Figure 3.

Deletion of RPD3 differentially affects conformation of AT- and GC-rich isochore domains. (a) Interaction frequencies (the average of three measurements) between loci located within the AT-rich isochore of chromosome III (filled circles) or within the GC-rich isochore domains on the right arm of chromosome III (open circles) were determined in G1-arrested rpd3Δ cells. Error bars are standard error of the mean. Dotted and solid lines indicate fits to equation 1 (Table 1). (b) Interaction frequencies between loci located in the AT-rich isochore of chromosome III obtained in rpd3Δ cells (open squares) and wild type cells (filled squares). Data were normalized such that the average Log of the fold difference between wild-type (WT) cells and rpd3Δ cells was zero. Solid and dotted lines indicate fits of the data to equation 1. (c) Interaction frequencies between loci located in the GC-rich isochore of the right arm of chromosome III obtained in rpd3Δ cells (open squares) and WT cells (filled squares) after normalization. Solid and dotted lines indicate fits of the data to equation 1. (d) Interaction frequencies in the GC-rich isochore on the right arm of chromosomes III and VI (GC (III) and GC (VI)) are significantly reduced compared to interaction frequencies in the AT-rich isochore on chromosome III (AT (III)). Data from two biological repeats are shown.