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H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state.

Brickner DG, Cajigas I, Fondufe-Mittendorf Y, Ahmed S, Lee PC, Widom J, Brickner JH - PLoS Biol. (2007)

Bottom Line: This form of transcriptional memory is chromatin based; the histone variant H2A.Z is incorporated into nucleosomes within the recently repressed INO1 promoter and is specifically required for rapid reactivation of both INO1 and GAL1.Furthermore, H2A.Z is required to retain INO1 at the nuclear periphery after repression.Therefore, H2A.Z-mediated localization of recently repressed genes at the nuclear periphery represents an epigenetic state that confers memory of transcriptional activation and promotes reactivation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America.

ABSTRACT
Many genes are recruited to the nuclear periphery upon transcriptional activation. The mechanism and functional significance of this recruitment is unclear. We find that recruitment of the yeast INO1 and GAL1 genes to the nuclear periphery is rapid and independent of transcription. Surprisingly, these genes remain at the periphery for generations after they are repressed. Localization at the nuclear periphery serves as a form of memory of recent transcriptional activation, promoting reactivation. Previously expressed GAL1 at the nuclear periphery is activated much more rapidly than long-term repressed GAL1 in the nucleoplasm, even after six generations of repression. Localization of INO1 at the nuclear periphery is necessary and sufficient to promote more rapid activation. This form of transcriptional memory is chromatin based; the histone variant H2A.Z is incorporated into nucleosomes within the recently repressed INO1 promoter and is specifically required for rapid reactivation of both INO1 and GAL1. Furthermore, H2A.Z is required to retain INO1 at the nuclear periphery after repression. Therefore, H2A.Z-mediated localization of recently repressed genes at the nuclear periphery represents an epigenetic state that confers memory of transcriptional activation and promotes reactivation.

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Localization at the Nuclear Periphery Is Necessary and Sufficient to Promote Reactivation of INO1(A) INO1 activation versus reactivation. Strain BY4741 cultures grown under long-term or short-term (3 h) repressing conditions were shifted into medium lacking inositol. INO1 mRNA abundance was quantified at the indicated times of inositol starvation using RT Q-PCR and expressed relative to ACT1 mRNA.(B) Wild-type (JBY397 for INO1, DBY32 for GAL1; four replicates of 30–50 cells) and nup2Δ (JBY462 for INO1, JBY467 for GAL1; two replicates of 30–50 cells) strains having the lac repressor–binding site array integrated at INO1 or GAL1 were scored for peripheral localization under activating conditions. The hatched blue line represents the baseline level of peripheral localization for the URA3 gene.(C) Schematic of the growth conditions: green arrows indicate growth under activating conditions; red arrows indicate growth under repressing conditions. After 3 h of repression with 100 μM inositol, wild-type (CRY1) or nup2Δ (JBY451-r1) mutant cells were shifted to medium lacking inositol, and INO1 mRNA levels were quantified at the indicated times.(D) Tethering of INO1 to the nuclear periphery enhances the rate of activation. Strains having the lac operator array integrated upstream of the INO1 gene were transformed with either wild-type Lac I-GFP (JBY397) or Lac I-FFAT-GFP (JBY399) to target the gene to the nuclear membrane [6]. These strains were shifted into medium lacking inositol for the indicated times, and INO1 mRNA levels were quantified.
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pbio-0050081-g004: Localization at the Nuclear Periphery Is Necessary and Sufficient to Promote Reactivation of INO1(A) INO1 activation versus reactivation. Strain BY4741 cultures grown under long-term or short-term (3 h) repressing conditions were shifted into medium lacking inositol. INO1 mRNA abundance was quantified at the indicated times of inositol starvation using RT Q-PCR and expressed relative to ACT1 mRNA.(B) Wild-type (JBY397 for INO1, DBY32 for GAL1; four replicates of 30–50 cells) and nup2Δ (JBY462 for INO1, JBY467 for GAL1; two replicates of 30–50 cells) strains having the lac repressor–binding site array integrated at INO1 or GAL1 were scored for peripheral localization under activating conditions. The hatched blue line represents the baseline level of peripheral localization for the URA3 gene.(C) Schematic of the growth conditions: green arrows indicate growth under activating conditions; red arrows indicate growth under repressing conditions. After 3 h of repression with 100 μM inositol, wild-type (CRY1) or nup2Δ (JBY451-r1) mutant cells were shifted to medium lacking inositol, and INO1 mRNA levels were quantified at the indicated times.(D) Tethering of INO1 to the nuclear periphery enhances the rate of activation. Strains having the lac operator array integrated upstream of the INO1 gene were transformed with either wild-type Lac I-GFP (JBY397) or Lac I-FFAT-GFP (JBY399) to target the gene to the nuclear membrane [6]. These strains were shifted into medium lacking inositol for the indicated times, and INO1 mRNA levels were quantified.

Mentions: We next compared the rate of activation of long-term repressed INO1 to the rate of reactivation of short-term repressed INO1 after 3 h of repression (∼1.5 generations). In contrast to GAL1, the reactivation of the INO1 gene after 3 h of repression was delayed compared with activation of the long-term repressed gene (Figure 4A). However, this rate of reactivation was clearly enhanced by the localization at the nuclear periphery. Nup2, a component of the nuclear pore complex that physically associates with transcriptionally active genes such as GAL1 [7,13], is required for recruitment of both INO1 and GAL1 to the nuclear periphery (Figure 4B). Mutants lacking Nup2 exhibited a delay in the reactivation of INO1 (Figure 4C), suggesting that recruitment to the nuclear periphery promotes more rapid reactivation.


H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state.

