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Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae.

Verzijlbergen KF, Faber AW, Stulemeijer IJ, van Leeuwen F - BMC Mol. Biol. (2009)

Bottom Line: Thus, Dot1 affects silencing by indirect mechanisms and does not act by the recruitment model commonly proposed for histone modifications.Our study shows that multiple histone modifications associated with euchromatin positively modulate the function of heterochromatin by distinct mechanisms.We discuss how euchromatic histone modifiers can make negative as well as positive contributions to gene silencing by competing with heterochromatin proteins within heterochromatin, within euchromatin, and at the boundary between euchromatin and heterochromatin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fred van Leeuwen, Division of Gene Regulation B4, Netherlands Cancer Institute, The Netherlands. k.verzijlbergen@nki.nl

ABSTRACT

Background: Methylation of lysine 79 on histone H3 by Dot1 is required for maintenance of heterochromatin structure in yeast and humans. However, this histone modification occurs predominantly in euchromatin. Thus, Dot1 affects silencing by indirect mechanisms and does not act by the recruitment model commonly proposed for histone modifications. To better understand the role of H3K79 methylation gene silencing, we investigated the silencing function of Dot1 by genetic suppressor and enhancer analysis and examined the relationship between Dot1 and other global euchromatic histone modifiers.

Result: We determined that loss of H3K79 methylation results in a partial silencing defect that could be bypassed by conditions that promote targeting of Sir proteins to heterochromatin. Furthermore, the silencing defect in strains lacking Dot1 was dependent on methylation of H3K4 by Set1 and histone acetylation by Gcn5, Elp3, and Sas2 in euchromatin. Our study shows that multiple histone modifications associated with euchromatin positively modulate the function of heterochromatin by distinct mechanisms. Genetic interactions between Set1 and Set2 suggested that the H3K36 methyltransferase Set2, unlike most other euchromatic modifiers, negatively affects gene silencing.

Conclusion: Our genetic dissection of Dot1's role in silencing in budding yeast showed that heterochromatin formation is modulated by multiple euchromatic histone modifiers that act by non-overlapping mechanisms. We discuss how euchromatic histone modifiers can make negative as well as positive contributions to gene silencing by competing with heterochromatin proteins within heterochromatin, within euchromatin, and at the boundary between euchromatin and heterochromatin.

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A competition model for positive and negative roles of euchromatic histone modifications in heterochromatin formation. Euchromatic histone modifications can have positive roles (arrows) and negative roles (blunt arrows) in heterochromatin formation. Competition between euchromatic histone modifiers and heterochromatin proteins for interactions with nucleosomes can occur at three locations and can have different outcomes (see text). 1) Competition within heterochromatin regions creates a semi-stable epigenetic state. 2) Competition at the interface between euchromatin and heterochromatin prevents local spreading of the Sir complex, thereby on the one hand avoiding ectopic silencing of regions adjacent to heterochromatin and on the other hand ensuring availability of limiting silencing proteins for the endogenous heterochromatic regions. 3) Competition throughout euchromatin prevents non-specific binding of the Sir2/3/4 complex to bulk chromatin, thereby enhancing targeting of Sir proteins to endogenous heterochromatic regions to ensure sufficient spreading of the Sir complex. By these mechanisms, the function of a euchromatic histone modification in gene silencing depends on the relative contribution that it makes to each of these mechanisms and to what extend the negative and positive functions counteract each other.
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Figure 7: A competition model for positive and negative roles of euchromatic histone modifications in heterochromatin formation. Euchromatic histone modifications can have positive roles (arrows) and negative roles (blunt arrows) in heterochromatin formation. Competition between euchromatic histone modifiers and heterochromatin proteins for interactions with nucleosomes can occur at three locations and can have different outcomes (see text). 1) Competition within heterochromatin regions creates a semi-stable epigenetic state. 2) Competition at the interface between euchromatin and heterochromatin prevents local spreading of the Sir complex, thereby on the one hand avoiding ectopic silencing of regions adjacent to heterochromatin and on the other hand ensuring availability of limiting silencing proteins for the endogenous heterochromatic regions. 3) Competition throughout euchromatin prevents non-specific binding of the Sir2/3/4 complex to bulk chromatin, thereby enhancing targeting of Sir proteins to endogenous heterochromatic regions to ensure sufficient spreading of the Sir complex. By these mechanisms, the function of a euchromatic histone modification in gene silencing depends on the relative contribution that it makes to each of these mechanisms and to what extend the negative and positive functions counteract each other.

