T a single product had been amplified in each real-time reaction.Cell Culture, Transfection, and RNA ExtractionHuman cervix carcinoma HeLa cells were maintained in Dulbecco modified Eagle’s medium (EuroClone, Milan, Italy), HepG2 cells were cultured in RPMI 1640 (EuroClone) additioned with sodium pyruvate (1 mM; Sigma-Aldrich). Both media were supplemented with 10 fetal bovine serum, 1 glutamine, and antibiotics (100 U/mL penicillin and 100 mg/mL streptomycin; EuroClone). Cells were grown at 37uC in a humidified atmosphere of 5 CO2 and 95 air, according to standard procedures. In each transfection experiment, an equal number of cells (250,000) were transiently transfected in 6-well plates with the Fugene HD reagent (Promega, Madison, WI, USA) and 4 mg of plasmid DNA, following the manufacturer’s instructions. Twentyfour hours after transfection, cells were washed twice with phosphate-buffered saline and total RNA was extracted by using the EUROzol reagent (EuroClone), according to the manufacturer’s instructions.Fluorescent RT-PCRTo quantify splice products, an aliquot (1 mL) of the total reverse-transcription reaction (20 mL) was used as template in a standard RT-PCR amplification using a fluorescein-labeled exonic forward primer (FGG x5-F-FAM: 59-[6FAM]AGAAGGTAGCCCAGCTTGA-39) and the exonic reverse oligonucleotide FGG x7-R (59-ATTCCAGTCTTCCAGTTCCA-39). For experiments in HepG2, the reverse primer was substituted with the commercial pTargeT sequencing primer (Promega) to discriminate transcripts produced by the transfected construct from the endogenous FGG mRNA. PCRs were carried out under standard conditions using the FastStart Taq DNA Polymerase (Roche) on a Mastercycler EPgradient (Eppendorf AG, Hamburg, Germany). PCR reactions were separated on an ABI-3130XL sequencer and the peak areas measured by the PD1-PDL1 inhibitor 1 GeneMapper v4.0 software. The level of pseudoexon inclusion was assessed by measuring the ratio of the fluorescence peak areas corresponding to the transcript including or skipping the pseudoexon. Because the two PCR products are amplified by the same primers, and the two amplicons have similar amplification efficiencies (as assessed by generating standard curves for each amplicon using real-time PCR, data not shown), the ratio of amplified products reflects the relative abundance of the templates before PCR.RNA InterferenceFor hnRNP H and F Hexokinase II Inhibitor II, 3-BP web knockdown 150,000 HeLa cells were seeded on 3.5-cm multiwell plates. After 24 hours, 5 mL Oligofectamine (Life Technologies) were mixed with 15 mL Opti-MEM I reduced serum medium (Life Technologies), incubated at room temperature for 7 minutes and added to 2.5 mL (25 pmol) of siRNA duplex (10 mM), which had been mixed with 175 mL Opti-MEM I. The mixture was incubated at room temperature for 20 minutes, and then added 1527786 to the cells. After 24 hours, effector and reporter constructs were transfected as described above. Cells were grown for an additional 24 hours followed by RNA and protein extraction. The 20-nt target sequences in hnRNP H and F were 59-GGAAATAGCTGAAAAGGCT-39 and 59-GCGACCGAGAACGACATTT-39, respectively. A pre-designed siRNA targeting luciferase (Target Sequence: 59-CGTACGCGGAATACTTCGA-39) (EuroClone) was used as negative control. Silencing efficiency was assessed by Western blotting performed according to standard protocols. The effect of siRNA treatment against hnRNP H and F on pseudoexon inclusion was assessed by real-time RT-PCR with transcriptspecific amplicons, as further det.T a single product had been amplified in each real-time reaction.Cell Culture, Transfection, and RNA ExtractionHuman cervix carcinoma HeLa cells were maintained in Dulbecco modified Eagle’s medium (EuroClone, Milan, Italy), HepG2 cells were cultured in RPMI 1640 (EuroClone) additioned with sodium pyruvate (1 mM; Sigma-Aldrich). Both media were supplemented with 10 fetal bovine serum, 1 glutamine, and antibiotics (100 U/mL penicillin and 100 mg/mL streptomycin; EuroClone). Cells were grown at 37uC in a humidified atmosphere of 5 CO2 and 95 air, according to standard procedures. In each transfection experiment, an equal number of cells (250,000) were transiently transfected in 6-well plates with the Fugene HD reagent (Promega, Madison, WI, USA) and 4 mg of plasmid DNA, following the manufacturer’s instructions. Twentyfour hours after transfection, cells were washed twice with phosphate-buffered saline and total RNA was extracted by using the EUROzol reagent (EuroClone), according to the manufacturer’s instructions.Fluorescent RT-PCRTo quantify splice products, an aliquot (1 mL) of the total reverse-transcription reaction (20 mL) was used as template in a standard RT-PCR amplification using a fluorescein-labeled exonic forward primer (FGG x5-F-FAM: 59-[6FAM]AGAAGGTAGCCCAGCTTGA-39) and the exonic reverse oligonucleotide FGG x7-R (59-ATTCCAGTCTTCCAGTTCCA-39). For experiments in HepG2, the reverse primer was substituted with the commercial pTargeT sequencing primer (Promega) to discriminate transcripts produced by the transfected construct from the endogenous FGG mRNA. PCRs were carried out under standard conditions using the FastStart Taq DNA Polymerase (Roche) on a Mastercycler EPgradient (Eppendorf AG, Hamburg, Germany). PCR reactions were separated on an ABI-3130XL sequencer and the peak areas measured by the GeneMapper v4.0 software. The level of pseudoexon inclusion was assessed by measuring the ratio of the fluorescence peak areas corresponding to the transcript including or skipping the pseudoexon. Because the two PCR products are amplified by the same primers, and the two amplicons have similar amplification efficiencies (as assessed by generating standard curves for each amplicon using real-time PCR, data not shown), the ratio of amplified products reflects the relative abundance of the templates before PCR.RNA InterferenceFor hnRNP H and F knockdown 150,000 HeLa cells were seeded on 3.5-cm multiwell plates. After 24 hours, 5 mL Oligofectamine (Life Technologies) were mixed with 15 mL Opti-MEM I reduced serum medium (Life Technologies), incubated at room temperature for 7 minutes and added to 2.5 mL (25 pmol) of siRNA duplex (10 mM), which had been mixed with 175 mL Opti-MEM I. The mixture was incubated at room temperature for 20 minutes, and then added 1527786 to the cells. After 24 hours, effector and reporter constructs were transfected as described above. Cells were grown for an additional 24 hours followed by RNA and protein extraction. The 20-nt target sequences in hnRNP H and F were 59-GGAAATAGCTGAAAAGGCT-39 and 59-GCGACCGAGAACGACATTT-39, respectively. A pre-designed siRNA targeting luciferase (Target Sequence: 59-CGTACGCGGAATACTTCGA-39) (EuroClone) was used as negative control. Silencing efficiency was assessed by Western blotting performed according to standard protocols. The effect of siRNA treatment against hnRNP H and F on pseudoexon inclusion was assessed by real-time RT-PCR with transcriptspecific amplicons, as further det.