Brickner DG, Cajigas I, Fondufe-Mittendorf Y, Ahmed S, Lee PC, Widom J, Brickner JH - PLoS Biol. (2007)

Localization at the Nuclear Periphery Is Necessary and Sufficient to Promote Reactivation of INO1(A) INO1 activation versus reactivation. Strain BY4741 cultures grown under long-term or short-term (3 h) repressing conditions were shifted into medium lacking inositol. INO1 mRNA abundance was quantified at the indicated times of inositol starvation using RT Q-PCR and expressed relative to ACT1 mRNA.(B) Wild-type (JBY397 for INO1, DBY32 for GAL1; four replicates of 30–50 cells) and nup2Δ (JBY462 for INO1, JBY467 for GAL1; two replicates of 30–50 cells) strains having the lac repressor–binding site array integrated at INO1 or GAL1 were scored for peripheral localization under activating conditions. The hatched blue line represents the baseline level of peripheral localization for the URA3 gene.(C) Schematic of the growth conditions: green arrows indicate growth under activating conditions; red arrows indicate growth under repressing conditions. After 3 h of repression with 100 μM inositol, wild-type (CRY1) or nup2Δ (JBY451-r1) mutant cells were shifted to medium lacking inositol, and INO1 mRNA levels were quantified at the indicated times.(D) Tethering of INO1 to the nuclear periphery enhances the rate of activation. Strains having the lac operator array integrated upstream of the INO1 gene were transformed with either wild-type Lac I-GFP (JBY397) or Lac I-FFAT-GFP (JBY399) to target the gene to the nuclear membrane [6]. These strains were shifted into medium lacking inositol for the indicated times, and INO1 mRNA levels were quantified.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC1828143&req=5

pbio-0050081-g004: Localization at the Nuclear Periphery Is Necessary and Sufficient to Promote Reactivation of INO1(A) INO1 activation versus reactivation. Strain BY4741 cultures grown under long-term or short-term (3 h) repressing conditions were shifted into medium lacking inositol. INO1 mRNA abundance was quantified at the indicated times of inositol starvation using RT Q-PCR and expressed relative to ACT1 mRNA.(B) Wild-type (JBY397 for INO1, DBY32 for GAL1; four replicates of 30–50 cells) and nup2Δ (JBY462 for INO1, JBY467 for GAL1; two replicates of 30–50 cells) strains having the lac repressor–binding site array integrated at INO1 or GAL1 were scored for peripheral localization under activating conditions. The hatched blue line represents the baseline level of peripheral localization for the URA3 gene.(C) Schematic of the growth conditions: green arrows indicate growth under activating conditions; red arrows indicate growth under repressing conditions. After 3 h of repression with 100 μM inositol, wild-type (CRY1) or nup2Δ (JBY451-r1) mutant cells were shifted to medium lacking inositol, and INO1 mRNA levels were quantified at the indicated times.(D) Tethering of INO1 to the nuclear periphery enhances the rate of activation. Strains having the lac operator array integrated upstream of the INO1 gene were transformed with either wild-type Lac I-GFP (JBY397) or Lac I-FFAT-GFP (JBY399) to target the gene to the nuclear membrane [6]. These strains were shifted into medium lacking inositol for the indicated times, and INO1 mRNA levels were quantified.
Mentions: We next compared the rate of activation of long-term repressed INO1 to the rate of reactivation of short-term repressed INO1 after 3 h of repression (∼1.5 generations). In contrast to GAL1, the reactivation of the INO1 gene after 3 h of repression was delayed compared with activation of the long-term repressed gene (Figure 4A). However, this rate of reactivation was clearly enhanced by the localization at the nuclear periphery. Nup2, a component of the nuclear pore complex that physically associates with transcriptionally active genes such as GAL1 [7,13], is required for recruitment of both INO1 and GAL1 to the nuclear periphery (Figure 4B). Mutants lacking Nup2 exhibited a delay in the reactivation of INO1 (Figure 4C), suggesting that recruitment to the nuclear periphery promotes more rapid reactivation.

Bottom Line: This form of transcriptional memory is chromatin based; the histone variant H2A.Z is incorporated into nucleosomes within the recently repressed INO1 promoter and is specifically required for rapid reactivation of both INO1 and GAL1.Furthermore, H2A.Z is required to retain INO1 at the nuclear periphery after repression.Therefore, H2A.Z-mediated localization of recently repressed genes at the nuclear periphery represents an epigenetic state that confers memory of transcriptional activation and promotes reactivation.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois, United States of America.

ABSTRACT
Many genes are recruited to the nuclear periphery upon transcriptional activation. The mechanism and functional significance of this recruitment is unclear. We find that recruitment of the yeast INO1 and GAL1 genes to the nuclear periphery is rapid and independent of transcription. Surprisingly, these genes remain at the periphery for generations after they are repressed. Localization at the nuclear periphery serves as a form of memory of recent transcriptional activation, promoting reactivation. Previously expressed GAL1 at the nuclear periphery is activated much more rapidly than long-term repressed GAL1 in the nucleoplasm, even after six generations of repression. Localization of INO1 at the nuclear periphery is necessary and sufficient to promote more rapid activation. This form of transcriptional memory is chromatin based; the histone variant H2A.Z is incorporated into nucleosomes within the recently repressed INO1 promoter and is specifically required for rapid reactivation of both INO1 and GAL1. Furthermore, H2A.Z is required to retain INO1 at the nuclear periphery after repression. Therefore, H2A.Z-mediated localization of recently repressed genes at the nuclear periphery represents an epigenetic state that confers memory of transcriptional activation and promotes reactivation.

Show MeSH
Related in: MedlinePlus