A set of five highly specific antibodies for H3K9Ac, H3K14Ac, H4K5Ac, H4K12Ac and H4K16Ac developed and titrated for ChIP (Suka et al., 2001) were used for ChIP of chromatin extracts from wt, hos2?, clr6-1, clr3? and sir2? cells. The mutant alleles were first backcrossed with the standard laboratory strain (972 h-) to ensure isogenic strain backgrounds . Cell cultures were then grown to mid logarithmic growth phase (5 x106 cells/ml) in rich medium before fixation and ChIP. The resulting ChIP DNA was labeled with Cy5. The wt control ChIP DNA was labeled with Cy3 and simultaneously hybridized with the Cy5 labeled DNA to the IGR+ORF microarrays to produce genome wide mutant versus wt histone acetylation maps.
