Genome-wide Identification of Dal80-bound Promoters
Explore the correlation between Dal80 binding and gene regulation through ChIP-Seq signal analysis, highlighting the impact on Dal80-sensitive, high-expression genes. Control experiments demonstrate Dal80 binding across gene bodies independently of intragenic GATA sites. Discover the necessity of transcription elongation for Dal80 binding across the MEP2 locus.
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A B TSS-ATG distance 250 No tag Dal80-Myc13 300 200 Density (tag/nt) 200 Distance (bp) 150 100 100 0 chr.16 431400 432000 432600 433200 433800 434400 435000 50 ALD6 0 peak_1747 Supplemental Figure 1 Related to Figure 1. Genome-wide identification of Dal80-bound promoters.
A Correlation between Dal80 binding and regulation Regulated Unaffected Total Bound 216 (124) 1098 (1190) 1314 Unbound 330 (422) 4154 (4062) 4484 Total 546 5252 5798 P<0.00001 (Chi-square test of independence) ChIP-Seq signal, Dal80-regulated genes B 300 Dal80- Myc13 No tag Dal80-bound Unbound 250 200 MetaSignal 150 100 50 -600 ATG 600 Supplemental Figure 2 Related to Figure 3. Dal80 binding across gene bodies correlates with Dal80-sensitive, high expression levels.
A Dal80-Myc13 ChIP 70 IP/IN Promoter 60 ORF 50 40 30 20 10 0 Gln Pro Gln Pro Gln Pro Gln Pro Gln Pro Gln Pro Gln Pro Gln Pro No tag Dal80-Myc No tag Dal80-Myc No tag Dal80-Myc No tag Dal80-Myc DAL5 GAP1 GDH2 MEP2 B O3O4 O1O2 O5O6 O1O2 O3O4 O5O6 GAL10 GAL1 P3P4 P1P2 180 Gal4 ChIP at the GAL1-10 locus GAL10 O3O4 GAL10 O1O2 GAL10 O5O6 GAL1-10 P3P4 GAL1-10 P1P2 GAL1 O1O2 GAL1 O3O4 GAL1 O5O6 DAL5 U1U2 IP/IN 160 140 120 100 80 60 40 20 0 Glucose Galactose C P5P6 P13P14 P9P10 O1O2 O11O12 O9O10 MEP2 120 Dal80-Myc13 ChIP at the MEP2 locus IP/IN MEP2 P5P6 MEP2 P13P14 100 MEP2 P9P10 MEP2 O1O2 80 MEP2 O11O12 60 MEP2 O9O10 40 20 0 No tag Dal80-Myc Dal80-Myc No treatment RNase treatment before IP Supplemental Figure 3 Related to Figure 4. Dal80 binding across the ORF of well-characterized NCR-sensitive genes Control experiments.
A B URA3 mRNA levels polII ChIP at URA3 40 800 TBP1-normalized expression levels IP/IN 35 700 30 600 25 500 20 400 15 300 10 200 5 100 0 0 wt wt PMEP2-URA3 PMEP2-URA3 C D UGA4 mRNA levels polII ChIP at UGA4 18 900 TBP1-normalized expression levels 16 IP/IN 800 700 14 12 600 10 500 8 400 6 300 4 200 2 100 0 0 LZ LZ wt wt Supplemental Figure 4 Related to Figure 5. Dal80 binding within gene bodies occurs independently of intragenic GATA sites Control experiments.
A TBP1-normalized expression levels MEP2 mRNA levels 140 120 100 80 60 40 20 0 Gln Pro Gln Pro wt rpb1-1 B 2500 IP/IN polII ChIP at the MEP2 locus 2000 1500 1000 500 0 Gln Pro Gln Pro wt rpb1-1 Supplemental Figure 5 Related to Figure 6. Transcription elongation is necessary for Dal80 binding across MEP2 Control experiments.
