Verlap extension PCR ofAnalysis of Recurrent Mutations in HAS1 IntronGenomic DNA

Verlap extension PCR ofAnalysis of Recurrent Mutations in HAS1 IntronGenomic DNA was prepared from PBMC using Trizol reagent (Invitrogen). HAS1 intron 3 region was amplified from 50 ng genomic DNA using 59outer SNPs/39exon4 NT-157 primer set at 94uC for Table 1. Summary of primer sequences.Primer E3 E5 E5I4 59Vb-specific 59outer SNPs 39exon 4 HAS1seq59 HAS1seq39 b2m b2mOrientation sense antisense antisense sense sense antisense sense antisense sense antisenseSequence 59GGGCTTGTCAGAGCTACT T39 59AGGGCGTCTCTGAGTAGCAG 39 59CTGGAGGTGTACCTGCACGGGGGC39 59GCGGTCCTCTAGAATCCTGCCCAG39 59TGTTCAGATCGGTTGCAGAGT39 59CATGCACACACGCTAGGATA39 59GGGGTCTGTGCTGATCCTGG39 59AACTGCTGCAAGAGGTTATTCC39 59CCAGCAGAGAATGGAAAGTC39 59GATGCTGCTTACATGTCTCGdoi:10.1371/Calyculin A chemical information journal.pone.0053469.tIntronic Changes Alter HAS1 Splicing30 s, 60uC for 30 s, and 72uC for 30 s for 35 cycles. The amplicon was treated with ExoSAP-IT reagent (USB) to 1326631 remove excess primers and deoxyribonucleotides and subjected to direct sequencing using HAS1seq59 or HAS1seq39 primer and BigDye Terminator v3.1 (Applied Biosystems). Sequencing reaction was run on an ABI Prism 3130xl Genetic Analyzer (Applied Biosystems) and data were analyzed by DNA Sequencing Analysis Software v5.1 and SeqScape Software v2.5. Primer sequences are summarized in Table 1. Polymerase error rate in this study is shown to be less than 1 in 14,000 bp.Results 1. In vitro Analysis of Minigene Construct Characterizes Alternative Splicing of Human HASHAS1 splicing analysis has been established in a mammalian expression system where splicing products can be assessed by RTPCR. Transient expression driven by the HAS1 minigene G345 construct (Figure 1A) yielded mainly full-length transcripts (FL) and varieties of alternatively spliced products similar to those found in ex vivo analysis [19] including a newly identified isoform termed HAS1Vd. Among HAS1 splice variants, Va (exon 4 skipped) is the most abundant, being detected along with FL on agarose gel when E3/E5 primer set was used (Figure 1B). Other variants are best determined by DNA fragment analysis using a selective primer set. HAS1Vb (exon 4 skipped and 59 bp downstream intron 4 retained) is of most interest due to its relevance in MM patients. Amplification by E3/E5I4 primer set predictably detected only HAS1Vb as E5I4 primer binds to exon 5/intron 4 junction. However, we always found another isoform, termed HAS1Vd, co-amplified with HAS1Vb, suggesting it is a common spliced product that has not been reported in the clinical studies (Figure 1C). Sequencing analysis showed that both Vb and Vd utilized the same alternative 39SS that retained 59 bp of downstream intron 24786787 4 (259): these two variants differed only in the inclusion (Vd) or exclusion (Vb) of exon 4 (133 bp). Overall, the splicing profile of G345 mimics normal HAS1 splicing and thus provides a model to study intronic sequence manipulation of the human HAS1 minigene.Figure 1. In vitro splicing analysis of human HAS1 minigene. Constructs FLc and G345 are shown in (A). Arrows show where PCR primers bind (E3, E5 and E5I4). The length of each intron in G345 is shown in bp. Each construct was transfected into HeLa cells and HAS1 splicing was studied by RT-PCR. Using E3/E5 primer set, products were analyzed by agarose gel electrophoresis (B). For E3/E5I4 primer set, amplicons were analyzed by DNA fragment analysis (C). Splice junctions for each product are also illustrated. ? mock