Fig. 1

fRIP-Seq reveals widespread binding of chromatin-associated proteins to mRNAs and lncRNAs. a Formaldehyde cross-linking RNA–protein complexes enables identification of target RNAs by high-throughput sequencing. b We mapped RNA interaction partners for 24 proteins in triplicate and performed hierarchical clustering of log2 fRIP/input fold change over the ~25,000 genes present in at least one condition. Replicates cluster together for every protein. Binding patterns vary between proteins. Neither total RNA recovery from fRIP-Seq (orange 1–10 nanogram range, green 10–50 nanogram range, purple 50+ nanograms) or published nucleic acid binding properties (orange DNA, green both DNA and RNA, purple RNA) can explain the observed clustering solution. c The lncRNA Xist is significantly bound by HNRNPU and PRC2 components SUZ12 and EZH2 in our data, validating these known interactions. fRIP-Seq coverage suggests potential binding patterns along the transcript. The coverage scales (y-axis) have maximum coverage 500, except for CHD4 and EZH2, which have maximum coverage 1500 and 3000, respectively