To explore the PRC2-associated RNA in Arabidopsis on a genome-wide scale, we designed a high-throughput sequencing followed by PRC2 RNA-IP. We used the transgenic plants to purify the Myc-tagged CLF protein, the homologs of EZH2 (the methyltransferase of PRC2 complex) in mammal. Overall design: The CLF-RNA complex was co-immunoprecipitated from the 3-week-old plants. The RNAs were de-crosslinked from CLF and purified by TRIzol reagent. Then, RNA-seq libraries were constructed and sequenced by using Illumina platforms.