10. Llave C, Xie Z, Kasschau KD, Carrington JC
(2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA.
Science 297:2053–2056. https://doi.org/10.
1126/science.1076311
11. Fagard M, Boutet S, Morel JB et al (2000)
AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene
silencing in plants, quelling in fungi, and
RNA interference in animals. Proc Natl Acad
Sci U S A 97:11650–11654. https://doi.org/
10.1073/pnas.200217597
12. Park W, Li J, Song R et al (2002) CARPEL
FACTORY, a Dicer homolog, and HEN1, a
novel protein, act in microRNA metabolism in
Arabidopsis thaliana. Curr Biol 12:1484–1495.
https://doi.org/10.1016/s0960-9822(02)
01017-5
13. Palatnik JF, Allen E, Wu X et al (2003) Control
of leaf morphogenesis by microRNAs. Nature
425:257–263.
https://doi.org/10.1038/
nature01958
14. Aukerman MJ, Sakai H (2003) Regulation of
flowering time and floral organ identity by a
MicroRNA and its APETALA2-like target
genes. Plant Cell 15:2730–2741. https://doi.
org/10.1105/tpc.016238
15. Peragine A, Yoshikawa M, Wu G et al (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. https://doi.org/10.
1101/gad.1231804
16. Vaucheret H, Vazquez F, Crete P, Bartel DP
(2004) The action of ARGONAUTE1 in the
miRNA pathway and its regulation by the
miRNA pathway are crucial for plant development. Genes Dev 18:1187–1197. https://doi.
org/10.1101/gad.1201404
17. Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that
selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A
102:11928–11933.
https://doi.org/10.
1073/pnas.0505461102
18. Chen X (2004) A microRNA as a translational
repressor of APETALA2 in Arabidopsis flower
development.
Science
303:2022–2025.
https://doi.org/10.1126/science.1088060
19. Allen E, Xie Z, Gustafson AM, Carrington JC
(2005) microRNA-directed phasing during
trans-acting siRNA biogenesis in plants. Cell
121:207–221.
https://doi.org/10.1016/j.
cell.2005.04.004
20. Fahlgren N, Montgomery TA, Howell MD
et al (2006) Regulation of AUXIN
RESPONSE FACTOR3 by TAS3 ta-siRNA
affects developmental timing and patterning
in Arabidopsis. Curr Biol 16:939–944.
https://doi.org/10.1016/j.cub.2006.03.065
21. Bennetzen JL, Park M (2018) Distinguishing
friends, foes, and freeloaders in giant genomes.
Curr Opin Genet Dev 49:49–55. https://doi.
org/10.1016/j.gde.2018.02.013
22. Matzke MA, Mosher RA (2014) RNA-directed
DNA methylation: an epigenetic pathway of
increasing complexity. Nat Rev Genet
15:394–408.
https://doi.org/10.1038/
nrg3683
23. Ferrafiat L, Pflieger D, Singh J et al (2019) The
NRPD1 N-terminus contains a Pol IV-specific
motif that is critical for genome surveillance in
Arabidopsis. Nucleic Acids Res. https://doi.
org/10.1093/nar/gkz618
24. Law JA, Du J, Hale CJ et al (2013) Polymerase
IV occupancy at RNA-directed DNA methylation
sites
requires
SHH1.
Nature
498:385–389.
https://doi.org/10.1038/
nature12178
25. Wendte JM, Haag JR, Pontes OM et al (2019)
The Pol IV largest subunit CTD quantitatively
affects siRNA levels guiding RNA-directed
DNA methylation. Nucleic Acids Res.
https://doi.org/10.1093/nar/gkz615
26. Ream TS, Haag JR, Wierzbicki AT et al (2009)
Subunit compositions of the RNA-silencing
enzymes Pol IV and Pol V reveal their origins
as specialized forms of RNA polymerase
II. Mol Cell 33:192–203. https://doi.org/
10.1016/j.molcel.2008.12.015
27. Haag JR, Ream TS, Marasco M et al (2012) In
vitro transcription activities of Pol IV, Pol V,
and RDR2 reveal coupling of Pol IV and RDR2
for dsRNA synthesis in plant RNA silencing.
Mol Cell 48:811–818. https://doi.org/10.
1016/J.MOLCEL.2012.09.027
28. Singh J, Mishra V, Wang F et al (2019) Reaction mechanisms of Pol IV, RDR2, and DCL3
drive RNA channeling in the siRNA-directed
DNA methylation pathway. Mol Cell
75:576–589.e5. https://doi.org/10.1016/j.
molcel.2019.07.008
29. Zhai J, Bischof S, Wang H et al (2015) A one
precursor one siRNA model for Pol
IV-dependent
siRNA
biogenesis.
Cell
163:445–455.
https://doi.org/10.1016/j.
cell.2015.09.032
30. Blevins T, Podicheti R, Mishra V et al (2015)
Identification of Pol IV and RDR2-dependent
precursors of 24 nt siRNAs guiding de novo
DNA methylation in Arabidopsis. elife
4. https://doi.org/10.7554/eLife.09591
31. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS
(2009) RNA polymerase V transcription guides
Genome-Scale and Northern Blot Analyses of siRNAs
409
(2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA.
