library_construction_protocol: For ChIP-seq, , the fresh whole liver lobes were homogenized in 4 ml PBS containing 1% formaldehyde and kept for 8 min at room temperature (RT). For dual crosslinking, the fresh whole liver lobes were homogenized in 4 ml PBS containing 2mM EGS for 20 min at RT. After quencing and cell lysis, chromatin was sonicated by Covaris S2 with the options of 30 sec on/off, intensity 5, cycles/burst 200, duty 20% at 4°C. For PRO-seq, the largest mouse liver lobe was homogenized and the dissociated cells were filtered by 100mm mesh and centrifuged. The precipitated cells were re-suspended and lysed.  The extracted nucleus was re-suspended with the storage buffer and frozen till the next step. After the nuclear run-on, the RNA was extracted by Trizol LS (ThermoFisher). For mRNA-seq, the frozen liver samples were homogenized with Trizol (ThermoFisher) and RNA was extracted according to the manufacturer's instructions. For ChIP-seq, the DNA fragments ranging from 125 to 175bp were size selected by AMPure magnetic beads (Beckman). Then, the DNA is adenylated, ligated to NEXTflex DNA barcode adaptors (PerkinElmer) and amplified (Enzymatics). For PRO-seq, the libraries were made with TruSeq small RNA Library primers nad the amplified libraries were size-separated by 8% PAGE gels and the DNA ranging from 140 bp to 200 bp was cut out and eluted by the crush/soak methods. For mRNA-seq, the mRNA was extracted from 10 mg of total RNA (RIN values > 8) pooled from three mice by NEXTflex Poly (A) Beads (PerkinElmer), fragmented by heat, reversely transcribed, ligated and amplified with NEXTflex DNA barcode adaptors (PerkinElmer). For all libraries, the size and quality of the libraries were validated by TapeStation (Agilent) and the amounts were measured by Qubit (ThermoFisher)