Fig. 6

Comparison of phenotypes arising from lncRNA genomic deletion mutants and phenotypes arising from RNAi-mediated knock-down of lncRNA transcript. To compare the effects of the disruption of a lncRNA genomic locus to the knock-down of the corresponding lncRNA transcript by RNAi, the mean brood size reduction compared to the control (a) and the ratio of the length at 50 h relative to the control (b) were plotted. These are shown as a scatter plot of the mean reduction (a, blue circle) or the mean ratio (b, blue circle) with the 95% confidence interval of the mean (orange lines). If the mutations or the RNAi yield an effect, data fall below the line y = 1 and to the left of x = 1. If mutants and RNAi yield similar effects, data fall along the red line; above the red line indicates that RNAi has a greater effect, while below the red line indicates that the genomic mutation has a greater effect. c Expression (log₂ FPKM) across C. elegans development for linc-239 and linc-339. d RT-PCR analysis of neighbouring genes in linc-239 (mj441) deletion mutant. Diagram shows the relative position of the lncRNA and the surrounding protein-coding genes. Col-73 expression (left panel) and F11G11.1 expression (right panel) are measured using end-point RT-PCR at three different cDNA concentrations. Actin is used as loading control. e qRT-PCR analysis of col-73 and F11G11.13 expression in linc-239 (mj441) mutants. Error bars = 95% CI, significance is tested using t test with multiple t test correction. f RT-PCR analysis of the T01C8.3 gene in linc-339 (mj601) deletion mutants (left panel) and in linc-339 RNAi knock-down (right panel) at three different cDNA concentrations. Actin is used as loading control. g qRT-PCR analysis of T01C8.3 expression in linc-339 (mj339) and linc-339 RNAi. Error bars = 95% CI, significance is tested using t test with multiple t test correction