Science 297:2053–2056. https://doi.org/10.
1126/science.1076311
11. Fagard M, Boutet S, Morel JB et al (2000)
AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene
silencing in plants, quelling in fungi, and
RNA interference in animals. Proc Natl Acad
Sci U S A 97:11650–11654. https://doi.org/
10.1073/pnas.200217597
12. Park W, Li J, Song R et al (2002) CARPEL
FACTORY, a Dicer homolog, and HEN1, a
novel protein, act in microRNA metabolism in
Arabidopsis thaliana. Curr Biol 12:1484–1495.
https://doi.org/10.1016/s0960-9822(02)
01017-5
13. Palatnik JF, Allen E, Wu X et al (2003) Control
of leaf morphogenesis by microRNAs. Nature
425:257–263.
https://doi.org/10.1038/
nature01958
14. Aukerman MJ, Sakai H (2003) Regulation of
flowering time and floral organ identity by a
MicroRNA and its APETALA2-like target
genes. Plant Cell 15:2730–2741. https://doi.
org/10.1105/tpc.016238
15. Peragine A, Yoshikawa M, Wu G et al (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. https://doi.org/10.
1101/gad.1231804
16. Vaucheret H, Vazquez F, Crete P, Bartel DP
(2004) The action of ARGONAUTE1 in the
miRNA pathway and its regulation by the
miRNA pathway are crucial for plant development. Genes Dev 18:1187–1197. https://doi.
org/10.1101/gad.1201404
17. Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that
selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A
102:11928–11933.
https://doi.org/10.
1073/pnas.0505461102
18. Chen X (2004) A microRNA as a translational
repressor of APETALA2 in Arabidopsis flower
development.
Science
303:2022–2025.
https://doi.org/10.1126/science.1088060
19. Allen E, Xie Z, Gustafson AM, Carrington JC
(2005) microRNA-directed phasing during
trans-acting siRNA biogenesis in plants. Cell
121:207–221.
https://doi.org/10.1016/j.
cell.2005.04.004
20. Fahlgren N, Montgomery TA, Howell MD
et al (2006) Regulation of AUXIN
RESPONSE FACTOR3 by TAS3 ta-siRNA
affects developmental timing and patterning
in Arabidopsis. Curr Biol 16:939–944.
https://doi.org/10.1016/j.cub.2006.03.065
21. Bennetzen JL, Park M (2018) Distinguishing
friends, foes, and freeloaders in giant genomes.
Curr Opin Genet Dev 49:49–55. https://doi.
org/10.1016/j.gde.2018.02.013
22. Matzke MA, Mosher RA (2014) RNA-directed
DNA methylation: an epigenetic pathway of
increasing complexity. Nat Rev Genet
15:394–408.
https://doi.org/10.1038/
nrg3683
23. Ferrafiat L, Pflieger D, Singh J et al (2019) The
NRPD1 N-terminus contains a Pol IV-specific
motif that is critical for genome surveillance in
Arabidopsis. Nucleic Acids Res. https://doi.
org/10.1093/nar/gkz618
24. Law JA, Du J, Hale CJ et al (2013) Polymerase
IV occupancy at RNA-directed DNA methylation
sites
requires
SHH1.
Nature
498:385–389.
https://doi.org/10.1038/
nature12178
25. Wendte JM, Haag JR, Pontes OM et al (2019)
The Pol IV largest subunit CTD quantitatively
affects siRNA levels guiding RNA-directed
DNA methylation. Nucleic Acids Res.
https://doi.org/10.1093/nar/gkz615
26. Ream TS, Haag JR, Wierzbicki AT et al (2009)
Subunit compositions of the RNA-silencing
enzymes Pol IV and Pol V reveal their origins
as specialized forms of RNA polymerase
II. Mol Cell 33:192–203. https://doi.org/
10.1016/j.molcel.2008.12.015
27. Haag JR, Ream TS, Marasco M et al (2012) In
vitro transcription activities of Pol IV, Pol V,
and RDR2 reveal coupling of Pol IV and RDR2
for dsRNA synthesis in plant RNA silencing.
Mol Cell 48:811–818. https://doi.org/10.
1016/J.MOLCEL.2012.09.027
28. Singh J, Mishra V, Wang F et al (2019) Reaction mechanisms of Pol IV, RDR2, and DCL3
drive RNA channeling in the siRNA-directed
DNA methylation pathway. Mol Cell
75:576–589.e5. https://doi.org/10.1016/j.
molcel.2019.07.008
29. Zhai J, Bischof S, Wang H et al (2015) A one
precursor one siRNA model for Pol
IV-dependent
siRNA
biogenesis.
Cell
163:445–455.
https://doi.org/10.1016/j.
cell.2015.09.032
30. Blevins T, Podicheti R, Mishra V et al (2015)
Identification of Pol IV and RDR2-dependent
precursors of 24 nt siRNAs guiding de novo
DNA methylation in Arabidopsis. elife
4. https://doi.org/10.7554/eLife.09591
31. Wierzbicki AT, Ream TS, Haag JR, Pikaard CS
(2009) RNA polymerase V transcription guides
Genome-Scale and Northern Blot Analyses of siRNAs
409