He_Supp. Fig.1

1. He_Supp. Fig.1 ( ) rdm5 nrpd1a ATG (1) TGA (4362) ( rdm6 - 2 nrpd1b) ( ) rdm6 - 1 nrpd1b 1377 bp deletion ATG (1) TAA (5931) ( ) rdm8 ago4 6 bp deletion ATG (1) TAA (2775) ( ) rdm9 hen1 TGA (2829) ATG (1) rdm10 (hda6) 13 bp deletion TAA (1416) ATG (1) rdm11 (drd1) 35 bp deletion TAA (2667) ATG (1) A AT1G63020 B AT2G40030 C AT3G23780 D AT2G27040 E AT4G20910 F AT5G63110 G AT2G16390

2. He_Supp. Fig.2 A nrpd1b B ago4 ros1 ros1 ros1rdm6-1 ros1rdm8 WT WT 23 °C 23 °C 23 °C 23 °C 23 °C 23 °C 4 °C 4 °C 4 °C 4 °C 4 °C 4 °C RD29A RD29A LUC NPTII NPTII COR15A COR15A TUB8 TUB8 rRNA rRNA C hda6 D drd1 ros1 ros1rdm10 WT ros1 ros1rdm11 WT 23 °C 23 °C 23 °C 4 °C 4 °C 4 °C 23 °C 23 °C 23 °C 4 °C 4 °C 4 °C RD29A RD29A LUC LUC NPTII NPTII COR15A COR15A TUB8 TUB8 rRNA rRNA

3. He_Supp. Fig.3 A 5S rDNA repeat Southern ros1nrpd1b ros1nrpd1b ros1nrpd1b ros1hda6 ros1ago4 ros1hda6 ros1ago4 ros1hda6 ros1ago4 ros1drd1 ros1drd1 ros1drd1 ros1 ros1 ros1 WT WT WT HpaII MspI HaeIII B ros1nrpd1b ros1hda6 ros1ago4 ros1drd1 ros1 ros1 ros1 ros1 WT WT WT WT AtSN1 HaeIII AtSN1 No Digest D C ros1ago4 ros1hda6 ros1drd1 ros1nrpd1b ros1hda6 ros1ago4 ros1drd1 ros1 ros1 ros1 WT WT WT ros1 WT AtGP1 siRNA1003 microRNA173 AtMU1 U6 snRNA TUB8

4. He_Supp. Fig.4 nrpd4-2 nrpd1a nrpd1b Col-0 Cluster4 siRNA AtSN1 siRNA siRNA1003 AtGP1 siRNA AtMU1 siRNA siRNA02 siRNA255 microRNA171 tRNA and 5S rRNA A B 180 bp CEN nrpd4-2 nrpd4-2 nrpd4-2 nrpd1a nrpd1b nrpd1a nrpd1b nrpd1a nrpd1b Col-0 Col-0 Col-0 HpaII MspI HaeIII

5. He_Supp. Fig.5 B A SD-Trp-Leu-His +50 mM 3AT SD-Trp-Leu C