1. Barrier Function at HMR
Masaya Oki, Rohinton T. Kamakaka 
Molecular Cell 
Volume 19, Issue 5, Pages (September 2005)
DOI: /j.molcel
Copyright © 2005 Elsevier Inc. Terms and Conditions

2. Figure 1 Mapping Histone Modifications at HMR
The distribution of modified histones and Sir3p was mapped by using ChIP in wild-type (wt) W-303 strains. The location of the PCR probes used is depicted alphabetically in the schematic figure.
Molecular Cell  , DOI: ( /j.molcel )
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3. Figure 2 Mapping Histone Modifications
Quantitative ChIP was performed as previously described (Litt et al., 2001). The bar graphs show the fold enrichment of sequences after ChIP with antibodies against Sir3p, H3 Ac-K9, H3 Ac-K14, H4 Ac-K8, and H4 Ac-K16. The y axis shows the fold enrichment between the same amount of the input fraction and the immunoprecipitated sample, whereas the x axis indicates the probe. SD values were ascertained from at least three independent ChIP experiments. The location of the probes is shown in the schematic figure.
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2005 Elsevier Inc. Terms and Conditions

4. Figure 3 Mapping the Distribution of Histones and Enzymes
(A) Mapping the distribution of SAGA. Wt strains containing Myc-tagged Ada2p (ROY3478) and Spt7p (ROY3017) were chromatin immunoprecipitated with anti-Myc monoclonal antibodies. The enrichment of these proteins was calculated as described for Figure 2 except that the enrichment was normalized to the TEL6R 0.5 kb probe.
(B) Mapping Ada2p in a t-RNA barrier mutant. A t-RNA mutant strain containing Myc-tagged Ada2p (ROY3583) was used for the quantitative ChIP analysis to map the distribution of this protein as described in (A). The hatched bars represent the distribution of Ada2p in the mutant. The data for Ada2p distribution in a wt strain (solid bars) are the same as in (A) and are included for ease of comparison.
(C) Mapping histone distribution at the HMR barrier. Distributions of histone H3 (ROY1685) or HA-tagged H2B (ROY3730) were mapped by quantitative ChIP as described in (A) by using antibodies that recognized unmodified histone H3 (solid bars) or the HA epitope (hatched bars).
(D) Mapping H3 in a t-RNA barrier mutant. A t-RNA mutant strain (ROY1681) was used for the ChIP analysis to map the distribution of H3 (hatched bars). The data for H3 distribution in a wt strain (solid bars) are the same as in (C).
(E) Mapping Sir3p in a t-RNA barrier mutant. A t-RNA mutant strain (ROY1681) was used for the ChIP analysis to map the distribution of Sir3p (hatched bars). The data for Sir3p distribution in a wt strain (solid bars) are the same as in Figure 2.
The SD values were ascertained from at least two independent crosslinked samples and three independent immunoprecipitation experiments.
Molecular Cell  , DOI: ( /j.molcel )
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5. Figure 4 Mapping the Distribution of Sir3p in Mutants
The distribution of Sir3p was determined in a wt strain and in ada2Δ (ROY3804), sas2Δ (ROY3658), eaf3Δ (ROY3847) (A), or isw2Δ (ROY3878) (B). The data for Sir3p distribution in a wt strain (solid bars) are the same as in Figure 2. The SD values were ascertained from at least two independent crosslinked samples and three independent immunoprecipitation experiments.
Molecular Cell  , DOI: ( /j.molcel )
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6. Figure 5 Mapping the Distribution of Sir3p
(A) Mapping the distribution of Sir3p in an ada2Δ t-RNA (ROY3810), sas2Δ t-RNA (ROY3663), and eaf3Δ t-RNA double mutants (ROY3849).
(B) Mapping of Sir3p distribution in an isw2Δ t-RNA double mutant (ROY3881). The data for Sir3p distribution in a wt strain (solid bars) are the same as in Figure 2 and are shown for ease of comparison. The SD values were ascertained from at least two independent crosslinked samples and three independent immunoprecipitation experiments.
(C) GIT1 expression analysis. Isogenic wt (ROY1685), t-RNA delete (ROY1681), ada2Δ (ROY3804), and t-RNA ada2Δ double (ROY3810) strains were grown in YPD, and total RNA was prepared for expression analysis. The GIT1 expression was normalized to ACT1. The primers used are as described (Tackett et al., 2005).
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2005 Elsevier Inc. Terms and Conditions