Cross-linked chromatin from wild-type, set1Δ, or set2Δ strains (indicated above each panel) was precipitated with anti-H3, anti-acetyl H4, or anti-acetyl H3 (indicated below panels). PCR analysis of the precipitated DNA was carried out on the YEF3 (A), PMA1 (B), and PYK1 and ADH1 (C) genes (numbered primer locations shown schematically at the top, PCR products below). TEL is from a non-transcribed region near the telomere of chromosome VI.
D. The signals for acetyl H4 or acetyl H3 were quantitated and normalized to the total H3 signal and the ratios were graphed (X axis shows primer number and Y axis shows ratio). Error bars show the standard deviation from at least three independent experiments.
E. Quantitation for the telomere primer pair was carried out as in D.

A. ChIP from wild-type, rad6Δ, or bre1Δ strains using anti-H3, anti-H3K4me3, anti-H3K4me2, or anti-H3K4me1 (left panels) and anti-H3, anti-acetyl H4, or anti-acetyl H3 (right panels) were carried out on YEF3. Primer locations are shown schematically at top. Similar results were seen at all other genes tested.
B. The results from part A for acetyl H4 and acetyl H3 were normalized to the total H3 signal and the ratios were graphed. Error bars show the standard deviation from multiple experiments.
C. Vector or plasmids expressing wild-type Set1 or a mutant Set1 lacking the RRM domain (ΔRRM) were transformed into a set1Δ strain and ChIP for histone modifications was carried out as in parts A and B.
D. Results from part C were quantitated and graphed as in part B.

A. ChIP from wild-type, set3Δ, rxt1Δ, or pho23Δ strains using anti-H3, anti-acetyl H4, or anti-acetyl H3 was performed on YEF3. The right panel shows quantification of the results from three repeats of the experiment. Error bars show the standard deviation from multiple experiments.
B. ChIP from wild-type, set3Δ, or hos2Δ strains using anti-H3, anti-acetyl H4, or anti-acetyl H3 was carried out on PMA1, PYK1, ADH1, or RPS13. Error bars show standard deviation.
C. ChIP from wild-type, set3Δ, hos2Δ, hst1Δ, cpr1Δ, or snt1Δ strains using anti-H3, anti-acetyl H4, or anti-acetyl H3 was carried out on YEF3. The right panel shows quantification of the results from multiple experiments for primer pair 2. Error bars show standard deviation. Quantitation of the full primer set appears in Fig S6.

A. Hos2-TAP or Set3-TAP was precipitated from SET1 or set1Δ cells (indicated in parentheses) using IgG sepharose. The precipitates (IP) were analyzed by immunoblot analysis for TAP tagged proteins (TAP) and associated histones (H3).
B. Chromatin fragments were immobilized on beads via TAP-tagged Hhf2 (histone H4) from either SET1 or set1Δ cells. Bead bound nucleosomes were incubated with whole cell extracts from wild-type Set3-HA or PHD finger mutant Set3-HA(W140A) strains. The precipitated proteins (IP) were analyzed by immunoblot analysis for TAP tagged histone H4 or epitope tagged Set3 (HA).
C. ChIP of Hos2-TAP was performed using chromatin from SET1 or set1Δ cells. The left panel shows PCR products and right panel shows quantitation of multiple repeats of the experiment. Signals for YEF3 regions were normalized to that of the telomeric probe (TEL) and input.
D. ChIP of Hos2-TAP was performed as in part C using chromatin from cells expressing wild type Set3 or mutant Set3(W140A).
E. Chromatin from SET3, set3Δ, or set3Δ cells with plasmid-borne SET3-HA or set3-HA(W140A) were precipitated with anti-H3, anti-acetyl H4, or anti-acetyl H3. PCR analysis of the precipitated DNA was carried out on the YEF3.

A. TAP-purified Set3 complex (40 μl) was visualized by silver staining.
B. Peptide binding assays were performed with 30μl purified Set3 complex and 1μg of the indicated histone peptides immobilized on beads. Precipitated protein was analyzed by immunoblot analysis with antibody recognizing the TAP tag.
C and D. Histone peptide binding assays were performed with whole cell extracts containing Hos2-TAP and either wild type Set3 or PHD finger mutant Set3(W140A). Precipitated Hos2 protein was analyzed by immunoblot analysis.
E. ChIP of Hos2-TAP was performed using chromatin from set1Δ cells containing empty vector, wild type SET1, or SET1 (ΔRRM). PCR analysis of the precipitated DNA was carried out on YEF3. Error bars show standard deviation.
F. Chromatin from an untagged strain, HOS2-TAP, or HOS2-TAP(rad6Δ) cells were precipitated with IgG sepharose. PCR analysis of the precipitated YEF3 DNA was performed and signals were normalized to a telomeric control region. Error bars show standard deviation.

A. The indicated deletion strains were spotted in 3-fold dilutions on Synthetic Complete media plates lacking uracil (SC-URA, 2 days growth shown) or SC-URA plates containing 6-AU or MPA (3 days).
B. A set3Δ strain was transformed with pRS415 (+Vector), pRS415-SET3-HA (+SET3), or pRS415-set3(W140A)-HA (+set3(W140A)) and spotted in 3-fold dilutions on SC plates (2 days) or SC plates containing MPA (3 days). For comparison, a SET3 strain (WT) containing pRS415 (+Vector) is shown as a control.
C. Chromatin from SET3 or set3Δ strains grown in galactose medium was precipitated with anti-H3, anti-acetyl H4, or anti-acetyl H3 and PCR carried out on GAL1. Error bars show standard deviation. PCR products are shown in Fig S7A.
D. ChIP from SET3 or set3Δ strains using anti-Rpb3 was carried out on GAL1. Cells were grown in galactose and then shifted to glucose for the indicated times. The number shown is the ratio between the specific GAL1 signal and the internal non-transcribed control. Error bars show standard deviation. PCR products appear in Fig S7B.
E. Cells with the indicated genotypes were grown in raffinose medium and then shifted to galactose medium for the indicated times. GAL1 mRNA levels were determined by RT-PCR and normalized to ACT1 mRNA. The left panel shows PCR products and right panel shows quantitation of multiple repeats of the experiment.

At 5′ ends of genes, RNApII recruits the Set1-COMPASS complex, which methylates histone H3K4. HATs such as SAGA, NuA3, and NuA4 direct histone acetylation to promoters by interacting with upstream regulatory factors and/or trimethylated H3K4. Just downstream, H3K4me2 serves as a binding site for the Set3 PHD finger. The resulting association of Set3C facilitates histone deacetylation by the Hos2 and Hst1 subunits. Further downstream, interaction of Set2 with Ser2-phosphorylated RNApII leads to methylation of H3K36. This mark recruits Rpd3C(S) via the Eaf3 chromodomain, leading to deacetylation of histones in 3′ regions of genes.