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. 2007;8(6):R116.
doi: 10.1186/gb-2007-8-6-r116.

GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p

Job Dekker  1
Affiliations

GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p

Job Dekker. Genome Biol. 2007.

Abstract

Background: Base-composition varies throughout the genome and is related to organization of chromosomes in distinct domains (isochores). Isochore domains differ in gene expression levels, replication timing, levels of meiotic recombination and chromatin structure. The molecular basis for these differences is poorly understood.

Results: We have compared GC- and AT-rich isochores of yeast with respect to chromatin conformation, histone modification status and transcription. Using 3C analysis we show that, along chromosome III, GC-rich isochores have a chromatin structure that is characterized by lower chromatin interaction frequencies compared to AT-rich isochores, which may point to a more extended chromatin conformation. In addition, we find that throughout the genome, GC-rich and AT-rich genes display distinct levels of histone modifications. Interestingly, elimination of the histone deacetylase Rpd3p differentially affects conformation of GC- and AT-rich domains. Further, deletion of RPD3 activates expression of GC-rich genes more strongly than AT-rich genes. Analyses of effects of the histone deacetylase inhibitor trichostatin A, global patterns of Rpd3p binding and effects of deletion of RPD3 on histone H4 acetylation confirmed that conformation and activity of GC-rich chromatin are more sensitive to Rpd3p-mediated deacetylation than AT-rich chromatin.

Conclusion: We find that GC-rich and AT-rich chromatin domains display distinct chromatin conformations and are marked by distinct patterns of histone modifications. We identified the histone deacetylase Rpd3p as an attenuator of these base composition-dependent differences in chromatin status. We propose that GC-rich chromatin domains tend to occur in a more active conformation and that Rpd3p activity represses this propensity throughout the genome.

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Figures

Figure 1
Figure 1
Isochore domains along chromosome III differ in conformation and activity. (a) Interaction frequencies (the average of three measurements) between loci located within the AT-rich isochore (positions 100-190 kb) of chromosome III (filled circles) or within the GC-rich isochore domain on the right arm of chromosome III (positions 190-280 kb; open circles) were determined in G1-arrested wild-type cells and plotted against genomic distance that separates each pair of loci. Error bars are standard error of the mean (SEM). Dotted and solid lines indicate fits of the data to equation 1 (Table 1). (b) Yeast genes were grouped in six groups dependent on the average base composition of the 4 kb region centered on the start site of the gene is (see Materials and methods). For each group the average steady state transcript level in wild-type cells was determined using data obtained by Bernstein et al. [30]. The genome-wide average transcript level was set at zero. The difference between the most GC-rich group and the most AT-rich group is statistically significant (P < 0.001). Error bars indicate SEM.
Figure 2
Figure 2
GC-rich and AT-rich genes differ in levels of acetylation of specific histone tail residues in wild-type cells. Genes were grouped in six groups dependent on the average base composition of the 4 kb region centered on the start site of the gene. For each group average levels of acetylation of different histone tail residues were determined using a dataset obtained by Kurdistani and co-workers [36]. (a-d) GC-rich genes display higher levels of H4K8, H4K12, H3K9 and H3K18 acetylation compared to AT-rich genes. (e) Comparison of the average levels of 11 histone modifications for GC-rich genes (GC > 40.4%) and AT-rich genes (GC < 36.6%). H3 and H4 acetylation is higher for GC-rich genes, whereas H2A and H2B acetylation is not different for the two types of isochore domains.
Figure 3
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.
Figure 4
Figure 4
Rpd3p displays base composition-dependent activity. (a) Patterns of base composition (line) and gene activation (gray area) in rpd3Δ cells along chromosome III as determined by sliding window analysis using a window size of 30 kb and the transcription start sites as midpoints (step size 1 open reading frame). The genome-wide dataset describing the effect of deletion of RPD3 was produced by Fazzio et al. [37]. (b) Genes were grouped in six groups dependent on the average base composition of the 4 kb region centered on the start site of the gene. For each group the average Log of the fold change in transcription in an rpd3Δ mutant compared to wild type was calculated. More GC-rich genes are more activated than more AT-rich genes (P < 10-13 for the difference between the most GC-rich genes and the most AT-rich genes). (c) The moving average (window size 200, step size 1 open reading frame) of the Log of the fold change in transcript level in rpd3Δ is plotted against transcript level in wild type. (d) A similar analysis as in (c) is performed with genes that are in the most GC-rich group and in the most AT-rich group (window size of 100 genes). GC-rich genes are more up-regulated in rpd3Δ cells.
Figure 5
Figure 5
Deletion of UME6 does not differentially affect GC- and AT-rich genes. Average change in gene expression levels in ume6Δ cells compared to wild type for each of the six groups of genes with increasing GC content. Expression data are from Fazzio et al. [37].
Figure 6
Figure 6
Rpd3p binding in wild-type and histone acetylation in rpd3Δ cells in AT-rich and GC-rich isochors. (a) Average levels of Rpd3p binding to each of the six groups of genes with increasing GC content. Rpd3p binding data are from Humphrey et al. [42]. (b) Average change in H4 acetylation of the upstream region of each of the six groups of genes with increasing GC content. Acetylation data were obtained by Bernstein et al. [30].
Figure 7
Figure 7
Inhibition of the histone deacetylase activity of Rpd3p results in base composition-dependent gene activation. The dataset describing changes in gene expression upon TSA treatment was obtained from Bernstein et al. [41]. Genes were divided into six groups dependent upon their base composition (as in Figure 1b) and per group the average change in gene expression upon TSA treatment was determined. Error bars are standard error of the mean. Cells were treated for (a) 15 minutes, (b) 30 minutes and (c) 60 minutes with TSA. (d) Average change in gene expression levels in hda1Δ cells for each of the six groups of genes with increasing GC content. Expression data are from Bernstein et al. [41].
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