| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| IgG from rabbit serum | Sigma-Aldrich | Cat# I5006; RRID: AB_1163659 |
| c-Myc polyclonal | Thermo Fischer Scientific | Cat# PA5-85185; RRID: AB_2792331 |
| PGK1 monoclonal | Thermo Fischer Scientific | Cat# 459250;RRID: AB_2532235 |
| IRDye® 800CW anti-mouse | Li-cor | Cat# 925-32210; RRID: AB_2687825 |
| IRDye® 800CW anti-rabbit | Li-cor | Cat# 926-32211; RRID: AB_621843 |
| 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 Fischer Scientific | Cat#214030 |
| Bacto™ Peptone | Thermo Fischer Scientific | Cat# 211677 |
| Bacto™ Yeast Extract, technical | Thermo Fischer Scientific | Cat# 288620 |
| D-Glucose | Sigma-Aldrich | Cat# 8270-10KG |
| D-Raffinose | Bio-Connect Life Sciences | Cat# OR06197_2kg |
| D-Galactose | Sigma-Aldrich | Cat# G0750-500G |
| 1× Tris-EDTA buffer pH 8.0 | Invitrogen | Cat# 12090015 |
| D-Sorbitol | Sigma-Aldrich | Cat# S6021 |
| Potassium phosphate monobasic (powder) | Sigma-Aldrich | Cat# P9791 |
| Potassium phosphate dibasic (powder) | Sigma-Aldrich | Cat# P8281 |
| B-Mercaptoethanol | Sigma-Aldrich | Cat# M6250 |
| Lyticase from Arthrobacter luteus (powder) | Sigma-Aldrich | Cat# L2524 |
| Ribonucleoside Vanadyl Complex (RVC; liquid) | NEB | Cat# S1402S |
| Formamide (deionized) | Sigma-Aldrich | Cat# F9037 |
| UltraPure™ SSC, 20X | Thermo Fisher Scientific | Cat# 15557044 |
| Dextran sulfate sodium salt | Sigma-Aldrich | Cat# 67578 |
| ProLong® Gold Antifade Mountant with DAPI | Invitrogen | Cat# P36935 |
| Sodium chloride (NaCl) | Sigma-Aldrich | Cat# S9888 |
| Glycerol | Sigma-Aldrich | Cat# G5516 |
| Phosphate-buffered saline (PBS) | Thermo Fisher Scientific | Cat# 18912014 |
| MyTaq Red Mix 2x | Bioline | Cat#: BIO-25044 |
| DMSO | Sigma | Cat#: D4540 |
| DNase I recombinant, RNase-free | Sigma-Aldrich (Roche) | Cat# 04716728001 |
| cOmplete EDTA-free protease inhibitor cocktail tablets | Sigma-Aldrich (Roche) | Cat# 11873580001 |
| Pefabloc SC-Protease-Inhibitor | Carl Roth | Cat# A154.3 |
| Dynabeads M-280 Tosylactivated | Thermo Fisher Scientific | Cat# 14204 |
| RNace-It Ribonuclease Cocktail | Agilent | Cat# 400720 |
| Recombinant GST-TEV protease | Challal et al.79 | N/A |
| Guanidine hydrochloride | Sigma-Aldrich | Cat# G4505 |
| Ni-NTA Agarose | Qiagen | Cat# 30230 |
| Imidazole | Sigma-Aldrich | Cat# I0125 |
| RNaseOUT Recombinant Ribonuclease Inhibitor | Thermo Fisher Scientific | Cat# 10777019 |
| T4 RNA Ligase 2, truncated KQ | NEB | Cat# M0373L |
| T4 Polynucleotide Kinase | NEB | Cat# M0201L |
| T4 RNA Ligase 1 (ssRNA Ligase) | NEB | Cat# M0204L |
| Proteinase K, recombinant, PCR grade | Sigma-Aldrich (Roche) | Cat# 03115887001 |
| SuperScript IV Reverse Transcriptase | Thermo Fisher Scientific | Cat# 18090050 |
| Exonuclease I | NEB | Cat# M0293S |
| RNase H | NEB | Cat# M0297S |
| LA Taq | Takara | Cat# RR002M |
| Zymolase 100T | US biological | Cat# Z1004.250 |
| Micrococcal nuclease | Sigma-Aldrich | Cat# N5386-200UN |
| Sorbitol | Sigma Aldrich | Cat# 1077581000 |
| Ammonium acetate solution | Sigma Aldrich | Cat# A2706 |
| NP-40 | Sigma Aldrich | Cat# 92016 |
| SDS | Sigma Aldrich | Cat# L3771 |
| Spermidine | Sigma Aldrich | Cat# S0266 |
| Phenol/chloroform (PCI 15:14:1) | Sigma-Aldrich | Cat# P2069-100ML |
| RNaseA/T1 | Thermo Fisher Scientific | Cat# EN0551 |
| Agarose MP | Sigma Aldrich | Cat# 11388991001 |
| 3-indole acetic acid (IAA, auxin) | Sigma Aldrich | Cat# I3750-100G-A |
| NuPAGE™ SDS Running buffer 20x | Thermo Fisher Scientific | Cat# LA0041 |
| NuPAGE™ 3-8%Tris-Acetate protein gels | Thermo Fisher Scientific | Cat#EA0375PK2 |
