Table S2.

Oligonucleotides

Name	Sequence (5′-3′)	Use	Comment
5′-URA3 F	TAAGGAACGTGCTGCTACTC	ChIP-qPCR	Figs. 4 B and C and 5 B–E
5′-URA3 R	TTGGCGGATAATGCCTTTAGCG	ChIP-qPCR	Figs. 4 B and C and 5 B–E
5′-ScURA3 F	CATGTCGAAAGCTACATATAAGGAAC	ChIP-qPCR	Fig. 4D
5′-ScURA3 R	CTTAACTGTGCCCTCCATGGAA	ChIP-qPCR	Fig. 4D
3′-URA3 F	GCTCAAAGAGACATGGGTGaA (lowercase “a” mismatches in S288c)	ChIP-qPCR	Figs. 4 B and C and 5 B–D
3′-URA3 R	GCCGCATCTTCTCAAATATGC	ChIP-qPCR	Figs. 4 B and C and 5 B–D
549.7kb S	TGAAGATGACATTGCTCCTTT	ChIP-qPCR	All ChIP
549.7kb AS	TGGATAATGGATCTGAAACCG	ChIP-qPCR	All ChIP
534kb S	ACAAGCATCATTCATAGCCT	ChIP-qPCR	All ChIP
534kb AS	ATCGTGGCTAGGACATTTTG	ChIP-qPCR	All ChIP
SL-LEU-R31F	CCTGGAATGGAGACCGTTTTCT	ChIP-qPCR	Fig. 5E
SL-LEU-R31B	GGGTTGTGCTATTGTCTTTATGCC	ChIP-qPCR	Fig. 5E
atest	TAAAATCCTCGCACTATCGCTG	qPCR	Fig. S2
btest	CTATATGCAATAAAAAGGGTACAAGA	qPCR	Fig. S2
ctest	GAATACAAGGTTATCAGCCGTC	qPCR	Fig. S2
5′ ACT1 (F)	CGTTACCCAATTGAACACGGT	qPCR, RT-qPCR	Figs. S1 and S2
3′ ACT1 (R)	AAGGACAAAACGGCTTGGAT	qPCR, RT-qPCR	Figs. S1 and S2
URA3 RT-qPCR F	AGAATTGTCATGCAAGGGCTC	RT-qPCR	Fig. S1
URA3 RT-qPCR R	TCAAATATGCTTCCCAGCCT	RT-qPCR	Fig. S1
URA3f downstream F	CAAAGTTGTGCTTTGGAT	ChIP-qPCR	Fig. S5
URA3f downstream R	ACTTTCTAAGACGCTAGGA	ChIP-qPCR	Fig. S5
URA3p-LoxP-SpHis5MX-LoxP R	ATTTGTGAGTTTAGTATACATGCATTTACTTATAATACAGATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCT	Strain construction	Strains HJ4, HJ5, HJ6, HJ7, and HJ19
URA3p-LoxP-SpHis5MX-LoxP F	ACTGCACAGAACAAAAACCTGCAGGAAACGAAGATAAATCATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain HJ5
URA3pΔTATA1-LoxP-SpHis5MX-LoxP F	CAGAAGGAAGAACGAAGGAAGGAGCACAGACTTAGATTGGATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain HJ6
URA3pΔUAS-LoxP-SpHis5MX-LoxP F	GTTCTTTTTTTTGATTCCGGTTTCTTTGAAATTTTTTTGA ATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain HJ7
URA3pΔdA-dT1-LoxP-SpHis5MX-LoxP F	TTCAGGGTCCATAAAGCTTTTCAATTCATCTTTTTTTTTTTTGTTCTTTTATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain HJ19
ΔURA3p::LoxP-SpHis5MX-LoxP F	GCATTTCTTTGTGGCTGTGGTTTCAGGGTCCATAAAGCTTATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain HJ4
dAdT-LoxP-HIS5-LoxP in LYS2 F	CAAGATTTCAAATTAGACGAGTTCAAGCATCATTTAGTGGACTTTGCTTTCAATTCATCTTTTTTTTTTTTGTTCTTTTTTTTGATTCCG	Strain construction	Strain MSB155
pURA3-LoxP-HIS5-LoxP in LYS2 F	CAAGATTTCAAATTAGACGAGTTCAAGCATCATTTAGTGGACTTTGCTTTTGTGGCTGTGGTTTCAGGGTC	Strain construction	Strains HJ22 and HJ23
Lys2-dAdT-LoxP R	GGTGATCAGAGAGATTTTAGTTATGCAATTGGATGGATATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCTA	Strain construction	Strains HJ22, HJ23, and MSB155
git1-trp1Δ::LoxP-SpHIS5MXf-LoxP F	AGTGCACAAACAATACTTAAATAAATACTACTCAGTAATAACATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain MSB30
git1-trp1Δ::LoxP-SpHIS5MXf-LoxP R	AAAAGAAATTTTGAGGTTAAAGGATGGAGGAAGAAATCGATACCAATTATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCT	Strain construction	Strain MSB30
git1-trp1Δ::LoxP-SpHIS5MXr-LoxP F	AATTTTGAGGTTAAAGGATGGAGGAAGAAATCGATACCAATTATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain MSB31
git1-trp1Δ::LoxP-SpHIS5MXr-LoxP R	CAGGCAAGTGCACAAACAATACTTAAATAAATACTACTCAGTAATAACATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCT	Strain construction	Strain MSB31
LoxP-MX-LoxP URA3 R	AGTCTGTGCTCCTTCCTTCGTTCTTCCTTCTGCTCGGAGATTACCGAAATAACTTCGTATAATGTATGCTATACGAAGTTATTAGGTCT	Strain construction	Strains MSB153 and MSB156
LoxP-amdMX-LoxP URA3fΔrdAdT F	TAATCCTTCACATCATGAAATATAAGCTAAATCGCATTTCTTATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain MSB156
LoxP-HIS3MX-LoxP URA3ΔrdAdT F	ATTTATGGTGAAGGATAAGTTTTGACCATCAAAGAAGGTTAAATAACTTCGTATAGCATACATTATACGAAGTTATATTAAGGGTTCTC	Strain construction	Strain MSB153
URA3pDupstreamdAdT F	GGTCAAATAATCCTTCACATCATGAAATATAAGCTAAATCGCATTTCTTTCCATAAAGCTTTTCAATTCATC	Strain construction	Strain HJ24
upstream URA3 NRG1 to AAA	ACATCATGAAATATAAGCTAAATCGCATTTCTTTGTGGCTGTGGTTTCAAAATCCATAAAGCTTTTCAATTCATC	Strain construction	Strain HJ25
frURA3t R	GACTTATGGAACATGGAACC	Strain construction	Strains HJ24 and HJ25