REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-V5 tag (mouse) antibody	Thermo Fisher Scientific	R96025; RRID: AB_2556564
Anti-hexokinase (rabbit) antibody	US Biological	H2035; RRID: AB_2629457
Anti-Myc tag (mouse) antibody	Merck Millipore	05-724; RRID: AB_309938
Anti-FLAG tag (mouse) antibody	Sigma-Aldrich (Merck)	F3165; RRID: AB_259529
Anti-V5 agarose affinity gel	Sigma-Aldrich (Merck)	A7345; RRID: AB_10062721
Anti-Mouse IgG IRDye® 800CW (goat)	LICOR (NE USA)	925-32210; RRID: AB_2687825
Anti-rabbit IgG IRDye 680RD (donkey)	LICOR (NE USA)	925-68073; RRID: AB_2716687
Anti-H3 (rabbit) antibody	Abcam	ab1791; RRID: AB_302613)
Anti-H3K56ac (rabbit) antibody	Sigma-Aldrich/Millipore (Merck)	07-677-I; RRID: AB_390167
Chemicals, peptides, and recombinant proteins
dATP [α-32P]	PerkinElmer	NEG512H500UC
Proteinase K	Thermo Fisher Scientific	EO0491
rDNase	Machery-Nagel	740963
RNA Fragmentation Reagents (Ambion)	Thermo Fisher Scientific	AM8740
Shrimp Alkaline Phosphatase (rSAP)	NEB	M0371L
Cap-Clip Acid Pyrophosphatase	CellScript	C-CC15011H
T4 RNA ligase 1 (high concentration)	NEB	M0437M
SuperScript IV Reverse Transcriptase	Thermo Fisher Scientific	18090050
RNasin Plus Ribonuclease Inhibitor	Promega	N2115
RNase H	NEB	M0297L
RNase cocktail	Thermo Fisher Scientific	AM2286
Dynabeads MyOne Streptavidin C1	Thermo Fisher Scientific	65002
Phenol:chloroform: Isoamyl alcohol (125:24:1)	Ambion	AM9520
Random hexamers	ThermoFisher Scientific	N8080127
HighPrep PCR beads	MagBio	AC-60050
Novex 6% TBE gels	Invitrogen	EC62655BOX
Costar SpinX column	Corning Incorporrated	8161
glass pre-filters	Whatman	1823010
linear acrylamide	Ambion	AM9520
5-Methylcytosine-dNTPs	Zymo Research	D1030
NEbuffer 2	NEB	B7002S
NAD+	NEB	B9007S
E.coli DNA ligase	NEB	M0205S
DNA polymerase I	NEB	M0209S
GsuI	ThermoFisher Scientific	ER0461
Halt Protease Inhibitor Cocktail (100X)	ThermoFisher Scientific	78429
SUPERase•In RNase Inhibitor (20 U/μL)	ThermoFisher Scientific	AM2694
FLAG® Peptide	Millipore	F3290
Critical commercial assays
Poly(A)Purist MAG kit	Ambion	AM1922
KAPA RNA hyperPrep kit	Roche	KK8540
Qbit RNA high sensitivity assay kit	ThermoFisher Scientific	Q32852
KAPA Hyper Prep Kit	Roche	KK8504
Qubit dsDNA HS assay kit	Invitrogen	Q32851
RNeasy MinElute Cleanup Kits	QIAGEN	74204
Platinum SYBR mix	ThermoFisher Scientific	11733046
2100 Bioanalyzer	Agilent	G2939BA
KAPA Hi-Fi hot start ready mix	Roche	KK2601
KAPA single indexed adapters Set A	Roche	KK8701
KAPA single indexed adapters Set B	Roche	KK8702
Prime-It II Random Primer Labeling Kit	Agilent	300385
IME1 and ACT1 single molecule RNA-FISH probes	Biosearch Technologies	N/A
Deposited data
mRNA-seq, TSS-seq, TES-seq and PolII associated RNA-seq	This paper	GEO: GSE138898
Experimental models: organisms/strains
S. cerevisiae: Strain background: BY, SK1 see Table S2	This paper	N/A
Oligonucleotides
Oligonucleotides and primers, see Table S3	This paper	N/A
Recombinant DNA
Plasmids, see Table S4	This paper	N/A
Software and algorithms
Cutadapt (version 1.9.1)	(Martin, 2011)	https://cutadapt.readthedocs.io/en/stable/
STAR (version 2.5.2)	(Dobin et al., 2013)	https://github.com/alexdobin/STAR
SAMTools (version 1.3.1)	(Li et al., 2009)	http://www.htslib.org/
BEDTools (version 2.26.0)	(Quinlan and Hall, 2010)	https://bedtools.readthedocs.io/en/latest/
BigWig and BigBed	(Kent et al., 2010)	http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
ImageJ (version 1.48k)	Schneider et al., 2012	https://imagej.nih.gov/ij/index.html
MATLAB 2018a	MATLAB - MathWorks - MATLAB and Simulink	RRID: SCR_001622
StarSearch	Raj Laboratory, University of Pennsylvania	https://rajlab.seas.upenn.edu/StarSearch/launch.html