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The histone H3K36 demethylase Rph1/KDM4 regulates the expression of the photoreactivation gene PHR1.

Liang CY, Hsu PH, Chou DF, Pan CY, Wang LC, Huang WC, Tsai MD, Lo WS - Nucleic Acids Res. (2011)

Bottom Line: Overexpression of Rph1 reduced the expression of PHR1 and increased UV sensitivity.The catalytically deficient mutant (H235A) of Rph1 diminished the repressive transcriptional effect on PHR1 expression, which indicates that histone demethylase activity contributes to transcriptional repression.Notably, overexpression of Rph1 and H3K36A mutant reduced histone acetylation at the URS, which implies a crosstalk between histone demethylation and acetylation at the PHR1 promoter.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.

ABSTRACT
The dynamics of histone methylation have emerged as an important issue since the identification of histone demethylases. We studied the regulatory function of Rph1/KDM4 (lysine demethylase), a histone H3K36 demethylase, on transcription in Saccharomyces cerevisiae. Overexpression of Rph1 reduced the expression of PHR1 and increased UV sensitivity. The catalytically deficient mutant (H235A) of Rph1 diminished the repressive transcriptional effect on PHR1 expression, which indicates that histone demethylase activity contributes to transcriptional repression. Chromatin immunoprecipitation analysis demonstrated that Rph1 was associated at the upstream repression sequence of PHR1 through zinc-finger domains and was dissociated after UV irradiation. Notably, overexpression of Rph1 and H3K36A mutant reduced histone acetylation at the URS, which implies a crosstalk between histone demethylation and acetylation at the PHR1 promoter. In addition, the crucial checkpoint protein Rad53 acted as an upstream regulator of Rph1 and dominated the phosphorylation of Rph1 that was required for efficient PHR1 expression and the dissociation of Rph1. The release of Rph1 from chromatin also required the phosphorylation at S652. Our study demonstrates that the histone demethylase Rph1 is associated with a specific chromatin locus and modulates histone modifications to repress a DNA damage responsive gene under control of damage checkpoint signaling.

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A model for Rph1-regulated PHR1 expression in response to DNA damage. Under normal conditions, Rph1 associates with URSPHR1, and PHR1 transcription is repressed (upper panel). Under DNA damage signaling, Rph1 dissociates from the PHR1 promoter to induce the expression of PHR1. Ac, histone acetylation; Me, H3K36 tri-methylation; Pi, phosphorylation; See ‘Discussion’ section for details.
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Figure 7: A model for Rph1-regulated PHR1 expression in response to DNA damage. Under normal conditions, Rph1 associates with URSPHR1, and PHR1 transcription is repressed (upper panel). Under DNA damage signaling, Rph1 dissociates from the PHR1 promoter to induce the expression of PHR1. Ac, histone acetylation; Me, H3K36 tri-methylation; Pi, phosphorylation; See ‘Discussion’ section for details.

Mentions: Collectively, we hypothesize a model to describe the regulatory event modulated by the H3K36 demethylase Rph1 at the PHR1 promoter in response to DNA damage signals in Figure 7. Roeder proposed a model of a ‘two-step process’ of transcriptional activation in eukaryotes: (i) The overall level of induction in response to activating signal involving first a ‘de-repression step’ that restores activity to the basal level, and followed by (ii) A ‘net-activation’ step that leads to the higher induction expression level (56). Here, we show that Rph1-mediated H3K36 demethylase activity is required to repress PHR1 expression and is involved in regulating the early step of transcriptional activation. Rph1 is specifically associated with URSPHR1 to generate a repressed or ground state of chromatin structure in the absence of UV irradiation. The physiological repressed chromatin structure at the URSPHR1 subsequently leads to decreased histone acetylation by cooperatively associating with the Rpd3 co-repressor complex. The checkpoint kinase Rad53 is required for the basal and inducible expression of PHR1. Upon UV-induced DNA damage, the fully activated Rad53 modulates the phosphorylation of Rph1, which subsequently dissociates from URSPHR1 to relieve the suppressed expression of PHR1. In addition, Rad53 may mediate the recruitment of other co-activators to increase the histone acetylations at the promoter in response to UV irradiation, which induces PHR1 expression for efficient DNA repair. This study highlights a distinct mechanism of the histone demethylase in transcriptional regulation at the promoter region instead of coding sequence. Thus, we reveal that the key regulatory step of Rph1 is to maintain a low level of H3K36 methylation at the PHR1 promoter in the basal state. Dismissal of Rph1 from the URSPHR1 region is mediated by a DNA damage signal to allow immediate histone acetylations as well as transcriptional initiation by recruiting RNA pol II.Figure 7.


