A) Left: A table showing data from the Ch16 mini-chromosome loss colony color-sectoring assay. Wild type (Hu199) and fft3Δ (Hu1666) colonies containing a mini-chromosome were picked from plates selecting for the mini-chromosome (Ade-), and plated onto YE+ low adenine plates. The colonies retaining the mini-chromosome are white, and loss events result in red sectors. The mini-chromosome loss frequency was quantified by determining the amount of half-sectored colonies. Right: A photograph showing the red-sectoring phenotype of fft3Δ cells. B) Top: Microscope images showing fft3Δ (Hu1867) cells stained with DAPI. Bottom: A table showing the frequencies of aberrant mitosis in wt (Hu29) and fft3Δ (Hu1867) cells.

A) A schematic presentation of centromere 3. tRNA genes are marked in red and the IRC elements in yellow. B) A genome browser view of cen3 showing the ChIP-chip occupancy profile for Fft3-myc (green), H3K9me2 (black) and Cnp1 (purple). Data on the Y-axis are presented in log2 scale and the X-axis shows genome positions in base pairs. H3K9me2 data are from .

A) The ChIP-chip distributions of histone H3 (blue) and H3K9me2 (green) at centromere 3 in wt and fft3Δ cells are shown in Genome Browser images. Y-axis: Linear scale. Mutant/wt ratios are indicated in black in log2 scale. B) A schematic diagram of centromere 3. tRNA genes are marked in red and the IRC elements in yellow. C) Genome browser images showing ChIP-chip data for Cnp1 (red) and H2A.Z^Pht1 (purple). Y-axis: Linear scale. Mutant/wt ratios are shown in black in log2 scale. D) Bar diagrams showing the results from real-time quantitative PCR analysis of ChIP signals. The enrichments at imr3 are relative to the act1+ euchromatic control locus except for the Cnp1 enrichment which is relative to cen1. The ChIP signals were normalized to input samples from the same chromatin extract. The error bars represent S.D. values from triplicate samples. *indicates a significant difference between wt and mutant (P<0.01; T-test, two-tailed, unpaired).

A genome browser view showing MNase cleavage maps (blue) from wt and fft3Δ cells. Y-axis: Log2 scale. Data are from . The mutant/wt ratio is shown in black in linear scale. tRNA genes are shown in red and IRC elements in yellow.

A) Chromosomal view of gene expression changes in fft3Δ versus wt. The position of upregulated genes (2-fold cutoff) is indicated in red. The subtelomeric regions of chromosome 2 are shown in more detail. B) Venn diagram showing the overlap between genes upregulated on chromosome 2 in fft3Δ cells and all subtelomeric genes 100 kb from tel2. The P value represents the hypergeometric probability.

A) Genome browser images showing the chromosome 2 occupancy of Fft3-myc (green, Y-axis: Log2 scale), H2A.Z in wt (purple, Y-axis: linear scale), H4K12ac in wt corrected for H4 occupancy (dark red, Y-axis: linear scale), and Micrococcal Nuclease (MNase) digested chromatin in wt (blue, Y-axis: linear scale). The MNase data are from . B) Genome browser views showing mutant/wt ratios for H2A.Z and H4K12ac ChIP-chip, and for MNase digested chromatin. Centromeric and subtelomeric regions are highlighted with light-pink rectangles.

A) Left panel: A genome browser view of subtelomere 2L. ChIP-chip data for Fft3-myc (green) and H3 (blue) are shown. A subtelomeric transition zone consisting of four copies of a membrane transporter gene and four LTR elements (red) is highlighted in blue. Right panel (top): Bar diagrams showing quantification of Fft3-myc ChIP signals by real time PCR. Enrichment at LTR elements, membrane transporter genes (using primers for SPBPB10D8.05c), and cnt1 was measured relative to centromeric dg repeats. Background normalization was performed using -antibody samples. The grey bars represent signals from the non-tagged control strain (Hu29). The error bars represent S.D. values from triplicate samples. *indicates a significant difference between Fft3-myc and the non-tagged control strain (P<0.01; T-test, two-tailed, unpaired). Right panel (bottom): Bar diagrams showing quantification of H3 ChIP in wt (blue) and fft3Δ (black) on LTR elements and membrane transporter genes relative to an euchromatin control gene (SPAC32A11.03c). The ChIP signals were normalized to input samples from the same chromatin extract. The error bars represent S.D. from triplicate samples. *indicates a significant difference between wt and fft3Δ cells (P<0.01; T-test, two-tailed, unpaired). B) A genome browser view of mononucleosomal signals in wt after MNase digestion. Data are from .