used as control. Genomic DNA was digested with AluI and RsaI, and then labeled with Genomic DNA Labeling Kit Plus (Agilent Technologies). Labeled DNA was purified with Microcon YM-30 (Millipore Corporation). The sample genomes were hybridized with Human Genome CGH 244 K Microarray slide (Agilent Technologies). The array slide was scanned by GenePix 4000 B (Axon Instruments Inc.) and analyzed with DNA Analytics ver 4.0 (Agilent Technologies).Establishment of Nalm-6-MSH+Two loxP sites in pENTR lox-Hyg were replaced with different mutant loxP (mloxP) sequences (lox66 and lox71) [24,25] (Method S1). The hygromycin-resistance gene was replaced with the neomycin-resistance gene. The resulting plasmid was named pENTR mloxP-Neo. All PCR reactions were performed with KOD FX (TOYOBO). MSH2 genomic fragment containing the region between a splicing acceptor of intron 8 and exon 9 was amplified by PCR using TK6 genomic DNA as template and primers of MSH2-I8 BamHI-Fw and MSH2-E9 Rv. The DNA fragment was digested with EcoRI/BamHI and the digested DNA was ligated into pBluescript II SK(+) (Agilent Technologies) at the same sites. The resulting plasmid was named pBluescript II SK(+)MSH2 I8-E9. MSH2 cDNA fragments containing the region between exon 9 and exon 16 were amplified by reverse transcription (RT)-PCR with TaKaRa RNA PCR Kit (AMV) Ver.3.0 using TK6 total RNA as template and primers of MSH2E8 Fw and MSH2-E16 XhoI-Rv, and ligated into pBluescript II SK(+)-MSH2 I8-E9 at the EcoRI/XhoI sites. The resulting plasmid was named pBluescript II SK(+)-MSH2 I8-E16. MSH2 genomic fragments containing the region between exon 16 and 39untranslated region (39-UTR) were amplified by PCR using TK6 genomic DNA as template and primers of MSH2-E16 Fw and MSH2-39UTR XhoI-Rv, and ligated into pBluescript II SK(+)-MSH2 I8-E16 at the HpaI/XhoI sites. The plasmid DNA was digested with BamHI/XhoI. The resulting DNA fragment containing the region from the splicing acceptor site of intron8 to the 39-UTR was blunt-ended and subcloned into pENTR mloxPNeo at the blunt-EcoRI site. Genomic fragments surrounding intron 8 of MSH2 with the DNA size of 2.4- and 3.0-kb, respectively, were amplified by PCR using Nalm-6 genomic DNA as template and were used as 59- and 39- arms, respectively, of MultiSite Gateway system. Two primer sets of MSH2-59arm Fw and Rv and MSH2-39arm Fw and Rv were used to amplify 59-arm and 39-arm, respectively. pENTR Pluripotin site mloxP-Neo containing the 
splicing acceptor, cDNA of exon 9 to exon 16 and the 39-UTR of the MSH2 gene, two plasmid DNAs containing 59-arm or 39-arm and pDEST DTA-MLS were mixed to generate a targeting vector to restore MSH2 expression in Nalm-6 cells according to the protocol of MultiSite Gateway system. Then, the targeting vector was linearized with PmeI and the linearized DNA was transfected into Nalm-6 cells. The transfected cells were selected in the medium containing G418 as described above. Targeted clones were identified by PCR screening using primers of MSH2 GT-Fw and 39-loxP. MSH2 mRNA was confirmed by RT-PCR with TaKaRa RNA PCR Kit (AMV) Ver.3.0 using primers of MSHMater.O and Life Technologies, respectively. 1516647 Gene targeting vectors were constructed by using MultiSite Gateway Three-Fragment Vector Construction Kit (Life Technologies) as previously described [21].Comparative Genome Hybridization (CGH) Array AnalysesGenomic DNA was extracted with Gentra Puregene Core Kit A (QIAGEN). The genome of human lymphoblastic cell line TK6 [22,23] was used as control. Genomic DNA was digested with AluI and RsaI, and then labeled with Genomic DNA Labeling Kit Plus (Agilent Technologies). Labeled DNA was purified with Microcon YM-30 (Millipore Corporation). The sample genomes were hybridized with Human Genome CGH 244 K Microarray slide (Agilent Technologies). The array slide was scanned by GenePix 4000 B (Axon Instruments Inc.) and analyzed with DNA Analytics ver 4.0 (Agilent Technologies).Establishment of Nalm-6-MSH+Two loxP sites in pENTR lox-Hyg were replaced with different mutant loxP (mloxP) sequences (lox66 and lox71) [24,25] (Method S1). The hygromycin-resistance gene was replaced with the neomycin-resistance gene. The resulting plasmid was named pENTR mloxP-Neo. All PCR reactions were performed with KOD FX (TOYOBO). MSH2 genomic fragment containing the region between a splicing acceptor of intron 8 and exon 9 was amplified by PCR using TK6 genomic DNA as template and primers of MSH2-I8 BamHI-Fw and MSH2-E9 Rv. The DNA fragment was digested with EcoRI/BamHI and the digested DNA was ligated into pBluescript II SK(+) (Agilent Technologies) at the same sites. The resulting plasmid was named pBluescript II SK(+)MSH2 I8-E9. MSH2 cDNA fragments containing the region between exon 9 and exon 16 were amplified by reverse transcription (RT)-PCR with TaKaRa RNA PCR Kit (AMV) Ver.3.0 using TK6 total RNA as template and primers of MSH2E8 Fw and MSH2-E16 XhoI-Rv, and ligated into pBluescript II SK(+)-MSH2 I8-E9 at the EcoRI/XhoI sites. The resulting plasmid was named pBluescript II SK(+)-MSH2 I8-E16. MSH2 genomic fragments containing the region between exon 16 and 39untranslated region (39-UTR) were amplified by PCR using TK6 genomic DNA as template and primers of MSH2-E16 Fw and MSH2-39UTR XhoI-Rv, and ligated into pBluescript II SK(+)-MSH2 I8-E16 at the HpaI/XhoI sites. The plasmid DNA was digested with BamHI/XhoI. The resulting DNA fragment containing the region from the splicing acceptor site of intron8 to the 39-UTR was blunt-ended and subcloned into pENTR mloxPNeo at the blunt-EcoRI site. Genomic fragments surrounding intron 8 of MSH2 with the DNA size of 2.4- and 3.0-kb, respectively, were amplified by PCR using Nalm-6 genomic DNA as template and were used as 59- and 39- arms, respectively, of MultiSite Gateway system. Two primer sets of MSH2-59arm Fw and Rv and MSH2-39arm Fw and Rv were used to amplify 59-arm and 39-arm, respectively. pENTR mloxP-Neo containing the splicing acceptor, cDNA of exon 9 to exon 16 and the 39-UTR of the MSH2 gene, two plasmid DNAs containing 59-arm or 39-arm and pDEST DTA-MLS were mixed to generate a targeting vector to restore MSH2 expression in Nalm-6 cells according to the protocol of MultiSite Gateway system. Then, the targeting vector was linearized with PmeI and the linearized DNA was transfected into Nalm-6 cells. The transfected cells were selected in the medium containing G418 as described above. Targeted clones were identified by PCR screening using primers of MSH2 GT-Fw and 39-loxP. MSH2 mRNA was confirmed by RT-PCR with TaKaRa RNA PCR Kit (AMV) Ver.3.0 using primers of MSHMater.