Homologous illegitimate random integration of foreign DNA into the X chromosome of a transgenic mouse line
© Yan et al; licensee BioMed Central Ltd. 2010
Received: 21 April 2010
Accepted: 13 August 2010
Published: 13 August 2010
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 . 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 . 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
Identity of the 3' integration site
Junction sequence analysis also showed that there was an additional 29-bp fragment (Figure 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 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
Identity of the 5' integration site
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 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 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 4C).
Transcription level of the X-linked transgene
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 , translocation , and deletions [23–25]. The length of the deleted genome segments might be from 2-3 kb  to 22 kb . 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.
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 . 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 6, Figure 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 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 6). This sequence motif is required to induce a localised conversion in Streptococcus pneumoniae transformation . The Ase I restriction endonuclease can recognise and cleave the sequence between the TT dinucleotide . 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 . 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 . In addition, in Pseudomonas stutzeri a similar phenomenon was observed, in which part of the short anchor segments recombined into the host genome . In eukaryotes, events of illegitimate integration whose homologous sequences are very short (≤5 bp) are also found in mammalian cells [7, 37], transgenic embryos , and mice . Taken together, our observations suggest that the HIRI process is present in all organisms undergoing transformation/transgenesis (Figure 9A).
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 6). Similar results have been found in the transgenic embryo . 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 . 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 . 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 , 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 . 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 . In fad2 mice, the transgene was expressed efficiently under the driven of the CMV enhancer and β-actin promoter (Figure 7, Figure 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 , 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 7F).
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  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.
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 , 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
Cycle Conditions used for TAIL-PCR
95°C, 5 min
94°C, 10 sec; 63°C, 30 sec; 72°C, 3 min
94°C, 10 sec; 25°C, 3 min; 72°C, 2.5 min
94°C, 10 sec; 63°C, 3 min; 72°C, 2.5 min; 94°C, 10 sec; 63°C, 3 min; 72°C, 2.5 min; 94°C, 10 sec; 44°C, 1 min; 72°C, 2.5 min
95°C, 5 min
94°C, 10 sec; 65°C, 3 min; 72°C, 2.5 min; 94°C, 10 sec; 65°C, 3 min; 72°C, 2.5 min; 94°C, 10 sec; 44°C, 1 min; 72°C, 2.5 min
95°C, 5 min
94°C, 10 sec; 65°C, 3 min; 72°C, 2.5 min; 94°C, 10 sec; 65°C, 3 min; 72°C, 2.5 min; 94°C, 10 sec; 44°C, 1 min; 72°C, 2.5 min
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 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.
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.
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.
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