KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| SPT5(for WB and ChiP-seq) | BD Biosciences | Cat# 611107, RRID:AB_398420 |
| SPT4 | Cell Signaling Technology | Cat# 64828, RRID:AB_2756442 |
| RPB1 NTD [D8L4Y] (for WB and ChiP-seq for human RPB1) | Cell Signaling Technology | Cat# 14958, RRID:AB_2687876 |
| RPB1 CTD [4H8) (for IP-MS) | Cell Signaling Technology | Cat# 2629, RRID:AB_2167468 |
| RPB1 CTD (for yeast RPB1 WB) | Abcam | Cat# ab26721, RRID:AB_777726 |
| RPB1 CTD [8WG16] (for yeast RPB1 ChiP-seq) | BioLegend | Cat# 664912, RRID:AB_2650945 |
| RPB1 CTD S2P | Millpore | Cat# 04–1571, RRID:AB_10627998 |
| RPB1 CTD S5P | Millpore | Cat# 04–1572, RRlD:AB_10615822 |
| RPB3 | Abcam | Cat# ab182150 |
| RPB5 | Proteintech | Cat# 15217–1-AP, RRlD:AB_2299932 |
| Tubulin | DSH8 | Cat# E7, RRID:AB_528499 |
| HSP90 | Santa Cruz Biotechnology | Cat# sc-13119, RRID:AB_675659 |
| Actin | Cell Signaling Technology | Cat# 3700, RRID:AB_2242334 |
| NELF-A | Proteintech | Cat# 10456–1-AP, RRID:AB_2216327 |
| NELF-C | Cell Signaling Technology | Cat# 12265, RRID: AB_2797862 |
| NELF-E | Abcam | Cat# ab170104, RRID:AB_2827280 |
| VCP | Thermo Fisher Scientific | Cat# MA3–004. RRID:AB_2214638 |
| BRD4 | Cell Signaling Technology | Cat# 13440, RRID:AB_2687578 |
| H3 | Shlatifard Laboratory | N/A |
| CUL3 (WB and ChiP-seq) | Bethyl | Cat# A301–109A, RRID:AB_873023 |
| CUL5 | Bethyl | Cat# A302–173A, RRID:AB_1659801 |
|
| ||
| Chemicals, peptides. and recombinant proteins | ||
|
| ||
| Auxin | Abcam | Cat# ab146403 |
| NMS-873(VCPl) | Sigma-Aidrich | Cat# SML1128 |
| Triptoldo | Tocris | Cat# 3253 |
| NVP-2 | MedChemExpress | Cat# HY-12214A |
| THAL-SNS-032 (dCDK9) | MedChemExpress | Cat# HY-123937 |
| dBET6 | Aobious | Cat# AOB37886 |
| KL-1 | DC Chemicals | Cat# DC11391 |
| KL-2 | DC Chemicals | Cat# DC11392 |
| Rapamycin | ApexBio Technology | Cat# A8167 |
| Benzonase | Sigma | Cat# E1014 |
| Dynabeads Protein G | Invitrogen | Cat# 10004D |
| 4-thiourdin | Sigma | Cat# T4509 |
| Biotin-XX-MTSEA | Bioturn | Cat# 90066 |
| Dynabeads MyOne Streptavidin C1 | ThermoFisher | Cat# 65001 |
|
| ||
| Deposited data | ||
|
| ||
| Sequencing data | This study | GEO: GSE168827 |
| Proteomics data | This study | ProteomaXchange: PXD023997 |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| OsTIR1 DLD-1 | Holland et al, 2012 | N/A |
| SPT5-AID OsTIR1 DLD1 #22–5F-5F | This study | N/A |
| SPT4-AID OsTlR1 DLD1 #5–1D | This study | N/A |
| DLD-1 | ATCC | Cat# CCL-221 |
| SPT5-AID7 AtAFB2 DLD1 #8–9C | This study | N/A |
| Mouse embryonic fibroblasts | Stem cell technology | Cat# 00325 |
| S2 | DGRC | RyBase: FBtc0000006 |
| HCT116 | ATCC | Cat# CCL-247 |
| PAF1-AID OsTlR1 DLD1 #5–3G | Chen et al., 2017 | N/A |
| NELF-C-AlD OsTlRI DLD1 #7–10B | Aoi et al., 2020 | N/A |
| NELF-E-AJD OsTlRI DLD1 #20–1B | Aoi et al., 2020 | N/A |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| Yeast Parental anchor strain: HHY168 | (Haruki et al., 2008): Euroscarf | Cat# Y40343 |
| Yeast SPT5-FRB-KanMXB (Derivative of HHY168) | This study | N/A |
| Yeast SPT5-FRB-KanMXB CDC48-FRB-GFP-His3MX6 (Derivative of HHY168) | This study | N/A |
|
| ||
| Recombinant DNA | ||
|
| ||
| CUL3 GIPZ Lentiviral shRNA #1 | Horizon Discovery | Cat# RMS4430–200161789 |
| CUL3 GIPZ Lentiviral shRNA #2 | Horizon Discovery | Cat# RHS4430–200258609 |
| NEDD4 GIPZ Lentiviral shRNA | Horizon Discovery | Cat# RHS4430–200286902 |
| VCP GIPZ Lentiviral shRNA #1 | Horizon Discovery | Cat# RHS4430–200285689 |
| VCP GIPZ Lentiviral shRNA #2 | Horizon Discovery | Cat# RHS4430–200306365 |
| Non-targeting GIPZ Lentiviral shRNA | Horizon Discovery | Cat# RHS4346 |
| SPT5-AID-Neo donor (YNP49) | This study | N/A |
| SPT5-AID-Hyg donor (YNP50) | This study | N/A |
| Cas9 for SPT5 (YNP50; gRNA CTTCATCCGACGAAGTCCAC) | This study | N/A |
| SPT5-AID7-Hyg donor (ANP38) | This study | N/A |
| SPT5-AID7-Neo donor (ANP39) | This study | N/A |
| SPT4-AID-Neo donor (ANP68) | This study | N/A |
| SPT4-AIO-Hyg donor (ANP69) | This study | N/A |
| Cas9 far SPT4 (ANP71; gRNA GTGCGGGAGCTGAAAAGTCG) | This study | N/A |
| CUL5 GIPZ Lentiviral shRNA #1 | Horizon Discovery | Cat# RHS4430–200181108 |
| CUL5 GIPZ Lentiviral shRNA #2 | Horizon Discovery | Cat# RHS4430–200267365 |
| CUL5 GIPZ Lentiviral shRNA #3 | Horizon Discovery | Cat# RHS4430–200276360 |
|
| ||
| Software and algorithms | ||
|
| ||
| bowtie 2.2.6 | Langmead and Salzberg,2012 | N/A |
| STAR 2.7.5 | Dobin et al., 2013 | N/A |
| outadapt 1.14 | Martin, 2011 | N/A |
| Max Quantvl.6.0.16 | Cox et al., 2014 | N/A |
| MSstats v4.0.0 | Choi et al., 2014 | N/A |
| imputeLCMD v2.0 | Lazar, 2015 | N/A |
| limma v3.48.0 | Ritchie et al., 2015 | N/A |
| deepTools 3.1.1 | Ramírez et al., 2016 | N/A |