REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-AGO1	Agrisera	Cat# AS09 527, RRID:AB_2224930
Rabbit polyclonal anti-AGO2	Agrisera	Cat# AS13 2682
Rabbit polyclonal anti-AGO4	Agrisera	Cat# AS09617, RRID:AB_10507623
Rabbit polyclonal anti-HYL1	Agrisera	Cat# AS06 136, RRID:AB_2233541
Rabbit polyclonal anti-ASK1	Lechner et al. (2002)	N/A
Rabbit polyclonal anti-CUL1	Shen et al. (2002)	N/A
Rabbit polyclonal anti-ROC1	Mybiosource	Cat# MBS4751158
Rabbit polyclonal anti-ACTIN	Agrisera	Cat# AS13 2640, RRID:AB_2722610
Rabbit polyclonal anti-CDC2 PSTAIRE	Santa Cruz Biotechnology	Cat# sc-53, RRID:AB_2074908
Rabbit polyclonal anti-BIP	Agrisera	Cat# AS09 481, RRID:AB_1832007
Rabbit polyclonal anti-UGPase	Agrisera	Cat# AS05 086, RRID:AB_1031827
Rabbit polyclonal anti-RFP	Chromotek	Cat# 6g6-100, RRID:AB_2631395
Mouse monoclonal anti-HA	Covance	Cat# MMS-101P-200, RRID:AB_10064068
Mouse monoclonal anti-HA	Sigma-Aldrich	Cat# H9658, RRID:AB_260092
Anti cMyc-HRP	Miltenyi	Cat# 130-092-113, RRID:AB_871937
Anti Flag-M2-HRP	Sigma-Aldrich	Cat# A8592, RRID:AB_439702
Anti GFP-HRP	Miltenyi	Cat# 130-091-833, RRID:AB_247003
Mouse monoclonal anti-GFP (JL8)	Clontech (Takara)	Cat# 632381, RRID:AB_2313808
peroxidase-conjugated goat anti-rabbit IgG	Thermo Fisher Scientific	Cat# G-21234, RRID:AB_2536530
peroxidase-conjugated goat anti-mouse IgG	Thermo Fisher Scientific	Cat# G-21040, RRID:AB_2536527
Bacterial and virus strains
Escherichia coli	Invitrogen	Top10
Agrobacterium tumefaciens		GV3101 Pmp90
Agrobacterium tumefaciens		C58C1
Chemicals, peptides, and recombinant proteins
Cycloheximide (use at 100 μM)	Sigma-Aldrich	C1988-1G
β−Estradiol (use at 10 or 20 μM)	Sigma-Aldrich	E8875
E64D (use at 50 or 100 μM)	Sigma-Aldrich	E8640
MLN-4924 (use at 25 μM)	Active Biochem	MLN-492
MG132 (use 10 or 100 μM)	CAS 13340782-6	Calbiochem
Bortezomib (use at 100 μM)	Selleckchem	S1013
Agar type A	Sigma Aldrich	A4550-500G
SYBR Green Master Mix	Roche	Cat N° 04707516001
ECL prime kit	GE Healthcare	Cat N° WBLUF0100
Clarity Western ECL substrate	Biorad	1705061
deoxynucleotide triphosphate (dNTP)	Promega	U1205
MS medium	Duchefa	MO255
Protease inhibitor: complete-EDTA free	Roche	04693132001
Igepal CA-630	Sigma Aldrich	I8896
Formaldehyde	Thermo Scientific	28906
μMACS HA Isolation Kit	Miltenyi Biotech	130-091-122
μ Columns	Miltenyi Biotech	130-042-701
Criterion TGX 4-15% gradient precast gels	Biorad	5671084
Nupage 4–12% gradient precast gels gels	Fisher Scientific	10472322
High capacity cDNA Reverse transcriptase	Fisher Scientific	4368813
Dnase I	Fisher Scientific	10649890
T4 Polynucleotide Kinase	Promega	M4103
T4 Polynucleotide Kinase	Thermo Fisher	EK0031
Glycogen	Thermo Fisher	R0561
Syringic acid	Sigma Aldrich	S6881
4-methylumbelliferyl-β-D-glucuronide	Duchefa	M1404
Pierce Anti-HA magnetic Beads	Thermo Fisher	88836
PureProteome Protein A Magnetic Bead System	Sigma Aldrich	LSKMAGA
Deposited data
mass spectrometry proteomics data deposited to the ProteomeXchange Consortium via the PRIDE [(Perez-Riverol et al., 2019)] partner repository.	Dataset identifier PXD024840 and https://doi.org/10.6019/PXD024840	N/A
Data for sRNA seq	GEO Series accession number GSE169324	N/A
Data for PARE seq	GEO Series accession number GSE169434	N/A
Experimental models: Organisms/strains
Nicothiana benthamiana		N/A
Arabidopsis thaliana ecotype Colombia		N/A
ago1-27	(Morel et al., 2002)	N/A
ago1-42	(Devers et al., 2020)	N/A
ago1-57	(Derrien et al., 2018)	N/A
fbw2-1	(Earley et al., 2010)	N/A
fbw2-4		SALK_144548
hen1-6		SALK_090960
hyl1-2		SALK_064863
sqn-1	(Smith et al., 2009)	N/A
XVE :P0-myc	(Derrien et al., 2012)	N/A
Hc1	(Elmayan et al., 1998; Martínez De Alba et al., 2011)	N/A
L1	(Elmayan et al., 1998; Martínez De Alba et al., 2011)	N/A
Hc1/sqn-1	(Elmayan et al., 1998; Martínez De Alba et al., 2011)	N/A
Hc1/4mAGO1	(Elmayan et al., 1998; Martínez De Alba et al., 2011)	N/A
35S:3HA-P19	(Incarbone et al., 2018)	N/A
Oligonucleotides
Primers for qPCR, see Table S4	This paper	N/A
Primers for genotyping, see Table S4	This paper	N/A
Primers for cloning, see Table S4	This paper	N/A
Probe sequence, see Table S4	This paper	N/A
Software and algorithms
ImageJ version 1.45		https://imagej.nih.gov/
Lightcycler 480 software, Release 1.5.0 SP3	Roche	Cat. No. 04994884001
Cutadapt v2.9	(Martin, 2011)	N/A
Bowtie2	(Langmead and Salzberg, 2012)	N/A
DESeq2	(Love et al., 2014)	N/A
CleaveLand v4.5	(Addo-Quaye et al., 2009)	N/A
PlantRegMap tool	(Tian et al., 2020)	N/A
ggplot2	(Wickham, 2016)	N/A
Graphical abstract picture	Created with BioRender.com	N/A