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Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters.

Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR - Mol. Biol. Cell (2011)

Bottom Line: In snf2 mutants, excess promoter nucleosomes correlate with reduced gene expression.Cells lacking SNF2 or ASF1 still accomplish the changes in promoter nucleosome structure associated with large-scale transcriptional reprogramming.However, chromatin reorganization in the mutants is reduced in extent compared to wild-type cells, even though transcriptional changes proceed normally.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA.

ABSTRACT
Most promoters in yeast contain a nucleosome-depleted region (NDR), but the mechanisms by which NDRs are established and maintained in vivo are currently unclear. We have examined how genome-wide nucleosome placement is altered in the absence of two distinct types of nucleosome remodeling activity. In mutants of both SNF2, which encodes the ATPase component of the Swi/Snf remodeling complex, and ASF1, which encodes a histone chaperone, distinct sets of gene promoters carry excess nucleosomes in their NDRs relative to wild-type. In snf2 mutants, excess promoter nucleosomes correlate with reduced gene expression. In both mutants, the excess nucleosomes occupy DNA sequences that are energetically less favorable for nucleosome formation, indicating that intrinsic histone-DNA interactions are not sufficient for nucleosome positioning in vivo, and that Snf2 and Asf1 promote thermodynamic equilibration of nucleosomal arrays. Cells lacking SNF2 or ASF1 still accomplish the changes in promoter nucleosome structure associated with large-scale transcriptional reprogramming. However, chromatin reorganization in the mutants is reduced in extent compared to wild-type cells, even though transcriptional changes proceed normally. In summary, active remodeling is required for distributing nucleosomes to energetically favorable positions in vivo and for reorganizing chromatin in response to changes in transcriptional activity.

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snf2 and asf1 mutants contain excess promoter nucleosomes. (A) Top, nucleosome occupancy (quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array) in the wild-type strain grown in glucose is subtracted from the occupancy in the snf2 mutant strain grown in glucose; positive values indicate excess nucleosomes in the mutant relative to wild-type (see scale on right). Nucleosome occupancy difference as a function of position is shown 800 base pairs upstream and downstream of the transcription start site (TSS) (Nagalakshmi et al., 2008) for 4532 genes. The occupancy difference is clustered into two groups using K-means. The upper cluster shows excess nucleosomes in the snf2 mutant. (B) Top, asf1 mutant grown in glycerol vs. wild-type grown in glycerol. (C) Top, snf2 mutant 20 min after downshift to glycerol vs. downshifted wild-type. (D) Top, asf1 mutant 20 min after upshift to glucose vs. upshifted wild-type. (A–D) Bottom, average nucleosome occupancy in the two clusters for each mutant–wild-type combination. Solid lines correspond to the cluster with excess nucleosomes in the mutant strain.
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Figure 2: snf2 and asf1 mutants contain excess promoter nucleosomes. (A) Top, nucleosome occupancy (quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array) in the wild-type strain grown in glucose is subtracted from the occupancy in the snf2 mutant strain grown in glucose; positive values indicate excess nucleosomes in the mutant relative to wild-type (see scale on right). Nucleosome occupancy difference as a function of position is shown 800 base pairs upstream and downstream of the transcription start site (TSS) (Nagalakshmi et al., 2008) for 4532 genes. The occupancy difference is clustered into two groups using K-means. The upper cluster shows excess nucleosomes in the snf2 mutant. (B) Top, asf1 mutant grown in glycerol vs. wild-type grown in glycerol. (C) Top, snf2 mutant 20 min after downshift to glycerol vs. downshifted wild-type. (D) Top, asf1 mutant 20 min after upshift to glucose vs. upshifted wild-type. (A–D) Bottom, average nucleosome occupancy in the two clusters for each mutant–wild-type combination. Solid lines correspond to the cluster with excess nucleosomes in the mutant strain.

