Analysis of a structured intronic region of the LMP2 pre-mRNA from EBV reveals associations with human regulatory proteins and nuclear actin

Figures

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  Fig. 1. Validation of protein interactors. a Secondary structure model of the intronic sequence. hnRNP A1, hnRNP U and HuR binding sites predicted by RBPmap are color coded. b Fold enrichment of the LMP2 pre-mRNA following RIPs carried out with antibodies against hnRNP A1, hnRNP U, hnRNP L, HuR, PSF and NONO. c Fold enrichment of pre-mRNA (junction spanning primers) and intron (internal primers) following RIPs with anti-actin antibody. Data represents the average (with standard deviation) of independent experiments all normalized to control RIP with IgG. All RIPs (except for RIPs for NONO and hnRNP L) were carried out as either 2 or 3 independent experiments. All primer sequences used for the experiments are included in Additional file 6: Table S4

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  Fig. 2. RT-PCR and qPCR analysis of spliced and unspliced transcripts following disruption of actin polymerization in BJAB B1 cells. a A cartoon of LMP2B with locations of exons RT-PCR primer sites and a model of the structured region is at the top. Below this are the results of RT-PCR analyses of spliced and unspliced transcripts in the presence of Latrunculin. b Spliced and unspliced variants quantified by qPCR analysis. Data shown are first normalized to housekeeping gene HPRT and plotted as a fold difference compared to the control at each time point. All data represents the mean (with standard deviation) from two independent experiments (*p < 0.05). All primer sequences used for the experiments are included in Additional file 6: Table S4