The RNA synthesis was conducted following the protocol from the manufacturer (MAXIscript Kit, part number AM1308–AM1326; Thermo Fisher Scientific). Briefly, the transcripts of COOLAIR, COLDAIR, and COLDWRAP were amplified with RT-PCR and driven by the T7 promoter, and then RNAs were generated with biotin–uridine triphosphate using an in vitro Transcription Kit (AM1312, Thermo Fisher Scientific). The primers used for RNA pull-down are described in Data file S1.

The pull-down assays were conducted by incubating beads with 3 μg of RNA. The beads were washed and mixed gently with soluble protein (3 μg) for 30 min at 4°C. The beads were washed five to eight times with 50 mM tris (pH 7.5), 150 mM NaCl, 1 mM DTT, 0.05% NP-40, and RNasin (40 U/ml). Proteins were resolved by SDS-PAGE and immunoblotted with anti-His (M30111 M, lot: 273884; Abmart).

For the RNA Co-IP, 0.5 g of 10-day-old seedlings was ground in a mortar and pestle in buffer [50 mM tris (pH 7.5), 150 mM NaCl, 20 mM KCl, 1 mM MgCl2, 1 mM DTT, 0.05% NP-40, bovine serum albumin (0.125 mg/ml), and RNasin (40 U/ml)]. Beads with 3 μg of RNA were incubated with cell extracts for 30 min at 4°C. After being washed five to eight times with 50 mM tris (pH 7.5), 150 mM NaCl, 1 mM DTT, 0.05% NP-40, and RNasin (40 U/ml), the samples were separated by SDS-PAGE and immunoblotted with anti-FCA (R3399-1, lot: 15088; Abicode).

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