Table 3. Co-expression analysis of high-fluence UV-B induction of miRNAs/phasi-RNAs abundances during berry development which are inversely correlated with predicted target mRNA expressions in the same skin tissues in response to UV-C pre-veraison and UV-B five weeks post-veraison from independent experiments (Suzuki et al. 2015; Carbonell-Bejerano et al. 2014).
| UV-B Fold Change& (bold= up; italics = down) | Inverse correlation of mRNA target expression vs. miRNA/siRNA? | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| High-Fluence Greenhouse | Low-Fluence Greenhouse | High-Fluence Field | |||||||||||||||
| miRNA/siRNA | LFC, UV-B | -3 WAV | Verai-son | +3 WAV | +6 WAV | -3 WAV | Verai-son | +3 WAV | +6 WAV | -3 WAV | Verai-son | +3 WAV | +6 WAV | Validated Targets* (n; annotation) | FC, UV-C$ | FC, UV-B† | FC P-val^ |
| miR156f | 0.68 | 1.332 | 2.755 | 3.266 | 5.520 | 0.644 | 10.25 | 1.863 | 0.567 | 1.440 | 2.149 | 1.144 | 1.430 | 11; SPB | 0.75 | 0.89 | 0.02 |
| miR530b | −0.77+ | n.d. | 2.556 | 0.488 | 1.183 | 0.258 | 0.853 | 0.200 | 0.065 | n.d. | 5.908 | 5.853 | 6.316 | 2; Plus3, DYW | 0.80 | 0.86 | 0.09 |
| miR477c | −0.32+ | 0.010 | 3.253 | 3.129 | 2.772 | 0.017 | 0.104 | 0.116 | 0.003 | 3.082 | 1.177 | 3.039 | 0.374 | 2; GRAS-domain | n.d. | 0.84 | 0.51 |
| TAS4a, miR828 target | 0.32 | 0.561 | 3.540 | 5.119 | 1.249 | 0.102 | 2.155 | 0.554 | 0.357 | 2.772 | 2.602 | 1.961 | 1.192 | 2; MYBA6/A7 | 0.63 | 0.97 | 0.30 |
| TAS4b, miR828 target | 1.10 | 0.089 | 1.704 | 2.115 | 60.16 | 1.006 | 2.713 | 2.562 | 0.572 | 4.956 | 7.022 | 6.213 | 2.953 | ||||
| TAS4c, miR828 target | 0.14 | 5.381 | 4.825 | 1.712 | 0.955 | 0.180 | 1.348 | 1.342 | 0.513 | 0.318 | 1.777 | 1.953 | 0.750 | ||||
| miR828 target MYB, phasi-RNA producing | −0.29+ | 0.218 | 1.425 | 1.023 | 1.725 | 0.130 | 2.948 | 1.260 | 0.377 | 1.151 | 1.367 | 0.569 | 1.316 | 5; MYBs | 0.70 | 0.87 | 0.04 |
| miR482 | 0.07 | 0.340 | 0.965 | 1.188 | 2.936 | 0.393 | 2.583 | 2.840 | 0.624 | 1.450 | 1.678 | 0.774 | 0.855 | 2;TAS11,slyTAS5-Like | 0.80 | 0.96 | 0.09 |
| TAS11-D3(-) miR482 target | 0.17 | 0.287 | 1.467 | 1.290 | 5.191 | 0.515 | 5.015 | 1.697 | 0.419 | 1.673 | 1.167 | 0.733 | 1.279 | 14; LRRs | 0.84 | 0.86 | 0.02 |
| miR403a-e average | −0.19 | 0.504 | 1.206 | 0.205 | 1.212 | 2.764 | 2.238 | 0.347 | 0.382 | 1.566 | 0.987 | 0.678 | 2.044 | 1; AGO2 | 1.1 | 1.07 | 0.17 |
| Overall 38 targets, two experiments | 5.3E-6 | ||||||||||||||||
& Normalized to 20M reads (+1 if zero reads). Denominator is corresponding normalized -UV-B sample (unity). n.d.: not detected.
sign negative overall because low-fluence UV-B effect dominant, or low read counts independently filtered out by PhaseTank.
See Supplementary Table 2a.
Data for 1 hr FC by UV-C treatment of pre-veraison berries from Suzuki et al. (2015). If called significantly different expression in response to UV-C, in bold.
Binomial distribution probability for FCs of al target mRNA responses to UV-C and UV-B inverse to miRNA/siRNA (up) under high-fluence UV-B.
Data for FC by UV-B treatment on 26 °Brix (ripe) berries irradiated for five weeks post-veraison from Carbonell-Bejerano et al. (2014). For miR403 target AGO2, includes 23°Brix sample (3 independent tests for significance).