. doi: 10.1126/science.2437652. [PubMed] [Cross Ref]
  • Krumlauf R, Chapman VM, Hammer RE, Brinster R, Tilghman SM. Differential expression of alpha-fetoprotein genes on the inactive X chromosome in extraembryonic and somatic tissues of a transgenic mouse line. Nature. 1986;319:224–226. doi: 10.1038/319224a0. [PubMed] [Cross Ref]
  • Hadjantonakis AK, Cox LL, Tam PP, Nagy A. An X-linked GFP transgene reveals unexpected paternal X-chromosome activity in trophoblastic giant cells of the mouse placenta. Genesis. 2001;29:133–140. doi: 10.1002/gene.1016. [PubMed] [Cross Ref]
  • Soriano P, Keitges EA, Schorderet DF, Harbers K, Gartler SM, Jaenisch R. High Rate of Recombination and Double Crossovers in the Mouse Pseudoautosomal Region during Male Meiosis. PNAS. 1987;84:7218–7220. doi: 10.1073/pnas.84.20.7218. [PubMed] [Cross Ref]
  • Harbers K, Soriano P, Muller U, Jaenisch R. High frequency of unequal recombination in pseudoautosomal region shown by proviral insertion in transgenic mouse. Nature. 1986;324:682–685. doi: 10.1038/324682a0. [PubMed] [Cross Ref]

Articles from BMC Molecular Biology are provided here courtesy of BioMed Central