Table 1.

Strains and conditions

Strain	Genotype
BY4741	MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
BY4741 bar1∆	BY4741 bar1::KanMX
DCY69	BY4741 HIS3:GAL1pr:FKH1 fkh2Δ:KanMX
DCY80	BY4741 HIS3:GAL1pr:FKH1-Flag:LEU2 fkh2Δ:KanMX
W303a	MATa leu2-3,112 trp1-1 can1-100 ura3-1 ADE2 his3-11,15
DCY85	W303a pRS316:CLN1pr:yeGFP-PEST
DCY86	W303a pRS316:HTA1pr:yeGFP-PEST
DCY61	W303a CLN1:CLN1pr:yeGFP-PEST
DCY38	W303a CLN2:CLN1pr:yeGFP-PEST
DCY40	W303a NRM1:CLN1pr:yeGFP-PEST
DCY39	W303a PHO8:CLN1pr:yeGFP-PEST

For Hi-C of pheromone-arrested cells, we used the strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 bar1::KanMX). Strains used for single-cell transcription analysis were congenic to W303. CLN1 promoter reporter strains were generated from laboratory stocks by standard methods. Reporters were integrated in the 5′ end of G1/S gene promoters without disrupting nearby ORFs. For all activation timing experiments, cells were grown in synthetic complete media with 2% (wt/vol) glucose (SCD) to logarithmic growth phase, sonicated, and plated on 1.5% (wt/vol) agarose SCD pads for imaging. Conditions for the Fkh1/2-depleted Hi-C experiment are described below.