REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K36me3	abcam	ab9050, RRID:AB_306966
H3K4me2	abcam	ab32356, RRID:AB_7329224
mouse α-V5	Thermo Fisher	R960-25, RRID:AB_2556564
α-GFP	Takara	632381, RRID:AB_2313808
rabbit α-hexokinase (α-Hxk2)	US Biological	H2035-01, RRID:AB_2629457
α-mouse antibody conjugated to IRDye 800CW	LI-COR Biosciences	926-32212, RRID:AB_621847
α-rabbit antibody conjugated to IRDye 680RD	LI-COR Biosciences	926-68071, RRID:AB_10956166
Chemicals, peptides, and recombinant proteins
Zinc-based alkaline fragmentation reagent	Ambion	AM8740
recombinant shrimp alkaline phosphatase	NEW ENGLAND BIOLABS	M0371
RNasin Plus	Promega	N2611
Cap-Clip acid pyrophosphatase	Tebu-Bio	C-CC15011H
T4 RNA ligase 1	NEW ENGLAND BIOLABS	M0437M
SuperScript IV reverse transcriptase	Invitrogen	18090010
RNase H	NEW ENGLAND BIOLABS	M0297
RNase cocktail enzyme mix	Ambion	AM2286
HighPrep PCR beads	MagBio	AC-60050
KAPA Hi-Fi hot start ready mix	Roche	KK2601
KAPA single indexed adapters Set B	Roche	KK8702
MyOne Streptavidin C1 Dynabeads	ThermoFisher Scientific	65001
oligo-dT DynaBeads	ThermoFisher Scientific	61002
R9.4.1 flow cell	Oxford Nanopore Technologies	FLO-MIN106
Protein A Dynabeads	Invitrogen	10001D
RNase A	Invitrogen	12091021
Proteinase K	Roche	3115879001
AMPure XP beads	Beckman Coulter	A63881
ULTRAhyb Ultrasensitive Hybridization Buffer	ThermoFisher Scientific	AM8669
Exonuclease III	New England Biolabs	M0206S
Mnase	Worthington	LS004797
Superscript III kit	ThermoFisher Scientific	18080044
Absolute Blue qPCR Mix	ThermoFisher Scientific	AB4162B
Critical commercial assays
Poly(A)Purist MAG kit	Ambion	AM1922
KAPA Hyper Prep Kit	Roche	KK8504
Direct RNA Sequencing Kit	Oxford Nanopore Technologies	SQK-RNA001
ThruPLEX DNA-seq Kit	Takara	R400427
NEXTflex™ Rapid Directional mRNA-Seq Kit	Bioo Scientific	NOVA-5138
Prime-It II Random Primer Labeling Kit	Agilent Technologies, Inc	300385
Deposited data
TL-seq, RNA-seq, Direct RNA Nanopore Sequencing, ChIP-seq, MNase-seq	This study	GEO: GSE140177
RNA-seq, Ribosome Profiling	Cheng et al. (2018)	GEO: GSE108778
Experimental models: organisms/strains
S. cerevisiae: UB3301: MATa /MATalpha UME6-3V5::His3MX/UME6-3V5::His3MX irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT	Brar-Ünal lab	N/A
S. cerevisiae: UB6183: MATa /MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::Δ9AUG-NDC80-3V5:LEU2/leu2::Δ9AUG-NDC80-3V5:LEU2 ndc80Δ(−1000 and ORF):KanMX4 /ndc80Δ(−1000 and ORF):KanMX4	Brar-Ünal lab	N/A
S. cerevisiae: UB6190: MATa /MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT ndc80Δ(−1000 and ORF):KanMX4 /ndc80Δ(−1000 and ORF):KanMX4 leu2::NDC80-3V5:LEU2/leu2::NDC80-3V5:LEU2	Brar-Ünal lab	N/A
S. cerevisiae: UB10579: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pUB88-Δ8AUG-uORF1-revert-5′UTR-NDC80-3V5:LEU2/leu2::pUB88-Δ8AUG-uORF1-revert-5′UTR-NDC80-3V5:LEU2 ndc80Δ(−1000 and ORF):KanMX4/ndc80Δ(−1000 and ORF):KanMX4	This study	N/A
S. cerevisiae: UB10581: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pUB88-Δ8AUG-uORF5-revert-5′UTR-NDC80-3V5:LEU2/leu2::pUB88-Δ8AUG-uORF5-revert-5′UTR-NDC80-3V5:LEU2 ndc80Δ(−1000 and ORF):KanMX4/ndc80Δ(−1000 and ORF):KanMX4	This study	N/A
