REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Mouse IgG HRP conjugated	GE Healthcare	RRID# AB_772210
Anti-Rabbit IgG HRP conjugated	GE Healthcare	Cat# NA934V
Anti-c-Myc 9E10	BioLegend	RRID# AB_2148451
Anti-c-Myc-Peroxidase	Roche	RRID# AB_390910
Monoclonal ANTI-FLAG M2	Sigma-Aldrich	RRID# AB_259529
Monoclonal ANTI-FLAG M2-Peroxidase	Sigma-Aldrich	RRID# AB_439702
Anti-HA-Peroxidase	Roche	RRID# AB_390917
Histone H2A antibody	Active Motif	RRID# AB_2687477
GAPDH antibody	GeneTex	RRID#AB_11174761
Anti-HA F7	Santa Cruz	Cat# sc-7392
Anti-HA (12CA5)	Roche	RRID# AB_514505
Chemicals, peptides, and recombinant proteins
α-factor	Zymo Research	Cat# Y1001
Nocodazole	Sigma-Aldrich	Cat# M1404
Indole-3-acetic acid (IAA)	Sigma-Aldrich	Cat# 45533
Formaldehyde Solution	Sigma-Aldrich	Cat# 252549
Proteinase K	ThermoFisher	Cat# EO0491
Benzonase nuclease	Sigma-Aldrich	Cat# E1014
RNase A	ThermoFisher	Cat# EN0531
Propidium iodide solution	Sigma-Aldrich	Cat# P4864
GelRed Nucleic Acid Gel Stain	Biotium	Cat# 41103
5-Fluoroorotic Acid	Zymo Research	Cat# F9001
DAPI	ThermoFisher	Cat# 62248
cOmplete Protease Inhibitors Cocktail	Sigma-Aldrich	Cat# 11836145001
Triton X-100	Sigma-Aldrich	Cat# T9284
NP-40 Alternative	Sigma-Aldrich	Cat# 492016
Sodium Deoxycholate	Sigma-Aldrich	Cat# S1827
2-Chloroacetamide	Sigma-Aldrich	Cat# C0267
Dithiothreitol	ThermoFisher	Cat# R0861
Sequencing grade modified trypsin	Promega	Cat# V5111
Copper (II) sulfate	Sigma-Aldrich	Cat# C1297
Critical commercial assays
Pierce ECL 2 western blotting substrate	ThermoFisher	Cat# 80196
Nitrocellulose Blotting Membrane	Sigma-Aldrich	Cat# GE10600002
Dynabeads Protein G	ThermoFisher	Cat# 10004D
Pierce Anti-c-Myc Magnetic Beads	ThermoFisher	Cat# 88842
NuPAGE LDS Sample Buffer	ThermoFisher	Cat# NP0007
NuPAGE bis-tris 4-12% gradient protein gel	ThermoFisher	Cat# NP0323BOX
Gateway LR Clonase II Enzyme mix	ThermoFisher	Cat# 11791020
Gateway BP Clonase II Enzyme mix	ThermoFisher	Cat# 11789020
TruSeq Stranded Yeast Ribo-Zero Gold Kit	Illumina	Cat# MRZY1324
TruSeq Stranded RNA LT kit with Ribo-Zero Gold	Illumina	Cat# RS-122-2301
KAPA HTP Library Prep Kit for Illumina	Roche	Cat# KK8234
PowerUp SYBR Green Master Mix	ThermoFisher	Cat# A25742
Deposited data
ChIP sequencing data	This study	GEO: GSE201194
RNA sequencing data	This study	GEO: GSE201194
Mass spectrometry data	This study	MassIVE: MSV000086339, ProteomeXchange: PXD022100
Unprocessed images presented in this manuscript	This study	https://www.stowers.org/research/publications/libpb-1710
Experimental models: Organisms/strains
All Saccharomyces cerevisiae strains used in this study are listed in Table S1	Lab stock and this study	N/A
Oligonucleotides
POA1-F AAACGGCCACATCAAATACC	Muñoz et al.20	N/A
POA1-R TCCAAGGGACTCCGAATATG	Muñoz et al.20	N/A
MRP10-F ACCCCCTCTTCCCAGACTAA	Muñoz et al.20	N/A
MRP10-R CCAGCACATTTAGGGCTCAT	Muñoz et al.20	N/A
MET10-F ACTTGTGTGGCCCTACTTGG	Muñoz et al.20	N/A
MET10-R CGACTTTGATGCCTCTTTCC	Muñoz et al.20	N/A
CEN3-F CGCCACTTTAACAAATGTGC	Muñoz et al.20	N/A
CEN3-R GCAGAACCACCGTAGCAGTT	Muñoz et al.20	N/A
CEN9-F TGTCACCTGGCTGTTTTGAG	Muñoz et al.20	N/A
CEN9-R TGGGTAATGTCAGCTGTGGA	Muñoz et al.20	N/A
GLT1-F TTTGACCCCAGCACATGTTA	Muñoz et al.20	N/A
GLT1-F GGGTGTGGAGTTTGTGGTCT	Muñoz et al.20	N/A
CEN3chip-F AAGTCACATGATGATATTTGAT	This study	N/A
CEN3chip-R ATTTCTTTTTTAACTTTCGGAA	This study	N/A
Recombinant DNA
Yeast genomic tiling collection	OpenBiosystems	Cat# YSC4613
pRS413-SCC2-7MYC Point and alanine block mutants	This study	N/A
pHyg-AID∗-6FLAG	Addgene	Cat# 99519
pHyg-AID∗-6HA	Addgene	Cat# 99520
Software and algorithms
Fiji (Image J) V2.3.1/1.53f	https://imageJ.net/	RRID# SCR_002285
FlowJo v9	FlowJo	RRID# SCR_008520
Prism V9.3.1	GraphPad	RRID# SCR_002798
PyMOL	http://www.pymol.org/	RRID# SCR_000305
ProLuCID	Xu et al.75	N/A
DTASelect v1.9	Tabb et al.76	N/A
NSAF v0.0.1	Zhang et al.77	N/A
STARTApp	Nelson et al.78	N/A
ReactomePA	Yu and He79	RRID# SCR_019316
HiSeq Control Software v2.2.58	Illumina	N/A
Illumina Primary Analysis version RTA v2.4.11	Illumina	N/A
Illumina Secondary Analysis bclfastq2 v2.17	Illumina	N/A
R 3.6-4.0	https://www.r-project.org/	RRID# SCR_001905
Bioconductor 3.10-3.13	http://www.bioconductor.org	RRID# SCR_006442
edgeR v3.28.0	http://www.bioconductor.org/packages/edgeR/	RRID# SCR_012802
TopHat 2.1.1	http://ccb.jhu.edu/software/tophat/index.shtml	RRID# SCR_013035
bowtie2 bowtie2-2.4.2	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml	RRID# SCR_016368
STAR STAR_2.6.1c	http://code.google.com/p/rna-star/	RRID# SCR_004463
Macs2 2.1.2	https://github.com/macs3-project/MACS	RRID# SCR_013291
Ensembl 96	http://www.ensembl.org/	RRID# SCR_002344