transfection; b2m, control. doi:10.1371/journal.pone.00.Verlap extension PCR ofAnalysis of Recurrent Mutations in HAS1 IntronGenomic DNA was prepared from PBMC using Trizol reagent (Invitrogen). HAS1 intron 3 region was amplified from 50 ng genomic DNA using 59outer SNPs/39exon4 primer set at 94uC for Table 1. Summary of primer sequences.Primer E3 E5 E5I4 59Vb-specific 59outer SNPs 39exon 4 HAS1seq59 HAS1seq39 b2m b2mOrientation sense antisense antisense sense sense antisense sense antisense sense antisenseSequence 59GGGCTTGTCAGAGCTACT T39 59AGGGCGTCTCTGAGTAGCAG 39 59CTGGAGGTGTACCTGCACGGGGGC39 59GCGGTCCTCTAGAATCCTGCCCAG39 59TGTTCAGATCGGTTGCAGAGT39 59CATGCACACACGCTAGGATA39 59GGGGTCTGTGCTGATCCTGG39 59AACTGCTGCAAGAGGTTATTCC39 59CCAGCAGAGAATGGAAAGTC39 59GATGCTGCTTACATGTCTCGdoi:10.1371/journal.pone.0053469.tIntronic Changes Alter HAS1 Splicing30 s, 60uC for 30 s, and 72uC for 30 s for 35 cycles. The amplicon was treated with ExoSAP-IT reagent (USB) to 1326631 remove excess primers and deoxyribonucleotides and subjected to direct sequencing using HAS1seq59 or HAS1seq39 primer and BigDye Terminator v3.1 (Applied Biosystems). Sequencing reaction was run on an ABI Prism 3130xl Genetic Analyzer (Applied Biosystems) and data were analyzed by DNA Sequencing Analysis Software v5.1 and SeqScape Software v2.5. Primer sequences are summarized in Table 1. Polymerase error rate in this study is shown to be less than 1 in 14,000 bp.Results 1. In vitro Analysis of Minigene Construct Characterizes Alternative Splicing of Human HASHAS1 splicing analysis has been established in a mammalian expression system where splicing products can be assessed by RTPCR. Transient expression driven by the HAS1 minigene G345 construct (Figure 1A) yielded mainly full-length transcripts (FL) and varieties of alternatively spliced products similar to those found in ex vivo analysis [19] including a newly identified isoform termed HAS1Vd. Among HAS1 splice variants, Va (exon 4 skipped) is the most abundant, being detected along with FL on agarose gel when E3/E5 primer set was used (Figure 1B). Other variants are best determined by DNA fragment analysis using a selective primer set. HAS1Vb (exon 4 skipped and 59 bp downstream intron 4 retained) is of most interest due to its relevance in MM patients. Amplification by E3/E5I4 primer set predictably detected only HAS1Vb as E5I4 primer binds to exon 5/intron 4 junction. However, we always found another isoform, termed HAS1Vd, co-amplified with HAS1Vb, suggesting it is a common spliced product that has not been reported in the clinical studies (Figure 1C). Sequencing analysis showed that both Vb and Vd utilized the same alternative 39SS that retained 59 bp of downstream intron 24786787 4 (259): these two variants differed only in the inclusion (Vd) or exclusion (Vb) of exon 4 (133 bp). Overall, the splicing profile of G345 mimics normal HAS1 splicing and thus provides a model to study intronic sequence manipulation of the human HAS1 minigene.Figure 1. In vitro splicing analysis of human HAS1 minigene. Constructs FLc and G345 are shown in (A). Arrows show where PCR primers bind (E3, E5 and E5I4). The length of each intron in G345 is shown in bp. Each construct was transfected into HeLa cells and HAS1 splicing was studied by RT-PCR. Using E3/E5 primer set, products were analyzed by agarose gel electrophoresis (B). For E3/E5I4 primer set, amplicons were analyzed by DNA fragment analysis (C). Splice junctions for each product are also illustrated. ? mock transfection; b2m, control. doi:10.1371/journal.pone.00.