Microarray deacetylation maps determine genome-wide
functions for yeast histone deacetylases
Daniel Robyr, Yuko Suka, Ioannis Xenarios, Siavash K. Kurdistani,
Amy Wang, Noriyuki Suka and Michael Grunstein
Cell 109, 437-446 (2002)
Supplemental data ( 1,
2,
3,
4,
5,
6)
Download acetylation data (Download
data )
Supplemental data
Supplemental_data_1
Generating acetylation microarrays. Chromatin fragments from
formaldehyde-treated histone deacetylase mutant cells (in that case rpd3D)
and their wild type (WT) isogenic counterparts were immunoprecipitated
(Chromatin IP) using highly specific antibodies raised against acetylated
histone sites (Suka et al., 2001). DNA from enriched chromatin fragments
was purified, amplified by PCR (DNA amplification) and labeled (Klenow)
with a fluorophore (Cy3 or Cy5). Wild type (WT) and mutant sets of
labeled DNA were then combined and hybridized to a DNA microarray containing
~6700 intergenic regions ( Intergenic_fragments_coordinates
) (IGRs) (Iyer et al., 2001; Ren et al., 2001). For a given IGR the ratio
of the normalized fluorescent intensities between the two probes indicates
whether the analyzed lysine residue is hypo- or hyper- acetylated upon
deletion of a deacetylase gene (as compared to the WT strain).
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Iyer, V. R., Horak, C. E., Scafe, C. S., Botstein, D., Snyder, M., and
Brown, P. O. (2001). Genomic binding sites of the yeast cell-cycle transcription
factors SBF and MBF. Nature 409, 533-538.
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Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon,
I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T.L.,
Wilson, C.J., Bell, S.P., and Young, R.A. (2001). Genome-wide location
and function of DNA binding proteins. Science 290:2306-2309.
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Suka, N., Suka, Y., Carmen, A. A., Wu, J., and Grunstein, M. (2001). New
antibodies for sites of acetylation determine novel histone site usage
in heterochromatin and euchromatin. Mol. Cell 8, 473-479.
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Supplemental_data_2
(pdf file)
Chromosomal display of sites affected by RPD3 at histone H4 K12.
Left (L) and right (R) chromosome arms are represented from their telomere
end to their centromere (black circle). Each intergenic region is illustrated
by a rectangle. Regions whose enrichment is increased (> 1.95 fold) relative
to the control are shaded in red. Note that chromosomes are not to scale
since ORFs were left out and intergenic regions were arbitrarily given
the same width for clarity.
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Supplemental_data_3
(pdf file)
Functional categories found among the Rpd3 and Hda1 target genes
based on the MIPS classification. The number of genes assigned
to a given category is listed in the left column. The number of genes whose
promoter is deacetylated by Rpd3 (at H4-K12) or Hda1 (at H3-K18) are shown
in the "Found" column (within the brackets are indicated the number of
genes for which we have data available for a particular category). The
probability (P-value) to observe more than k overlapping regions
between two data sets was calculated as follow:
where k is the observed overlap ("Found"), n is the number of genes
within a category and m is the number of IGRs hyperacetylated by
a factor of 1.95 or more (531 and 467 regions for Rpd3 and Hda1 respectively).
N is the total number of regions for which we have data available.
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Supplemental_data_4
(pdf file)
Intergenic and ORF regions identified in HAST domains. Intergenic
and ORF fragments are shown along with their genomic coordinates (bp) and
the acetylation increase at histone H3-K18 upon HDA1 disruption. The ORF
names and descriptions are also indicated. Acetylation fold increases
>1.95 fold are highlighted in orange and ORFs are written in blue in order
to distinguish them from intergenic regions. For simplicity, we have chosen
to define the domains from the edgemost sequences affected >1.95 fold by
hda1D.
The size and coordinates of these domains are shown in red.
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Supplemental_data_5
(pdf file)
Hierarchical cluster analysis comparing expression data from 300
mutants or conditions (Hughes et al., 2000) with 149 ORFs located in
the HAST domains. Changes of gene expression in high glucose (19 g/L) and
low glucose (~0 g/L) are also introduced in the clustering analysis (DeRisi
et al., 1997). The scale of gene activity is represented from green (repressed)
to red (derepressed). The cluster analysis was performed with Gene Cluster
(2.11) and visualized using TreeView (1.50) (Eisen et al., 1998).
-
DeRisi, J. L., Iyer, V. R., and Brown, P. O. (1997). Exploring the metabolic
and genetic control of gene expression of a genomic scale. Science 278,
680-686
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Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster
analysis and display of genome-wide expression patterns. Proc. Natl. Acad.
Sci. USA 95, 14863-14868.
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Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton,
R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., et al.
(2000). Functional discovery via a compendium of expression profiles. Cell
102,
109-126.
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Supplemental_data_6
(pdf file)
IGRs (and some ORFs) at which histone H4 K12 acetylation is most
affected by hos2D. Ribosomal protein
genes are highlighted in orange. Fold increases in H4 K12 hyperacetylation
in a hos2D mutant are shown.
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Download
Data (Data files are text tab delimited)
Intergenic_fragments_coordinates
File containing the coordinates of all intergenic regions used in this
study
Intergenic_Acetylation_Arrays
Normalized average acetylation fold changes in the specified mutant
strain versus the isogenic wild type strain (i.e. HDA1-H3K18: acetylation
changes at Lysine 18 of histone H3 in hda1D).
Please, refer to (Intergenic_fragments_coordinates)
for informations regarding the chromsomal location of the intergenic regions
(IGRs).
ORF_Acetylation_Arrays
Normalized average acetylation fold changes in the specified mutant
strain versus the isogenic wild type strain (i.e. HDA1-H3K18: acetylation
changes at Lysine 18 of histone H3 in hda1D).
INPUT_Control_Intergenic
Relative amount of INPUT DNA (no immunoprecipitation) from the mutant
and WT strains are tested as a control for aneuploidy. (Data for rpd3D
and hda1D; note that this control experiment
was performed once).
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