Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Saccharomyces cerevisiae) | BY4705 | PMID:9483801 | ATCC: 200869 | Laboratory of Dan Gottschling; WT |
| Genetic reagent (Schizosaccharomyces pombe) | SHY1058 | PMID:28918900 | h- RPB3-3x Flag::NatMX | WT |
| Genetic reagent (S. pombe) | SHY1110 | PMID:18216783 | h + leu1-32 ade6-216 OtrR1:ura4 Abp1-3xFlag::KanMX Cbh1-13xMyc::NatMX | Laboratory of Toshio Tsukiyama; WT |
| Genetic reagent (S. cerevisiae) | SHY1036 | PMID:28918900 | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3 | WT-degron tagging (BY4705 derivative) |
| Genetic reagent (S. cerevisiae) | SHY1235 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3 | WT-degron tagging (BY4705 derivative) |
| Genetic reagent (S. cerevisiae) | SHY1039 | PMID:31913117 | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, TAF1-3xV5 IAA7::KanMX | Taf1 degron |
| Genetic reagent (S. cerevisiae) | SHY1059 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2△::HPH | bdf2△ |
| Genetic reagent (S. cerevisiae) | RDY27 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF1-3xV5 IAA7::KanMX | Bdf1 degron |
| Genetic reagent (S. cerevisiae) | RDY28 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX | Bdf2 degron |
| Genetic reagent (S. cerevisiae) | RDY70 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX | Bdf2 degron |
| Genetic reagent (S. cerevisiae) | RDY73 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3 | Bdf1/2 degron |
| Genetic reagent (S. cerevisiae) | RDY1 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2△::HPH, BDF1-3xV5 IAA7::KanMX | bdf2△, Bdf1 degron |
| Genetic reagent (S. cerevisiae) | SHY1137 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, TOA1-3xV5 IAA7 | Toa1 degron |
| Genetic reagent (S. cerevisiae) | SHY1213 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, ssl2△::KanMX/pSH1947 (LEU2 SSL2-3xV5 IAA7) | Ssl2 degron |
| Genetic reagent (S. cerevisiae) | RDY29 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, HTZ1-3xV5 IAA7::KanMX | H2A.Z degron |
| Genetic reagent (S. cerevisiae) | RDY57 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, esa1△::KanMX/pRD8 (LEU2 ESA1-3xV5 IAA7) | Esa1 degron |
| Genetic reagent (S. cerevisiae) | RDY44 | Laboratory of Steven Hahn | pBDF2-MNase::TRP1 | Free MNase (BDF2 promoter) |
| Genetic reagent (S. cerevisiae) | RDY34 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF1-3xV5 IAA7, BDF2-MNase::TRP1 | Bdf1 degron, Bdf2-MNase |
| Genetic reagent (S. cerevisiae) | RDY33 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7, BDF1-MNase::TRP1 | Bdf2 degron, Bdf1-MNase |
| Genetic reagent (S. cerevisiae) | RDY59 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, esa1△::KanMX, BDF1-MNase::TRP1/pRD8 (LEU2 ESA1-3xV5 IAA7) | Esa1 degron, Bdf1-MNase |
| Genetic reagent (S. cerevisiae) | RDY85 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF1-3xFlag::NatMX | Bdf1-3xFlag |
| Genetic reagent (S. cerevisiae) | RDY86 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xFlag::NatMX | Bdf2-3xFlag |
| Genetic reagent (S. cerevisiae) | RDY30 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2△::HygMX, BDF1-3xV5 IAA7::KanMX, TAF1-MNase::TRP1 | bdf2△, Bdf1 degron, Taf1-MNase |
| Genetic reagent (S. cerevisiae) | RDY21 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2△::HygMX, BDF1-3xV5 IAA7::KanMX, TAF11-MNase::TRP1 | bdf2△, Bdf1 degron, Taf11-MNase |
| Genetic reagent (S. cerevisiae) | RDY26 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2△::HygMX, BDF1-3xV5 IAA7::KanMX, MED8-MNase::TRP1 | bdf2△, Bdf1 degron, Med8-MNase |
| Genetic reagent (S. cerevisiae) | RDY50 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2△::HygMX, BDF1-3xV5 IAA7::KanMX, MED17-MNase::TRP1 | bdf2△, Bdf1 degron, Med17-MNase |
| Genetic reagent (S. cerevisiae) | RDY51 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2△::HygMX, BDF1-3xV5 IAA7::KanMX, SPT3-MNase::TRP1 | bdf2△, Bdf1 degron, Spt3-MNase |
| Genetic reagent (S. cerevisiae) | SHY1172 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, MED14-3xV5 IAA7::KanMX, SPT3-MNase::TRP1 | Med14 degron, Spt3-MNase |
| Genetic reagent (S. cerevisiae) | SHY1301 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, MED14-3xV5 IAA7::KanMX, TAF1-MNase::TRP1 | Med14 degron, Taf1-MNase |