The histone H3K36 demethylase Rph1/KDM4 regulates the expression of the photoreactivation gene PHR1.

Liang CY, Hsu PH, Chou DF, Pan CY, Wang LC, Huang WC, Tsai MD, Lo WS - Nucleic Acids Res. (2011)

A model for Rph1-regulated PHR1 expression in response to DNA damage. Under normal conditions, Rph1 associates with URSPHR1, and PHR1 transcription is repressed (upper panel). Under DNA damage signaling, Rph1 dissociates from the PHR1 promoter to induce the expression of PHR1. Ac, histone acetylation; Me, H3K36 tri-methylation; Pi, phosphorylation; See ‘Discussion’ section for details.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105397&req=5

Figure 7: A model for Rph1-regulated PHR1 expression in response to DNA damage. Under normal conditions, Rph1 associates with URSPHR1, and PHR1 transcription is repressed (upper panel). Under DNA damage signaling, Rph1 dissociates from the PHR1 promoter to induce the expression of PHR1. Ac, histone acetylation; Me, H3K36 tri-methylation; Pi, phosphorylation; See ‘Discussion’ section for details.
Mentions: Collectively, we hypothesize a model to describe the regulatory event modulated by the H3K36 demethylase Rph1 at the PHR1 promoter in response to DNA damage signals in Figure 7. Roeder proposed a model of a ‘two-step process’ of transcriptional activation in eukaryotes: (i) The overall level of induction in response to activating signal involving first a ‘de-repression step’ that restores activity to the basal level, and followed by (ii) A ‘net-activation’ step that leads to the higher induction expression level (56). Here, we show that Rph1-mediated H3K36 demethylase activity is required to repress PHR1 expression and is involved in regulating the early step of transcriptional activation. Rph1 is specifically associated with URSPHR1 to generate a repressed or ground state of chromatin structure in the absence of UV irradiation. The physiological repressed chromatin structure at the URSPHR1 subsequently leads to decreased histone acetylation by cooperatively associating with the Rpd3 co-repressor complex. The checkpoint kinase Rad53 is required for the basal and inducible expression of PHR1. Upon UV-induced DNA damage, the fully activated Rad53 modulates the phosphorylation of Rph1, which subsequently dissociates from URSPHR1 to relieve the suppressed expression of PHR1. In addition, Rad53 may mediate the recruitment of other co-activators to increase the histone acetylations at the promoter in response to UV irradiation, which induces PHR1 expression for efficient DNA repair. This study highlights a distinct mechanism of the histone demethylase in transcriptional regulation at the promoter region instead of coding sequence. Thus, we reveal that the key regulatory step of Rph1 is to maintain a low level of H3K36 methylation at the PHR1 promoter in the basal state. Dismissal of Rph1 from the URSPHR1 region is mediated by a DNA damage signal to allow immediate histone acetylations as well as transcriptional initiation by recruiting RNA pol II.Figure 7.

Bottom Line: Overexpression of Rph1 reduced the expression of PHR1 and increased UV sensitivity.The catalytically deficient mutant (H235A) of Rph1 diminished the repressive transcriptional effect on PHR1 expression, which indicates that histone demethylase activity contributes to transcriptional repression.Notably, overexpression of Rph1 and H3K36A mutant reduced histone acetylation at the URS, which implies a crosstalk between histone demethylation and acetylation at the PHR1 promoter.

View Article: PubMed Central - PubMed

Affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.

ABSTRACT
The dynamics of histone methylation have emerged as an important issue since the identification of histone demethylases. We studied the regulatory function of Rph1/KDM4 (lysine demethylase), a histone H3K36 demethylase, on transcription in Saccharomyces cerevisiae. Overexpression of Rph1 reduced the expression of PHR1 and increased UV sensitivity. The catalytically deficient mutant (H235A) of Rph1 diminished the repressive transcriptional effect on PHR1 expression, which indicates that histone demethylase activity contributes to transcriptional repression. Chromatin immunoprecipitation analysis demonstrated that Rph1 was associated at the upstream repression sequence of PHR1 through zinc-finger domains and was dissociated after UV irradiation. Notably, overexpression of Rph1 and H3K36A mutant reduced histone acetylation at the URS, which implies a crosstalk between histone demethylation and acetylation at the PHR1 promoter. In addition, the crucial checkpoint protein Rad53 acted as an upstream regulator of Rph1 and dominated the phosphorylation of Rph1 that was required for efficient PHR1 expression and the dissociation of Rph1. The release of Rph1 from chromatin also required the phosphorylation at S652. Our study demonstrates that the histone demethylase Rph1 is associated with a specific chromatin locus and modulates histone modifications to repress a DNA damage responsive gene under control of damage checkpoint signaling.

Show MeSH
Related in: MedlinePlus