Fig. 2

Schematic representation of ChIRP, CHART and RAP to identify associated proteins and chromatin DNA. RNA–protein–DNA complexes were cross-linked in vivo and solubilized by sonication. Corresponding biotinylated oligonucleotides of three methods were designed and synthesized to be hybridized to target lncRNAs under stringent conditions. Associated proteins and chromatin DNA were efficiently pulled down with streptavidin magnetic beads. Co-purified RNA, protein and DNA were isolated with RNase elution and subjected analyzed downstream analysis. Isolated proteins were analyzed by mass spectrometry or Western blotting and chromatin DNA was used for q-PCR, deep sequencing