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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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Nucleosome occupancy in the CHA1-VAC17 locus of the snf2 mutant and wild-type (SNF2) cells. Nucleosome occupancy is quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array; larger numbers indicate increased nucleosome coverage. Top, steady-state growth in glucose; bottom, 20 min after downshift to glycerol.
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Figure 1: Nucleosome occupancy in the CHA1-VAC17 locus of the snf2 mutant and wild-type (SNF2) cells. Nucleosome occupancy is quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array; larger numbers indicate increased nucleosome coverage. Top, steady-state growth in glucose; bottom, 20 min after downshift to glycerol.

Mentions: To determine global nucleosome positions in nucleosome remodeling mutants, we isolated chromatin from wild-type cells as well as asf1 and snf2 mutants at steady state and 20 min after carbon downshift (wild-type, snf2Δ, asf1Δ) or upshift (wild-type, asf1Δ). Chromatin was digested by micrococcal nuclease, yielding DNA protected from digestion by inclusion in nucleosomes (Supplemental Figure S1); this nucleosomal DNA was hybridized to Affymetrix tiling arrays covering the entire yeast genome at four to five base pair offset. As an illustrative example, nucleosome occupancy in the CHA1-VAC17 locus (quantified as the log-intensity ratio between nucleosomal and control DNA hybridized to the tiling array) is shown in Figure 1.


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)

Nucleosome occupancy in the CHA1-VAC17 locus of the snf2 mutant and wild-type (SNF2) cells. Nucleosome occupancy is quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array; larger numbers indicate increased nucleosome coverage. Top, steady-state growth in glucose; bottom, 20 min after downshift to glycerol.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3113774&req=5

Figure 1: Nucleosome occupancy in the CHA1-VAC17 locus of the snf2 mutant and wild-type (SNF2) cells. Nucleosome occupancy is quantified as the log ratio of intensities from nucleosomal and control DNA hybridized to the tiling array; larger numbers indicate increased nucleosome coverage. Top, steady-state growth in glucose; bottom, 20 min after downshift to glycerol.
Mentions: To determine global nucleosome positions in nucleosome remodeling mutants, we isolated chromatin from wild-type cells as well as asf1 and snf2 mutants at steady state and 20 min after carbon downshift (wild-type, snf2Δ, asf1Δ) or upshift (wild-type, asf1Δ). Chromatin was digested by micrococcal nuclease, yielding DNA protected from digestion by inclusion in nucleosomes (Supplemental Figure S1); this nucleosomal DNA was hybridized to Affymetrix tiling arrays covering the entire yeast genome at four to five base pair offset. As an illustrative example, nucleosome occupancy in the CHA1-VAC17 locus (quantified as the log-intensity ratio between nucleosomal and control DNA hybridized to the tiling array) is shown in Figure 1.

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