Figure 4

Thy-ncR1 transcripts are cytoplasmic but are not susceptible to NMD. A. Subcellular distribution of Thy-ncR1 isoforms. HPB-ALL cells were fractionated into nuclear and cytoplasmic fractions. RNA prepared from each fraction was used for qRT-PCR analyses. The levels of Thy-ncR1 isoforms (exon 1-3, 2-3, and 4-5) and precursor retaining intron 1 (int1-ex2) were quantified in the nuclear and cytoplasmic fractions. GAPDH and β-actin mRNA are the controls for cytoplasmic RNA, and β-actin pre-mRNA (actin intron) is the control for nuclear RNA. Thy-ncR1 is not susceptible to NMD. B. Potential ORFs (closed boxes) in Thy-ncR1 exons. The scales (nt) are shown below the diagram. C. Depletion of hUPF1 from Jurkat cells treated with siRNA (si-hUPF1) was confirmed by immunoblot analysis with anti-hUPF1 antibody. D. qRT-PCR analyses of Thy-ncR1 isoforms and known NMD targets (gas5 and UHG) in control (NC, adjusted to 100%) and hUPF1-depleted cells (si-hUPF1) as shown in B. Bars represent means ± SD for three independent experiments.