| Nitrocellulose membrane | Bio-rad | Cat# 1620112 |
| Auxinole | Sigma Aldrich | Cat# SML3231-25MG |
| JFX650 dye | Grimm et al.80 | N/A |
| Critical commercial assays | ||
| LightCycler FastStart DNA Master SYBR Green I | Roche | Cat# 12239364001 |
| LightCycler 480 SYBR Green I Master | Roche | Cat# 04887352001 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher Scientific (Invitrogen) | Cat# Q32851 |
| Vivacon 500 | Sartorius | Cat# VN01H22 |
| QIAquick PCR Purification Kit | Qiagen | Cat# 28104 |
| PCR Isolate II PCR and Gel Kit | Bioline | Cat# BIO-52060 |
| Bioanalyzer High Sensitivity DNA kit | Agilent | Cat# 5067-4626 |
| ISOLATE II Plasmid Mini Kit | Bioline | Cat# BIO-52057 |
| KAPA HTP Library Preparation Kit | KAPA Biosystems | Cat# 07961901001 |
| Deposited data | ||
| MNase-seq data | this study | GEO: GSE196945 |
| Pol II CRAC-seq | this study | GEO: GSE217963 |
| Raw images and Western blots | this study | Mendeley Data: https://doi.org/10.17632/z2w34669gj.1 |
| Experimental models: Organisms/strains | ||
| Please refer to Table S1 | this study | N/A |
| Oligonucleotides | ||
| Please refer to Tables S3, S4, and S5 | this study | N/A |
| Recombinant DNA | ||
| Please refer to Table S2 | this study | N/A |
| Software and algorithms | ||
| ImageJ | Schneider et al.81 | https://imagej.nih.gov/ij/index.html |
| Python | custom code |
https://doi.org/10.5281/zenodo.7820986 https://doi.org/10.5281/zenodo.7820895 https://doi.org/10.5281/zenodo.7820931 https://doi.org/10.5281/zenodo.7821005 |
| Bowtie2 | Langmead and Salzberg82 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MATLAB (MatTrack v6) | Mazza et al.,83 kind gift from David Ball | https://doi.org/10.5281/zenodo.7821136 |
| DESeq2 | Love et al.84 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| RStudio | RStudio | RRID: SCR_000432 |
| Affinity Designer | Serif | https://affinity.serif.com/en-us/designer/; RRID: SCR_016952 |
| Other | ||
| "Megatron" W5 UV crosslinking unit | UVO3 Ltd | https://www.uvo3.co.uk/ |
| Mixer Mill MM 400 | Retsch | Cat# 20.745.0001 |
| Gelfree 8100 Fractionation Station | Expedeon | Cat# 48100 |
| 18 mm round cover slips coated with poly-L-lysine | Neuvitro | Cat# GG-18-1.5-pll |
| 25mm round cover glasses (#1.5, thickness) | VWR | Cat# 631-0172 |
| 25mm round cover glasses HI D=0.17m | Zeiss | Cat# 000000-1787-996 |
| Wash-N-Dry coverslip rack | Sigma Aldrich | Cat# Z688568-1EA |
| 400 mL tall glass beakers | Novodirect | Cat# 15439093 |
| Microscope slides, SuperFrost® | VWR | Cat# ISO8037/I |
| Attofluor™ Cell Chamber, for microscopy | Thermofisher Scientific | Cat# A7816 |
| Dumont Horlogemakers pincet Gebogen Nr. 7 (forceps, tweezers) | Vos Medisch | Cat# 1121 |
| Cell density meter | VWR | Cat#634-0882 |
| Parafilm® M (4 inches wide) | Merck | P7668 |
| Zeiss Plan-Apochromat 40×/1.40NA Oil | Zeiss | Cat# 420762-9900-000 |
| Zeiss 4-alpha Plan-Apochromat 100×/1.46NA Oil | Zeiss | Cat# 420792-9800-000 |
| Zeiss alpha Plan-Apochromat 100x 1.57NA oil | Zeiss | Cat# 420792-9771-000 |
| SPECTRA X light engine WL:360–680 nm | Lumencor | N/A |
| ORCA Flash 4v3 digital sCMOS camera | Hamamatsu | Cat# C13440-20CU |
| UNO Top stage incubator and objective heater | Okolab | N/A |
| Excitation filters, emission flters and dichroic mirrors | See method details | N/A |
Official websites use .gov
A
.gov website belongs to an official
government organization in the United States.
Secure .gov websites use HTTPS
A lock (
) or https:// means you've safely
connected to the .gov website. Share sensitive
information only on official, secure websites.