Gene / Gene family or function / Targeted by miRNA or tasiRNAa / Targeted by miRNA / Targeted by tasiRNA / Targeted by multiple small RNAs / Normalized 21 nt small RNA readsb / Phasing (Y/N)
Col-0 & rdr2 / dcl1 / rdr6 / dcl4
At2g27400 / TAS1a / see Table 2 / + / 41 / 0 / 0 / 1 / Yf
At1g50055 / TAS1b / see Table 2 / + / 23 / 0 / 0 / 4 / Yf
At2g39675 / TAS1c / see Table 2 / + / 41 / 0 / 0 / 1 / Yf
At2g39681 / TAS2 / see Table 2 / + / 92 / 0 / 0 / 11 / Yg,h
At3g17185 / TAS3a / see Table 2 / + / + / 41 / 11 / 0 / 19 / Yh
At5g49615 / TAS3b / see Table 2 / + / + / 4d / 0 / 0 / 1 / Y
At5g57735 / TAS3c / miR390 / + / + / 0 / 0 / 0 / 0 / N
AT1G62910 / PPR / see Table 2 / + / + / + / 31d,e / 1 / 0 / 0 / Yi
AT1G63130 / PPR / see Table 2 / + / + / + / 25d / 1 / 0 / 0 / Yi
AT1G62930 / PPR / see Table 2 / + / + / + / 17d / 1 / 0 / 0 / Yi
AT1G63080 / PPR / see Table 2 / + / + / + / 15d / 0 / 0 / 0 / Yi
AT1G63400 / PPR / see Table 2 / + / + / + / 9d / 1 / 0 / 0 / Yi
AT1G63150 / PPR / see Table 2 / + / + / + / 10d / 1 / 0 / 0 / Yi
AT1G63070 / PPR / see Table 2 / + / + / + / 7d / 0 / 0 / 0 / Y
AT1G63330 / PPR / see Table 2 / + / + / + / 4d / 1 / 0 / 0 / Yi
AT1G62590 / PPR / see Table 2 / + / + / + / 4d / 1 / 0 / 0 / Yi
AT1G12300 / PPR / see Figure 5 / + / + / 1 / 0 / 0 / 0 / N
AT1G62670 / PPR / see Figure 5 / + / + / + / 7c,d / 0 / 0 / 0 / Ni
AT1G62860 / PPR / see Figure 5 / + / + / + / 2d / 0 / 0 / 0 / Ni
AT1G12775 / PPR / see Figure 5 / + / + / 1d / 0 / 0 / 0 / N
AT1G63320 / PPR / see Figure 5 / + / 1 / 0 / 0 / 0 / N
AT1G63230 / PPR / see Figure 5 / + / + / + / 1 / 0 / 0 / 0 / Ni
AT1G63630 / PPR / see Figure 5 / + / 1d / 0 / 0 / 0 / N
AT1G12620 / PPR / see Figure 5 / + / + / 1 / 0 / 0 / 0 / N
AT5G38850 / TIR-NBS-LRR / 9e / 0 / 0 / 0 / Y
AT5G43740 / CC-NBS-LRR / miR472 / + / 2 / 1 / 0 / 0 / N
AT5G43730 / CC-NBS-LRR / miR472 / + / 1 / 1 / 0 / 0 / N
AT1G51480 / CC-NBS-LRR / miR472 / + / 1 / 0 / 0 / 0 / N
Supplemental Table S1. cont.
AT1G12820 / AFB3 / see Table 2 / + / 1d / 0 / 0 / 0 / Yi
AT3G26810 / AFB2 / miR393 / + / 1 / 0 / 0 / 0 / Ni
AT3G23690 / bHLH / miR393 / + / 1e / 0 / 0 / 0 / Ni
AT5G41610 / ATCHX18 / see Table 2 / + / + / 2d / 1 / 0 / 1 / Y
AT2G46800 / ZAT1 / miR856 / + / 1 / 0 / 0 / 0 / N
AT1G48410 / AGO1 / miR168 / + / 1c,e / 0 / 0 / 1 / Ni
AT5G60450 / ARF4 / tasiR2141/2142 / + / + / 1 / 0 / 0 / 1 / Ni
AT4G08990 / MET2-like / miR773 / + / 1e / 0 / 0 / 0 / N
AT4G36920 / AP2 / miR172 / + / 1 / 0 / 0 / 2 / N
AT4G19690 / ZIP8 / 1e / 0 / 0 / 0 / N
AT5G39370 / putative S-locus glycoprotein / 1d / 1 / 0 / 0 / N
AT4G08380 / proline-rich extensin-like / 0 / 0 / 0 / 0 / N
AT1G50440 / C3HC4-type RING zinc finger) / 1 / 0 / 0 / 0 / N
AT3G28917 / zinc finger homeobox / 0 / 0 / 0 / 0 / N
AT1G33420 / PHD finger / 1 / 0 / 0 / 0 / N
AT1G11700 / unclassified / 1 / 0 / 0 / 0 / N
AT5G49440 / unclassified - LINE / 1 / 0 / 0 / 0 / N
AT1G18010 / expressed proteins / 1 / 0 / 0 / 0 / N
AT1G18000
4:1472767-1472932 / ubiquitin fragment / 1 / 0 / 0 / 0 / N
4:1476401-1476524
5:9789580-9789665 / too few data / 0 / 0 / 0 / 0 / N
aSee Vaucheret, 2006; Jones-Rhoades et al., 2006; Lu et al., 2006; Fahlgren et al., 2007.
bNumber of reads are normalized for small RNA sequence population size.
cShown to generate siRNAs by Ronemus et al. (2006).
dShown to generate siRNAs by Lu et al. (2006).
eShown to generate siRNAs by Rajagopalan et al. (2006).
fShown to generate phased siRNAs by Vazquez et al. (2004) and Peragine et al. (2004).
gShown to generate phased siRNAs by Yoshikawa et al. (2005).
hShown to generate phased siRNAs by Allen et al. (2005).
iShown to generate phased siRNAs by Axtell et al. (2006).
Supplemental References
Allen, E., Xie, Z., Gustafson, A.M., and Carrington, J.C. (2005). microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207-221.
Axtell, M.J., Jan, C., Rajagopalan, R., and Bartel, D.P. (2006). A two-hit trigger for siRNA biogenesis in plants. Cell 127, 565-577.
Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., Law, T.F., Grant, S.R., Dangl, J.L., and Carrington, J.C. (2007). High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2, e219.
Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B. (2006). MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57, 19-53.
Lu, C., Kulkarni, K., Souret, F.F., Muthuvalliappan, R., Tej, S.S., Poethig, R.S., Henderson, I.R., Jacobsen, S.E., Wang, W., Green, P.J., and Meyers, B.C. (2006). MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res 16, 1276-1288.
Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H.L., and Poethig, R.S. (2004). SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18, 2368-2379.
Rajagopalan, R., Vaucheret, H., Trejo, J., and Bartel, D.P. (2006). A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev 20, 3407-3425.
Ronemus, M., Vaughn, M.W., and Martienssen, R.A. (2006). MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell 18, 1559-1574.
Vaucheret, H. (2006). Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20, 759-771.
Vazquez, F., Vaucheret, H., Rajagopalan, R., Lepers, C., Gasciolli, V., Mallory, A.C., Hilbert, J.L., Bartel, D.P., and Crete, P. (2004). Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16, 69-79.
Yoshikawa, M., Peragine, A., Park, M.Y., and Poethig, R.S. (2005). A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19, 2164-2175.