Mentions: When we examined nucleosome positioning in asf1 and snf2 mutants grown at steady state in either glycerol or glucose, we found that distinct subsets of promoters were altered in the mutants relative to wild-type (Figures 2 and S2A). While the promoter nucleosome occupancy patterns of a majority of genes in both snf2 or asf1 mutants were identical to those in wild-type, 20% of genes in glucose-grown snf2 (900/4532), 43% of genes in glucose-grown asf1 (1948/4532), and 25% of genes in glycerol-grown asf1 (1051/4532) contained an excess of nucleosomes in their promoters; few promoters in either mutant had decreased nucleosome levels. Deleting SNF2 or ASF1 affects promoters of distinct gene subsets with only limited overlap under glucose growth conditions (540 genes in common). The set of genes affected by SNF2 deletion is significantly enriched for TATA box–containing promoters (Huisinga and Pugh, 2004) (222/900 genes, p = 5.9 × 10−10) and for genes at which Snf2 has been shown to bind in vivo by prior chromatin immunoprecipitation experiments (p = 0.003) (Shivaswamy and Iyer, 2008). In contrast, promoters with additional nucleosomes in the asf1 mutant are depleted of TATA boxes, both in glucose (290/1948 genes, p = 2.1 × 10−5) and glycerol (111/1051 genes, p < 10−10). Previous studies have shown that NDRs exist not only over promoters but also over the transcription termination sites (TTS) of most genes (Mavrich et al., 2008; Kaplan et al., 2009). Both snf2 and asf1 mutants display an excess of nucleosomes over the TTS in largely distinct subsets of genes (Figure S3), but excess TTS nucleosomes are not correlated with excess promoter nucleosomes in either mutant. The positions of nucleosomes over coding regions were essentially unchanged in the mutants. In sum, we conclude that both the histone chaperone Asf1 and the Swi/Snf complex act under steady-state conditions to remove, or prevent the deposition of, nucleosomes at specific and largely nonoverlapping sets of promoter and terminator regions.


Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters.

Tolkunov D, Zawadzki KA, Singer C, Elfving N, Morozov AV, Broach JR - Mol. Biol. Cell (2011)

