Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| IgG from rabbit serum | Sigma-Aldrich | Cat# I5006; RRID:AB_1163659 |
| PGK1 monoclonal | Thermo Fisher Scientific | Cat# 459250; RRID:AB_2532235 |
| TAP Tag polyclonal | Thermo Fisher Scientific | Cat# CAB1001; RRID:AB_10709700 |
| IRDye® 800 anti-rabbit | LI-COR Biosciences | Cat# 926-32211; RRID:AB_621843 |
| IRDye® 680 anti-mouse | LI-COR Biosciences | Cat# 926-68070; RRID:AB_10956588 |
| Chemicals, peptides, and recombinant proteins | ||
| Yeast Nitrogen Base w/o AA, Carbohydrate & w/ AS (YNB) (Powder) | US Biological | Cat# Y2025 |
| Drop-out Mix Complete w/o Yeast Nitrogen Base (Powder) | US Biological | Cat# D9515 |
| Bacto™ Agar | Thermo Fisher Scientific | Cat#214030 |
| Bacto™ Peptone | Thermo Fisher Scientific | Cat# 211677 |
| Bacto™ Yeast Extract | Thermo Fisher Scientific | Cat# 212750 |
| D-Glucose | Sigma-Aldrich | Cat# 8270 |
| Glycerol | Honeywell | Cat# 49770 |
| Ethanol | Honeywell | Cat# 32221 |
| Potassium hydrogen phthalate | VWR | Cat# 26948.260 |
| Myo-inositol | Sigma-Aldrich | Cat# I5125 |
| 4-Amino benzoic acid potassium salt | Sigma-Aldrich | Cat# A0254 |
| Geneticin (G418) Sulfate | Santa Cruz Biotech | Cat# sc-29065A |
| Hygromycin B | Gibco™ | Cat# 10687010 |
| Nourseothricin-dihydrogen sulfate (CloNat) | Werner BioAgents | Cat# 5.002.000 |
| 1,10-phenanthroline | Sigma-Aldrich | Cat# 131377 |
| Rapamycin | LC Laboratories | Cat# R-5000 |
| DMSO | Sigma-Aldrich | Cat# D4540 |
| Formaldehyde solution 37% | Sigma-Aldrich | Cat# 252549 |
| Tris(hydroxymethyl)aminomethane | Millipore | Cat# 1083821000 |
| Glycine | Acros Organics | Cat# 220910050 |
| Hydrochloric acid (fuming) | Honeywell | Cat# 30721 |
| Dynabeads™ M-270 Epoxy | Thermo Fisher Scientific | Cat# 14302D |
| PMSF | Roche | Cat# 10837091001 |
| cOmplete™ EDTA-free Protease Inhibitor Cocktail | Roche | Cat# 11873580001 |
| Ribonuclease A from bovine pancreas | Sigma-Aldrich | Cat# R5000 |
| Proteinase K from Tritirachium album | Sigma-Aldrich | Cat# P2308 |
| Agencourt AMPure XP beads | Beckman Coultier | Cat# A63881 |
| DAPI | Invitrogen™ | Cat# D1306 |
| MyTaq Red Mix 2x | Meridian Bioscience | Cat# BIO-25044 |
| Phusion™ High-Fidelity DNA Polymerase (2 U/μL) | Thermo Fisher Scientific | Cat# F530L |
| Deoxynucleoside Triphosphate Set | Roche | Cat# 11969064001 |
| DNAse I | New England Biolabs | Cat# M0303S |
| Trichloroacetic acid | Sigma-Aldrich | Cat# T6399 |
| Tris/Glycine/SDS running buffer | Bio-Rad | Cat# 161-0772 |
| 40% Acrylamide/Bis Solution, 37.5:1 | Bio-Rad | Cat# 1610149 |
| TEMED | Sigma-Aldrich | Cat# T9281 |
| Ammonium Persulfate | Thermo Fisher Scientific | Cat# 17874 |
| Agarose MP | Sigma-Aldrich | Cat# 11388991001 |
| Trypsin from bovine pancreas | Sigma-Aldrich | Cat# T1426 |
| Guanidinium hydrochloride | Sigma-Aldrich | Cat# G3272 |
| TCEP | Sigma-Aldrich | Cat# C4706 |
| 2-Chloroacetamide | Sigma-Aldrich | Cat# 22790 |
| Critical commercial assays | ||
| QIAquick PCR Purification Kit | Qiagen | Cat# 28106 |
| KAPA Hyper Prep Kit | Roche | Cat# 07962347001 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher Scientific | Cat# Q33231 |
| High Sensitivity DNA Kit | Agilent | Cat# 5067-4626 |
| SensiFAST SYBR No-ROX Kit | Meridian Bioscience | Cat# BIO-98020 |
| QIAquick Gel Extraction Kit | Qiagen | Cat# 28706 |
| RNeasy Kit | Qiagen | Cat# 74106 |
| TruSeq Stranded mRNA Kit | Illumina | Cat# 20020594 |