S. cerevisiae: UB10583: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pUB88-Δ8AUG-uORF9-revert-5′UTR-NDC80-3V5:LEU2/leu2::pUB88-Δ8AUG-uORF9-revert-5′UTR-NDC80-3V5:LEU2 ndc80Δ(−1000 and ORF):KanMX4/ndc80Δ(−1000 and ORF):KanMX4	This study	N/A
S. cerevisiae: UB14584: MATa/MATalpha pCUP-IME1::NAT/pCUP-IME1::NAT pCUP-IME4::NAT/pCUP-IME4::NAT amn1(BY4741 allele)unmarked/amn1(BY4741 allele)unmarked	This study	N/A
S. cerevisiae: UB18175: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::SWI4-3V5-NDC80term::LEU2/leu2::SWI4-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18176: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pSWI4LUTI(−1200 to −934)Δ-SWI4-3V5-NDC80term::LEU2/leu2::pSWI4LUTI(−1200 to −934)Δ-SWI4-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18181: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pAPL4LUTIΔ(−415 to −800)-APL4-3V5-NDC80term::LEU2/leu2::pAPL4Δ(−415 to −800)-APL4-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18185: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::CDC60-3V5-NDC80term::LEU2/leu2::CDC60-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18186: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pCDC60LUTI(−1000 to −483)Δ-CDC60-3V5-NDC80term::LEU2/leu2::pCDC60LUTI(−1000 to −483)Δ-CDC60-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18188: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pHSP60LUTIΔ(−1000 to −501)-HSP60-3V5-NDC80term::LEU2/leu2::pHSP60Δ(−1000 to −501)-HSP60-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18190: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::pMSC6LUTI(−800 to −335)Δ-MSC6-3V5-NDC80term::LEU2/leu2::pMSC6LUTI(−800 to −335)Δ-MSC6-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18238: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::MSC6-3V5-NDC80term::LEU2/leu2::MSC6-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18336: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::HSP60-3V5-NDC80term::LEU2/leu2::HSP60-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18539: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::APL4-3V5-NDC80term::LEU2/leu2::APL4-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB18838: MATa trp1::pGPD1-LexA-ER-HA-B112::TRP1 his3::8xLexO-HSP60leader-ubiGFP::HIS3	This study	N/A
S. cerevisiae: UB19257: MATa/MATalpha trp1::pGPD1-LexA-ER-HA-B112::TRP1/trp1::pGPD1-LexA-ER-HA-B112::TRP1 irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT his3::8xLexO-HSP60leader-ubiGFP::HIS3/his3::8xLexO-HSP60leader-ubiGFP::HIS3	This study	N/A
S. cerevisiae: UB20485: MATa trp1::pGPD1-LexA-ER-HA-B112::TRP1 his3::8xLexO-hsf1-mut1-HSP60leader-ubiGFP::HIS3	This study	N/A
S. cerevisiae: UB20649: MATa/MATalpha irt1::pCUP1-3HA-IME1::KANMX/irt1::pCUP1-3HA-IME1::KANMX ime4::pCUP1-3HA-IME4::KANMX/ime4::pCUP1-3HA-IME4::KANMX Ume6-3v5::His3MX/Ume6-3v5::His3MX	This study	N/A
S. cerevisiae: UB22629: MATa/MATalpha irt1::pCUP1-3HA-IME1::KANMX/irt1::pCUP1-3HA-IME1::KANMX pCUP-IME4::NAT/pCUP-IME4::NAT ume6::UME6(T99N)-3V5::KanMX/ume6::UME6(T99N)-3V5::KanMX	This study	N/A
