library_construction_protocol: Nuclei of mouse ESCs were extracted using cytolysis buffer (0.1% BSA, 200 U RNase inhibitor, 0.2% NP-40, 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM MgCl2) and fixed using 1% formaldehyde. Fixed nuclei were used for biotin-tagging reaction using in-situ click working solution (50 mM Hepes pH 7.5, 2.5 mM THPTA, 2.5 mM CuSO4, 4 mM Biotin-PEG3-azide, 10 mM Sodium ascorbate) and incubated at 25°C,350 rpm with 10 s on and 10s off on a ThermoMixer for 0.5 h. The nuclei were further processed for in-situ reverse transcription and lysed for biotinylated RNA pull-down. VAHTS Universal V6 RNA-seq Library Prep kit (Vazyme #NR604) was used for RNA library construction. Library construction was conducted according to the manufacturer's protocol (with UMI barcoded dual index, RK21702) and the libraries were sequenced on the Illumina platform.