| DC™ Protein Assay Kit II | Bio-Rad | Cat# 5000112 |
| Pierce™ Bradford Protein Assay Kit | Thermo Fisher Scientific | Cat# 23200 |
| Deposited data | ||
| ChIP-sequencing data | This study | GEO: GSE227470 |
| RNA-sequencing data | This study | GEO: GSE227470 |
| ChIP-exo data Fpt1 | This study | GEO: GSE227470 |
| ChIP-exo data others | (Rossi et al, 2021) | GEO: GSE147927 |
| Epi-Decoder tDNA-Ty1 locus data | This study | NCBI BioProject: PRJNA945378 |
| Epi-Decoder HO locus data | (Poramba-Liyanage et al, 2020) | NCBI BioProject: PRJNA610036 (SRX7842936) |
| Proteomics data | This study | PXD045463 |
| Immunoblots and microscopy data | This study | Mendeley Data: 10.17632/stwm3b4jsf.1 |
| Experimental models: Organisms/strains | ||
| Please refer to Table S11 | This study | N/A |
| Oligonucleotides | ||
| Please refer to Table S13 | This study | N/A |
| Recombinant DNA | ||
| Please refer to Table S12 | This study | N/A |
| Software and algorithms | ||
| ImageJ | (Schneider et al, 2012) | RRID:SCR_003070 |
| ChIP-exo data analysis | This study | https://doi.org/10.5281/zenodo.8381412 |
| GraphPad Prism 9 | GraphPad | RRID:SCR_002798 |
| ScriptManager (version v.014) | (Lang et al, 2022) | RRID:SCR_021797 |
| Picard | Picard | RRID:SCR_006525 |
| BWA-MEM (version 0.7.17-r1188 and 0.7.9a) | (Li & Durbin, 2009) | https://github.com/lh3/bwa |
| GenomicRanges | (Lawrence et al, 2013) | RRID:SCR_000025 |
| Rtracklayer | (Lawrence et al, 2009) | RRID:SCR_021325 |
| RStudio | Rstudio | RRID:SCR_000432 |
| Micro-manager | (Edelstein et al, 2014) | RRID:SCR_000415 |
| Tornadoplot R/Github package | This study | https://doi.org/10.5281/zenodo.8348229 |
| DEseq2 | (Love et al, 2014) | RRID:SCR_015687 |
| FlowJo (version 10.6.1) | FlowJo | RRID:SCR_008520 |
| STAR (version 2.7.1a) | (Dobin et al, 2013) | https://github.com/alexdobin/STAR |
| eXpress (Bioconda Package) | (Roberts & Pachter, 2013) | https://anaconda.org/bioconda/express |
| ShinyGO 0.77 | (Ge et al, 2019) | RRID:SCR_019213 |
| EMBOSS (version 6.6.0) | (Rice et al, 2000) | RRID:SCR_008493 |
| BLAST (version 2.2.31+) | (Camacho et al, 2009) | RRID:SCR_004870 |
| OrthoFinder (version 2.2.7) | (Emms & Kelly, 2019) | RRID:SCR_017118 |
| MAFFT (version 7.271) | (Katoh & Standley, 2013) | RRID:SCR_011811 |
| IQ-Tree (version 1.6.8) | (Nguyen et al, 2015) | RRID:SCR_021163 |
| DIA-NN (version 1.8) | (Demichev et al, 2020) | RRID:SCR_022865 |
| Perseus (version 2.0.10.0) | (Tyanova et al, 2016) | RRID:SCR_015753 |
| Other | ||
| Cover Slips round 25mm (#1.5 thickness) | VWR | Cat# 631-0172 |
| Attofluor™ Cell Chamber, for microscopy | Thermo Fisher Scientific | Cat# A7816 |
| Zeiss 4-alpha Plan-Apochromat 1003/1.46NA Oil | Zeiss | Cat# 420792-9800-000 |
| ORCA Flash 4v3 digital sCMOS camera | Hamamatsu | Cat# C13440-20CU |
| UNO Top stage incubator and objective heater | Okolab | N/A |
| Zirconia-Silicate Beads, 0.5 mm | Biospec | Cat# 11079105Z |
| Amersham™ Protran® nitrocellulose membrane | GE Healthcare Life Science | Cat# 10600002 |
| Sep-Pak C18 1cc cartridges | Waters | Cat# WAT054960 |
| Microlab STAR liquid handling system | Hamilton | N/A |
| Rotor HDA | Singer Instruments | N/A |
| Singer Plusplates™ | Singer Instruments | Cat# PLU-003 |
| Singer Repads™ | Singer Instruments | Cat# REP-004 |
| 2100 Bioanalyzer Instrument | Agilent | Cat# G2939BA |
| DynaMag™−2 Magnet | Invitrogen™ | Cat# 12321D |
| Bioruptor® Pico sonication device | Diagenode | Cat# B01060010 |