S. cerevisiae: UB26122: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::APL4uORFdel-3V5-NDC80term::LEU2/leu2::APL4uORFdel-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB26123: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::HSP60uORFdel-3V5-NDC80term::LEU2/leu2::HSP60uORFdel-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB26124: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::MSC6uORFdel-3V5-NDC80term::LEU2/leu2::MSC6uORFdel-3V5-NDC80term::LEU2	This study	N/A
S. cerevisiae: UB26705: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::HSP60-3V5-NDC80term::LEU2/ leu2::HSP60-3V5-NDC80term::LEU2 upf1::NAT/upf1::NAT	This study	N/A
S. cerevisiae: UB26707: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::APL4-3V5-NDC80term::LEU2/ leu2::APL4-3V5-NDC80term::LEU2 upf1::NAT/upf1::NAT	This study	N/A
S. cerevisiae: UB26708: MATa/MATalpha irt1:cup1::Hphmx/irt1:cup1::Hphmx ime4::cup1::NAT/ime4::cup1::NAT leu2::MSC6-3V5NDC80term::LEU2/ leu2::MSC6-3V5-NDC80term::LEU2 upf1::NAT/upf1::NAT	This study	N/A
Oligonucleotides
3V5 probe primers	See Table S7	N/A
ACT1 qPCR primers	See Table S7	N/A
PFY1 qPCR primers	See Table S7	N/A
HSP60/UBI qPCR primers	See Table S7	N/A
APL4 qPCR primers	See Table S7	N/A
HSP60 qPCR primers	See Table S7	N/A
MSC6 qPCR primers	See Table S7	N/A
Software and algorithms
cutadapt, v2.3	Martin, 2011	https://cutadapt.readthedocs.io/en/stable/
STAR, v2.5.3a	Dobin et al., 2013	https://github.com/alexdobin/STAR
BSgenome, v1.50.0	Pagè, 2018	https://bioconductor.org/packages/release/bioc/html/BSgenome.html
CAGEr, v1.24.0	Haberle et al., 2015	https://bioconductor.org/packages/release/bioc/html/CAGEr.html
DESeq2, v1.22.2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
MinKNOW, v1.10.23	Oxford Nanopore Technologies	https://nanoporetech.com/
Albacore, v2.1.10	Oxford Nanopore Technologies	https://nanoporetech.com/
minimap2, v2.9-r720	Li, 2018	https://github.com/lh3/minimap2
Meme	Bailey and Elkan, 1994	https://meme-suite.org/tools/meme
bowtie2, v2.3.4.3	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
macs2, v2.1.1.20160309	Zhang et al., 2008	https://github.com/macs3-project/MACS
bedGraphToBigWig, v4	Kent et al., 2010	https://bioconda.github.io/recipes/ucsc-bedgraphtobigwig/README.html
deeptools2, v3.0.1	Ramírez et al., 2016	https://deeptools.readthedocs.io/en/develop/
phastCons	Siepel et al., 2005	http://compgen.cshl.edu/phast/phastCons-HOWTO.html
salmon, v0.13.1	Patro et al., 2017	https://combine-lab.github.io/salmon/
matplotlib	Hunter, 2007	https://matplotlib.org/
Image Studio Lite	LI-COR	https://www.licor.com/bio/image-studio-lite/
Graphpad Prism	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
bedtools	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
GSEA, v4.1.0	Subramanian et al., 2005 and Mootha et al., 2003	https://www.gsea-msigdb.org/gsea/index.jsp
DANPOS2, v2.2.2	Chen et al., 2013	https://sites.google.com/site/danposdoc/
custom code	this study	https://github.com/atresen/LUTI_key_features
Other
minION	Oxford Nanopore Technologies	MIN-101B
Bioruptor Pico	Diagenode	B01060010