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H3K4 monomethylation dictates nucleosome dynamics and chromatin remodeling at stress-responsive genes.

Nadal-Ribelles M, Mas G, Millán-Zambrano G, Solé C, Ammerer G, Chávez S, Posas F, de Nadal E - Nucleic Acids Res. (2015)

Bottom Line: Hog1 targets the RSC chromatin remodeling complex to stress-responsive genes and rsc deficient cells display reduced induction of gene expression.Monomethylation of H3K4 is specifically inhibiting RSC-independent chromatin remodeling and thus, it prevents osmostress-induced gene expression.Our findings point to a novel role for H3K4 monomethylation in dictating the specificity of chromatin remodeling, adding an extra layer of regulation to the transcriptional stress response.

View Article: PubMed Central - PubMed

Affiliation: Cell signaling unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain.

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SWR1 is licensed to act as a chromatin remodeler in the absence of RSC and histone methylation. (A) Deletion of BDF1, HTZ1 and inducible expression of pGAL1::SWR1 prevents induction of osmo-responsive genes in an rsc9ts set1Δ background. The indicated strains were grown in either YPD or YPD 17β-estradiol (17 β-E2) before being shifted to a non-permissive temperature (37ºC) for 2 h. The cells were subsequently exposed to an osmotic stress of 0.4 M NaCl. Total RNA was assayed by northern blot for STL1, CTT1 and ENO1 (as loading control) expression. Quantification data came from the same original blot and it was normalized to the loading control. The value of maximum gene expression of the wild type strain was used as 100% reference. (B) Impairment of the SWR1 complex leads to defective chromatin remodeling. Total H3 eviction from the coding region of STL1 was followed using ChIP assays in the same strains and under the same conditions as in (A). The levels of total H3 under untreated (black bars) conditions were used as a reference for the treated samples (0.4 M NaCl, 10 min, white bars). Data represent the mean and standard deviation of three independent experiments.
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Figure 6: SWR1 is licensed to act as a chromatin remodeler in the absence of RSC and histone methylation. (A) Deletion of BDF1, HTZ1 and inducible expression of pGAL1::SWR1 prevents induction of osmo-responsive genes in an rsc9ts set1Δ background. The indicated strains were grown in either YPD or YPD 17β-estradiol (17 β-E2) before being shifted to a non-permissive temperature (37ºC) for 2 h. The cells were subsequently exposed to an osmotic stress of 0.4 M NaCl. Total RNA was assayed by northern blot for STL1, CTT1 and ENO1 (as loading control) expression. Quantification data came from the same original blot and it was normalized to the loading control. The value of maximum gene expression of the wild type strain was used as 100% reference. (B) Impairment of the SWR1 complex leads to defective chromatin remodeling. Total H3 eviction from the coding region of STL1 was followed using ChIP assays in the same strains and under the same conditions as in (A). The levels of total H3 under untreated (black bars) conditions were used as a reference for the treated samples (0.4 M NaCl, 10 min, white bars). Data represent the mean and standard deviation of three independent experiments.

Mentions: Since lack of H3K4 methylation suppressed the RSC deficiency and permitted nucleosome remodeling in response to stress, we hypothesized that an alternative remodeler might act at stress-responsive genes in the absence of H3K4 methylation. To identify such a chromatin remodeler(s), we performed a targeted candidate screen in which we deleted genes encoding representative members of all chromatin remodeling complexes in yeast (a total of 20 were assayed), in the set1 rsc9ts background. We reasoned that in the absence of this alternative remodeler the set1 deficiency should not suppress the rsc9ts mutation. When monitoring gene expression in these mutant strains, we found that only the absence of BDF1 in that background rendered cells that were unable to induce gene (STL1 and CTT1 in lesser extend) expression upon stress (Figures 5A and 6A). We then tested whether Bdf1 was recruited to stress-responsive genes upon osmostress, using ChIP assays. Although Bdf1 indeed associates with STL1 upon stress in wild type, set1Δ and rsc9ts strains, its binding was more robust in set1 rsc9ts deficient cells (Figure 5B). Of note, we did not detect differences in Bdf1 recruitment when comparing wild type, set1Δ, rsc9ts and set1Δ rsc9ts mutant strains in the absence of stress (Supplementary Figure S5).


