1. A Transient Histone Hyperacetylation Signal Marks Nucleosomes for Remodeling at the PHO8 Promoter In Vivo 
Hans Reinke, Philip D. Gregory, Wolfram Hörz 
Molecular Cell 
Volume 7, Issue 3, Pages (March 2001)
DOI: /S (01)

2. Figure 1
Histone Acetylation Levels at the PHO8 Promoter upon Chromatin Remodeling and Transcriptional Activation
(A) Positions of the PCR fragments used for ChIP analysis of the PHO8 promoter are shown with respect to the nucleosomal organization of the repressed and activated promoter. Stable nucleosomes (filled circles), partially stable (shaded circles), and unstable nucleosomes (open circles) are indicated (Barbaric et al., 1992).
(B) Strains CY338 (Δpho4) and CY337 (wt) were phosphate starved for 16 hr and the chromatin fixed by formaldehyde treatment. Chromatin fragments were precipitated with an antibody specific for diacetylated histone H3. The amounts of coimmunoprecipitated DNA determined by quantitative PCR were normalized to the respective Input DNA and are shown in arbitrary units.
(C) H4 acetylation in strains CY338 and CY337 was determined by ChIP analysis employing an antibody against tetraacetylated histone H4
Molecular Cell 2001 7, DOI: ( /S (01) )

3. Figure 2
The PHO8 Promoter Is Highly Acetylated in a Δsnf2 Strain upon Phosphate Starvation
(A) Strains CY338 (Δpho4), CY407 (Δsnf2), and CY337 (wt) were subjected to ChIP analysis after phosphate starvation. Acetylation levels of histone H3 (A) and H4 (B) were determined at PHO8 and the PGK1 promoter.
(C and D) DNA quantification by ethidium bromide gel electrophoresis following PCR. DNA from the Δsnf2 strain was purified from the whole-cell extract before immunoprecipitation and subjected to quantitative PCR (Input). Antibodies against diacetylated H3 (C) and tetraacetylated H4 (D) were used for ChIP analyses of the Δsnf2 (IP Δsnf2) and wild-type (IP wt) strain. Each combination of IP DNA and Input DNA with each specific primer pair was analyzed using two different concentrations of the respective template DNA (2.5-fold dilution of template DNA in each even numbered lane) to confirm that the PCR reaction was in the linear range
Molecular Cell 2001 7, DOI: ( /S (01) )

4. Figure 3
Requirements for Histone H3 Hyperacetylation at the PHO8 Promoter
(A) Strain CY397 (snf2K798A) carries a point mutation in Snf2, which abolishes the ATPase activity of SWI/SNF. Cells were induced by phosphate starvation, and acetylation of histone H3 was determined by ChIP. Acetylation levels at the PHO8 promoter and the PGK1 control promoter were compared to those of strains CY407 (Δsnf2) and CY337 (wt).
(B) Quantification of IP DNA from strains CY397 and CY407 and Input DNA from strain CY397 on ethidium bromide gels following the quantitative PCR.
(C) Histone acetylation in strains CY338 (Δpho4) and CY408 (Δpho4,Δsnf2) was determined by ChIP analysis following phosphate starvation.
(D) Quantification of IP DNA by ethidium bromide gel electrophoresis following PCR. Antibodies against diacetylated H3 were used for ChIP analyses of the Δpho4 (IP Δpho4) and Δpho4,Δsnf2 (IP Δpho4,Δsnf2) strain; only Input DNA from strain CY 338 is shown. To confirm that the PCR reaction was in the linear range, we used the protocol described in the legend to Figure 2
Molecular Cell 2001 7, DOI: ( /S (01) )

5. Figure 4
Effect of Gcn5 and Rpd3 upon the Acetylation of the PHO8 Promoter
(A) H3 acetylation and (B) H4 acetylation of the PHO8 promoter were determined in the Gcn5 HAT domain mutant PKM (Gregory et al., 1998; Wang et al., 1998) and compared to the Δsnf2 (CY407) and wild-type (CY337) strains. Histone acetylation of the PHO8 promoter in strain CY637 (Δrpd3) is shown for histone H3 in (C) and for histone H4 in (D)
Molecular Cell 2001 7, DOI: ( /S (01) )

6. Figure 5 Histone H4 Acetylation across the PHO8 Promoter
The nucleosomal composition of the repressed PHO8 promoter is shown schematically (compare to Figure 1A); the area of chromatin destined for remodeling is indicated below. The black horizontal bars above show the positions of the PHO8 promoter regions analyzed and the relative degree of histone H4 acetylation levels in the strains indicated
Molecular Cell 2001 7, DOI: ( /S (01) )