snf2 and asf1 mutants contain excess promoter nucleosomes. (A) Top, nucleosome occupancy (quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array) in the wild-type strain grown in glucose is subtracted from the occupancy in the snf2 mutant strain grown in glucose; positive values indicate excess nucleosomes in the mutant relative to wild-type (see scale on right). Nucleosome occupancy difference as a function of position is shown 800 base pairs upstream and downstream of the transcription start site (TSS) (Nagalakshmi et al., 2008) for 4532 genes. The occupancy difference is clustered into two groups using K-means. The upper cluster shows excess nucleosomes in the snf2 mutant. (B) Top, asf1 mutant grown in glycerol vs. wild-type grown in glycerol. (C) Top, snf2 mutant 20 min after downshift to glycerol vs. downshifted wild-type. (D) Top, asf1 mutant 20 min after upshift to glucose vs. upshifted wild-type. (A–D) Bottom, average nucleosome occupancy in the two clusters for each mutant–wild-type combination. Solid lines correspond to the cluster with excess nucleosomes in the mutant strain.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 2: snf2 and asf1 mutants contain excess promoter nucleosomes. (A) Top, nucleosome occupancy (quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array) in the wild-type strain grown in glucose is subtracted from the occupancy in the snf2 mutant strain grown in glucose; positive values indicate excess nucleosomes in the mutant relative to wild-type (see scale on right). Nucleosome occupancy difference as a function of position is shown 800 base pairs upstream and downstream of the transcription start site (TSS) (Nagalakshmi et al., 2008) for 4532 genes. The occupancy difference is clustered into two groups using K-means. The upper cluster shows excess nucleosomes in the snf2 mutant. (B) Top, asf1 mutant grown in glycerol vs. wild-type grown in glycerol. (C) Top, snf2 mutant 20 min after downshift to glycerol vs. downshifted wild-type. (D) Top, asf1 mutant 20 min after upshift to glucose vs. upshifted wild-type. (A–D) Bottom, average nucleosome occupancy in the two clusters for each mutant–wild-type combination. Solid lines correspond to the cluster with excess nucleosomes in the mutant strain.
Mentions: When we examined nucleosome positioning in asf1 and snf2 mutants grown at steady state in either glycerol or glucose, we found that distinct subsets of promoters were altered in the mutants relative to wild-type (Figures 2 and S2A). While the promoter nucleosome occupancy patterns of a majority of genes in both snf2 or asf1 mutants were identical to those in wild-type, 20% of genes in glucose-grown snf2 (900/4532), 43% of genes in glucose-grown asf1 (1948/4532), and 25% of genes in glycerol-grown asf1 (1051/4532) contained an excess of nucleosomes in their promoters; few promoters in either mutant had decreased nucleosome levels. Deleting SNF2 or ASF1 affects promoters of distinct gene subsets with only limited overlap under glucose growth conditions (540 genes in common). The set of genes affected by SNF2 deletion is significantly enriched for TATA box–containing promoters (Huisinga and Pugh, 2004) (222/900 genes, p = 5.9 × 10−10) and for genes at which Snf2 has been shown to bind in vivo by prior chromatin immunoprecipitation experiments (p = 0.003) (Shivaswamy and Iyer, 2008). In contrast, promoters with additional nucleosomes in the asf1 mutant are depleted of TATA boxes, both in glucose (290/1948 genes, p = 2.1 × 10−5) and glycerol (111/1051 genes, p < 10−10). Previous studies have shown that NDRs exist not only over promoters but also over the transcription termination sites (TTS) of most genes (Mavrich et al., 2008; Kaplan et al., 2009). Both snf2 and asf1 mutants display an excess of nucleosomes over the TTS in largely distinct subsets of genes (Figure S3), but excess TTS nucleosomes are not correlated with excess promoter nucleosomes in either mutant. The positions of nucleosomes over coding regions were essentially unchanged in the mutants. In sum, we conclude that both the histone chaperone Asf1 and the Swi/Snf complex act under steady-state conditions to remove, or prevent the deposition of, nucleosomes at specific and largely nonoverlapping sets of promoter and terminator regions.

Bottom Line: In snf2 mutants, excess promoter nucleosomes correlate with reduced gene expression.Cells lacking SNF2 or ASF1 still accomplish the changes in promoter nucleosome structure associated with large-scale transcriptional reprogramming.However, chromatin reorganization in the mutants is reduced in extent compared to wild-type cells, even though transcriptional changes proceed normally.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA.

ABSTRACT
Most promoters in yeast contain a nucleosome-depleted region (NDR), but the mechanisms by which NDRs are established and maintained in vivo are currently unclear. We have examined how genome-wide nucleosome placement is altered in the absence of two distinct types of nucleosome remodeling activity. In mutants of both SNF2, which encodes the ATPase component of the Swi/Snf remodeling complex, and ASF1, which encodes a histone chaperone, distinct sets of gene promoters carry excess nucleosomes in their NDRs relative to wild-type. In snf2 mutants, excess promoter nucleosomes correlate with reduced gene expression. In both mutants, the excess nucleosomes occupy DNA sequences that are energetically less favorable for nucleosome formation, indicating that intrinsic histone-DNA interactions are not sufficient for nucleosome positioning in vivo, and that Snf2 and Asf1 promote thermodynamic equilibration of nucleosomal arrays. Cells lacking SNF2 or ASF1 still accomplish the changes in promoter nucleosome structure associated with large-scale transcriptional reprogramming. However, chromatin reorganization in the mutants is reduced in extent compared to wild-type cells, even though transcriptional changes proceed normally. In summary, active remodeling is required for distributing nucleosomes to energetically favorable positions in vivo and for reorganizing chromatin in response to changes in transcriptional activity.

Show MeSH
Related in: MedlinePlus