Fig. 1

Nuclear fractionation to isolate chromatin-associated RNAs from four tissues and the properties of rice cheRNAs. A Depiction of the nuclear fractionation procedure. B Immunoblot analysis of histone H3 and GAPDH in chromatin, the nucleoplasm, and the cytoplasmic fraction. C Density plot of transcript length distributions for cheRNAs, lncRNAs (annotated using NONCODEv6), and mRNAs (annotated using MSU7.0). D Number of exons per transcript for cheRNAs, annotated lncRNAs, and mRNAs. E Cumulative distribution of G/C content for cheRNAs, annotated lncRNAs, and mRNAs transcripts. F Density plot of transcript length distributions for intermediate-sized cheRNAs (including che-snoRNAs, cheRNA-tRNAs, and che-snRNAs, n = 440). G Density plot of G/C content for intermediate-sized cheRNA transcripts (including che-snoRNAs, che-tRNAs, and che-snRNAs, n = 440). H Principal component analysis (PCA) of transcript levels (FPKM) in the CPE and SNE fractions from four tissues with two biological repetitions