| Genetic reagent (S. cerevisiae) | SHY1327 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, TAF13-3xV5 IAA7::KanMX, MED8-MNase::TRP1 | Taf13 degron, Med8-MNase |
| Genetic reagent (S. cerevisiae) | SHY1331 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, TAF13-3xV5 IAA7::KanMX, SPT7-MNase::TRP1 | Taf13 degron, Spt7-MNase |
| Genetic reagent (S. cerevisiae) | RDY82 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, TAF1-3xFlag::NatMX | Bdf1/2 degron, Taf1-3xFlag |
| Genetic reagent (S. cerevisiae) | SHY1089 | Laboratory of Steven Hahn | RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, TAF13-3xV5 IAA7::KanMX, SUA7-13xMyc::HPH | Taf13 degron, TFIIB-13xMyc |
| Genetic reagent (S. cerevisiae) | RDY92 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, SUA7-3xFlag::NatMX | Bdf1/2 degron, TFIIB-3xFlag |
| Genetic reagent (S. cerevisiae) | RDY79 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, BUR1-3xFlag::NatMX | Bdf1/2 degron, Bur1-3xFlag |
| Genetic reagent (S. cerevisiae) | RDY81 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, CTK1-3xFlag::NatMX | Bdf1/2 degron, Ctk1-3xFlag |
| Genetic reagent (S. cerevisiae) | RDY94 | Laboratory of Steven Hahn | pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, SPT5-3xFlag::NatMX | Bdf1/2 degron, Spt5-3xFlag |
| Antibody | Rabbit polyclonal anti-Tfg2 | Laboratory of Steven Hahn | Rabbit #1260K | WB (1:2000) |
| Antibody | Mouse monoclonal anti-V5 | Invitrogen | Cat. #R960-25 | WB (1:1000) |
| Antibody | Rabbit monoclonal anti-H4K12ac | Cell Signaling Technology | Cat. #13944 | WB (1:1000) ChIP-seq (1:100) |
| Antibody | Mouse monoclonal anti-Flag | Sigma-Aldrich | Cat. #F3165 | ChIP-seq (1:100) |
| Antibody | Mouse monoclonal anti-Myc | Cell Signaling Technology | Cat. #2276 | ChIP-seq (1:100) |
| Antibody | Mouse monoclonal anti-Rpb1 CTD | Cell Signaling Technology | Cat. #2629 | ChIP-seq (1:50) |
| Antibody | Rabbit monoclonal anti-Phospho-Rpb1 CTD (Ser2) | Cell Signaling Technology | Cat. #13499 | ChIP-seq (1:50) |
| Antibody | Rabbit monoclonal anti-Phospho-Rpb1 CTD (Ser5) | Cell Signaling Technology | Cat. #13523 | ChIP-seq (1:50) |
| Recombinant DNA reagent | pFA6a-3V5-IAA7-KanMX6 | PMID:30192227 | Degron tagging vector | |
| Recombinant DNA reagent | pSH1855 | Laboratory of Steven Hahn | Degron tagging vector | |
| Recombinant DNA reagent | pGZ110 | PMID:26490019 | MNase tagging vector | |
| Recombinant DNA reagent | p2L-3Flag-NAT | Laboratory of Toshio Tsukiyama | 3xFlag tagging vector | |
| Recombinant DNA reagent | pFA6a-13Myc-Hyg | Laboratory of Toshio Tsukiyama | 13xMyc tagging vector | |
| Recombinant DNA reagent | pRS303 | PMID:2659436 | ATTC: 77138 | |
| Recombinant DNA reagent | pRD15 | Laboratory of Steven Hahn | pRS303 derivative-free MNase under BDF2 promoter | |
| Recombinant DNA reagent | pRS315 | PMID:2659436 | ATTC: 77144 | |
| Recombinant DNA reagent | pRS316 | PMID:2659436 | ATTC: 77145 | |
| Recombinant DNA reagent | pRD5 | Laboratory of Steven Hahn | pRS315 derivative-ESA1 gene with native promoter | |
| Recombinant DNA reagent | pRD21 | Laboratory of Steven Hahn | pRS316 derivative-ESA1 gene with native promoter and degron tag | |
| Commercial assay or kit | RiboPure yeast kit | Thermo Fisher Scientific | Cat. #AM1926 | |
| Commercial assay or kit | MyOne Streptavidin C1 Dynabeads | Thermo Fisher Scientific | Cat. #65002 | |
| Commercial assay or kit | Protein G Dynabeads | Thermo Fisher Scientific | Cat. #10003D | |
| Commercial assay or kit | RNeasy Kit | Qiagen | Cat. #74104 | |
| Commercial assay or kit | Qubit HS RNA assay | Thermo Fisher Scientific | Cat. #Q32852 | |
| Commercial assay or kit | Qubit HS DNA assay | Thermo Fisher Scientific | Cat. #Q32851 | |
| Commercial assay or kit | Ovation Universal RNA-seq Library Preparation Kit | Tecan | Cat. #0364-A01 | Including S. cerevisiae AnyDeplete reagent |
| Chemical compound, drug | MTSEA biotin-XX | Biotium | Cat. #90066-1 | |
| Chemical compound, drug | 4-thiouracil | Sigma-Aldrich | Cat. #440736 | |
| Chemical compound, drug | Indole-3-acetic acid | Sigma-Aldrich | Cat. #I3750 | |
| Software, algorithm | HTseq | PMID:25260700 | ||
| Software, algorithm | Bowtie 2 | PMID:22388286 | ||
| Software, algorithm | HOMER | PMID:20513432 | ||
| Software, algorithm | Clustal Omega | PMID:21988835 | ||
| Software, algorithm | Jalview v 2 | PMID:19151095 | ||
| Software, algorithm | PANTHER v 16.0 | PMID:33290554 |