H3K4 monomethylation dictates nucleosome dynamics and chromatin remodeling at stress-responsive genes.

Nadal-Ribelles M, Mas G, Millán-Zambrano G, Solé C, Ammerer G, Chávez S, Posas F, de Nadal E - Nucleic Acids Res. (2015)

SWR1 is licensed to act as a chromatin remodeler in the absence of RSC and histone methylation. (A) Deletion of BDF1, HTZ1 and inducible expression of pGAL1::SWR1 prevents induction of osmo-responsive genes in an rsc9ts set1Δ background. The indicated strains were grown in either YPD or YPD 17β-estradiol (17 β-E2) before being shifted to a non-permissive temperature (37ºC) for 2 h. The cells were subsequently exposed to an osmotic stress of 0.4 M NaCl. Total RNA was assayed by northern blot for STL1, CTT1 and ENO1 (as loading control) expression. Quantification data came from the same original blot and it was normalized to the loading control. The value of maximum gene expression of the wild type strain was used as 100% reference. (B) Impairment of the SWR1 complex leads to defective chromatin remodeling. Total H3 eviction from the coding region of STL1 was followed using ChIP assays in the same strains and under the same conditions as in (A). The levels of total H3 under untreated (black bars) conditions were used as a reference for the treated samples (0.4 M NaCl, 10 min, white bars). Data represent the mean and standard deviation of three independent experiments.
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Figure 6: SWR1 is licensed to act as a chromatin remodeler in the absence of RSC and histone methylation. (A) Deletion of BDF1, HTZ1 and inducible expression of pGAL1::SWR1 prevents induction of osmo-responsive genes in an rsc9ts set1Δ background. The indicated strains were grown in either YPD or YPD 17β-estradiol (17 β-E2) before being shifted to a non-permissive temperature (37ºC) for 2 h. The cells were subsequently exposed to an osmotic stress of 0.4 M NaCl. Total RNA was assayed by northern blot for STL1, CTT1 and ENO1 (as loading control) expression. Quantification data came from the same original blot and it was normalized to the loading control. The value of maximum gene expression of the wild type strain was used as 100% reference. (B) Impairment of the SWR1 complex leads to defective chromatin remodeling. Total H3 eviction from the coding region of STL1 was followed using ChIP assays in the same strains and under the same conditions as in (A). The levels of total H3 under untreated (black bars) conditions were used as a reference for the treated samples (0.4 M NaCl, 10 min, white bars). Data represent the mean and standard deviation of three independent experiments.
Mentions: Since lack of H3K4 methylation suppressed the RSC deficiency and permitted nucleosome remodeling in response to stress, we hypothesized that an alternative remodeler might act at stress-responsive genes in the absence of H3K4 methylation. To identify such a chromatin remodeler(s), we performed a targeted candidate screen in which we deleted genes encoding representative members of all chromatin remodeling complexes in yeast (a total of 20 were assayed), in the set1 rsc9ts background. We reasoned that in the absence of this alternative remodeler the set1 deficiency should not suppress the rsc9ts mutation. When monitoring gene expression in these mutant strains, we found that only the absence of BDF1 in that background rendered cells that were unable to induce gene (STL1 and CTT1 in lesser extend) expression upon stress (Figures 5A and 6A). We then tested whether Bdf1 was recruited to stress-responsive genes upon osmostress, using ChIP assays. Although Bdf1 indeed associates with STL1 upon stress in wild type, set1Δ and rsc9ts strains, its binding was more robust in set1 rsc9ts deficient cells (Figure 5B). Of note, we did not detect differences in Bdf1 recruitment when comparing wild type, set1Δ, rsc9ts and set1Δ rsc9ts mutant strains in the absence of stress (Supplementary Figure S5).

Bottom Line: Hog1 targets the RSC chromatin remodeling complex to stress-responsive genes and rsc deficient cells display reduced induction of gene expression.Monomethylation of H3K4 is specifically inhibiting RSC-independent chromatin remodeling and thus, it prevents osmostress-induced gene expression.Our findings point to a novel role for H3K4 monomethylation in dictating the specificity of chromatin remodeling, adding an extra layer of regulation to the transcriptional stress response.

View Article: PubMed Central - PubMed

Affiliation: Cell signaling unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain.

Show MeSH
Related in: MedlinePlus