library_construction_protocol: TT-seq: Six in vitro transcribed spike-in RNAs were added to the lysates (Qiazol, Qiagen) from 30 million cells, followed by extraction of RNA according to the manufacturer's protocol.  This was followed by fragmentation by sonication and biotinylation of the 4sU-containing RNA. Two biotinylation reactions were set up per sample (150 µg fragmented total RNA, 10 mM Tris pH 7.5, 1 mM EDTA pH 8.0, 200 µg/ml HPDP-biotin, 40% DMSO) and then pooled after purification with the µMACS Streptavidin Kit (Miltenyi). The 4sU-labeled RNA was eluted by cleaving the HDPD-biotin with 100 mM DTT and then purified and concentrated with the miRNeasy Micro kit (Qiagen). 100 µg of the purified 4sU-labeled RNA was then used as input for the Ovation library prep kit (Nugen). mNET-seq:  Cells were seeded the day before the experiment to get 100 million cells per sample the following day. We randomly assigned flasks for each treatment and treated cells with DMSO or dTAG7 ligand (final dTAG7 conc. 500 nM) for 1 or 4h, before extracting the chromatin-bound Pol II. The fractionation was done with 25 million cells per chromatin extraction. The cells were first washed with ice-cold DPBS, resuspended in 4 ml ice-cold HLB+N buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2 and 0.5% (vol/vol) NP-40) and incubated on ice for 5 minutes. The cell suspension was then underlaid with 1 ml HLB+NS buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 2.5 mM MgCl2, 0.5% (vol/vol) NP-40 and 10% (wt/vol) sucrose) and centrifuged to pellet the nuclei at 0.44 x g. The supernatant and membrane debris was then removed and the nuclei were resuspended in 125 µl NUN1 lysis buffer (20 mM Tris-HCl (pH 7.9), 75 mM NaCl, 0.5 mM EDTA and 50% (vol/vol) glycerol) to which we added 1.2 ml NUN2 buffer to precipitate the chromatin (20 mM HEPES-KOH (pH 7.6), 300 mM NaCl, 0.2 mM EDTA, 7.5 mM MgCl2, 1% (vol/vol) NP-40 and 1 M urea) and incubated on ice for 15 minutes with occasional vortexing. The lysates are then centrifuged at ≥16,000g for 10 minutes at 4 °C to pellet the chromatin. These were then washed with MNase buffer and then digested with MNase (NEB) for 2 minutes at 37°C. The digestion was stopped by adding 5 µl of 500 mM EGTA and transferring onto ice. The reactions were then centrifuged at ≥16,000g for 5 minutes at 4 °C and then supernatant was diluted with 1 ml NET-2E buffer (50 mM Tris-HCl (pH 7.4, 150 mM NaCl,0.05% (vol/vol) NP-40 and 1 % Empigen BB) per fractionation and pooled per sample for the IP. We added 50 µl of antibody-conjugated beads (Dynabeads M-280 Sheep Anti-Mouse IgG rebound with 30 µg anti-CTD antibody) and incubated in the cold room for 1.5 h. This was followed by 6 washes with NET-2E buffer and phosphorylation of 5' RNA ends with T4 PNK 3' phosphatase minus (NEB) by incubating the beads with phosphorylation buffer (1 x PNK Buffer, 0.1% Tween-20, 1.5 mM ATP, PNK) at 37°C for 6 min. We eluted the RNA with RNA extraction buffer (ZYMO Quick-RNA microPrep kit). We added 1 ng of fragmented S. cerevisae mRNA spike-in to the extraction buffer (1h dTAG7-treatment samples). In brief, these spike-ins were prepared from S. c. total RNA. Yeast cells were lysed in TSNTE buffer (2% triton x-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0) and acidic phenol by several rounds of shaking with zirconia beads in the FastPrep machine, followed by RNA extraction and DNAse treatment (TURBO DNA-free DNAse, Thermo Fisher Scientific). Yeast mRNA was isolated with two rounds of purification with the Dynabeads mRNA Purification kit (Thermo Fisher Scientific). Yeast mRNA was then chemically fragmented with NEBNext Magnesium RNA Fragmentation Module (NEB) for 5 min at 94°C and the ends were repaired with T4 PNK (NEB) to be compatible for library input. Next, short immunoprecipitated RNA fragments were size selected (under 200 nt) and purified from the eluates (with or without spiked-in fragmented yeast mRNA) according to the manufacturers protocol (ZYMO Quick-RNA microPrep kit) and eluted in 7.5 µl nuclease-free water. TT-seq RNA libraries were prepared for sequencing using standard Ovation library prep kit protocol (Nugen). mNET-seq RNA libraries were prepared for sequencing using standard Illumina/NEB protocols (TruSeq Small RNA Library Prep Kit/NEBNext Small RNA Library Prep).