Nf κb2

Total protein was extracted with radioimmunoprecipitation assay (RIPA) lysis buffer. The cell lysate was then quantified and boiled for 5 min before 30 μg of the samples were separated by10% SDS-PAGE. Proteins were then electrotransferred to polyvinylidene fluoride (PVDF) membranes (Millipore, USA) and blocked for 2 h with 3% BSA at room temperature. Subsequently, the membranes were incubated overnight at 4°C with primary antibodies for the detection of NF-κB2 (1:1,000; Proteintech, USA), MMP2 (1:1,000; Proteintech), HSP70 (1:500; Boster, USA), CD9 (1:1,000; Proteintech), FAP-1 (1:1,000; Abbkine, USA), vimentin (1:1,000; Proteintech), α-SMA (1:1,000; Proteintech), and β-actin (1:3,000; Proteintech). The membranes were then washed (3 × 10 min) with Tris-buffered saline containing Tween-20 (TBST). After incubation for 90 min at room temperature with anti-rabbit secondary detection antibodies (1:5,000; Proteintech), immunoreactive bands were visualized by enhanced chemiluminescence (Santa Cruz Biotechnology, Santa Cruz, CA, USA).

Denatured nuclear extractions or proteins were loaded onto polyacrylamide gels, and after electrophoresis, proteins were transferred onto PVDF membranes (Millipore), then blocked in 5% non-fat milk for 1 h at 25 °C. Incubation of primary antibodies was done overnight at 4 °C in 5% non-fat milk on TBS with 0.1% Tween-20. Primary antibodies were as follows: Med1 (CRSP1/TRAP220) (Bethyl, Cat.: A300-793A, 1:1000), Bmal1 (Cell Signaling Technology, Cat.: 14020 S, 1:1000), Rora (Proteintech, Cat.: 10616-1-AP, 1000), Pparδ (Proteintech, Cat.: 60193-1-Ig, Clone No.: 1B10E1, 1:1000), Tmem173 (Proteintech, Cat.: 19851-1-AP, 1:1000), Nfκb2 (Proteintech, Cat.: 10409-2-AP, 1:1000). The uncropped scans of blots of Bmal1, Rora, Pparδ, Med1, Tmem173, and Nfκb2 were represented in Supplementary Fig. 12.

Specific antisera were obtained from the following sources: HIV-1 Tat (ab42359 & ab43014), GFP (sc-9996), HA (Sigma, H9658-.2ML, clone HA-7 & Novus, NB600363), Flag (ThermoSientific, MA1-91878-1MG, clone FG4R), RNAPII-CTD (sc-56767, clone 8WG16), RNAPII CTD-Ser2P (Bethyl, A300-654A), RNAPII CTD-Ser5P (Active Motif, 39749), RNAPII CTD-Ser7P (Millipore, 04–1570), NF-κB/p65 (sc-372), NF-κB2 (ProteinTech, 10409-2-AP), H2B (Millipore, 07–371), H3 (Millipore, 05–928), TBP (sc-273), TAF4 (sc-136093), Cyclin T1 (sc-10750), CDK9 (sc-8338), RNF20 (ProteinTech, 21625-1-AP), KDM4A (Novus, NB110-40585), KDM4B (Novus, NB100-74605), KDM4C (NBP1-49600), KDM4D (NBP1-03357), KDM5A (NB110-40499), KDM5B (NB100-97821), JMJD6 (NBP1-71693), NELF-A (sc-32911), Csn3 (sc-100693), Csn8 (sc-393482), PRMT6 (ProteinTech, 15395-1-AP), SHMT1 (ProteinTech, 14149-1-AP), SHMT2 (ProteinTech, 11099-1-AP), BRCC36 (Novus, NBP1-76831), Ubquitin (Millipore, 05–944), K48Ub (Millipore, 05–1307), K63Ub (Millipore, 05–1313), p62 (ProteinTech, 18420-1-AP), Rabbit IgG (sc-2027), Mouse IgG (sc-2025) and HRP-conjugated 2nd antibodies (sc-2004, sc-2005 & sc-2033).