Mentions: Heterochromatin in yeast is characterized by the absence of post-translational modifications of histone proteins and biochemical and genetic studies indicate that binding of Sir proteins to nucleosomes is negatively affected by histone methylation and acetylation. Therefore, heterochromatin formation and spreading seems to be determined by a competition between binding of the Sir complex and action of euchromatic histone modifying enzymes. Competition between histone modifiers and the Sir proteins can in principle affect heterochromatin at three distinct genomic or chromatin locations (Figure 7). First, histone modifiers can compete with Sir proteins within heterochromatin domains. By doing so they are expected to destabilize heterochromatin domains. Indeed, when Sas2 or Dot1 are overexpressed and lead to increased global histone acetylation and methylation, respectively, Sir protein binding and silencing at telomeres is reduced [5,17,28,81]. Furthermore, the presence of Sas2 and Dot1 in yeast cells delays the onset of silencing at a previously active locus [82]. Second, modifying enzymes can deposit an anti-silencing mark at the interface between euchromatin and heterochromatin and thereby form a boundary. By this mechanism, loss of a histone modifying enzyme is expected to lead to increased spreading of heterochromatin into adjacent regions. When excessive spreading occurs of the limiting Sir proteins this may be accompanied by reduced Sir protein binding and impaired silencing of the distal wild-type silenced loci, as has been observed for strains lacking SAS2, BDF1 or GCN5+ELP3 [21,22,75,83]. Third, histone modifications throughout euchromatin can prevent non-specific binding of Sir proteins, which increases the availability of the limiting Sir proteins for heterochromatic regions [19]. By this model, loss of a modifying enzyme is expected to reduce targeting of Sir proteins to heterochromatic areas as well as their flanking regions, as has been described for DOT1 and SET1. In cells lacking Dot1 or Set1, Sir proteins do not spread excessively but become redistributed throughout the genome [5,25,26]. Also by this model, higher levels of a global and limiting histone modification are expected to improve targeting, silencing, and ectopic spreading of Sir proteins, in which case the degree of spreading will depend on how the increased mark affects competition within heterochromatin and at the boundary.


Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae.

Verzijlbergen KF, Faber AW, Stulemeijer IJ, van Leeuwen F - BMC Mol. Biol. (2009)

A competition model for positive and negative roles of euchromatic histone modifications in heterochromatin formation. Euchromatic histone modifications can have positive roles (arrows) and negative roles (blunt arrows) in heterochromatin formation. Competition between euchromatic histone modifiers and heterochromatin proteins for interactions with nucleosomes can occur at three locations and can have different outcomes (see text). 1) Competition within heterochromatin regions creates a semi-stable epigenetic state. 2) Competition at the interface between euchromatin and heterochromatin prevents local spreading of the Sir complex, thereby on the one hand avoiding ectopic silencing of regions adjacent to heterochromatin and on the other hand ensuring availability of limiting silencing proteins for the endogenous heterochromatic regions. 3) Competition throughout euchromatin prevents non-specific binding of the Sir2/3/4 complex to bulk chromatin, thereby enhancing targeting of Sir proteins to endogenous heterochromatic regions to ensure sufficient spreading of the Sir complex. By these mechanisms, the function of a euchromatic histone modification in gene silencing depends on the relative contribution that it makes to each of these mechanisms and to what extend the negative and positive functions counteract each other.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724485&req=5

Figure 7: A competition model for positive and negative roles of euchromatic histone modifications in heterochromatin formation. Euchromatic histone modifications can have positive roles (arrows) and negative roles (blunt arrows) in heterochromatin formation. Competition between euchromatic histone modifiers and heterochromatin proteins for interactions with nucleosomes can occur at three locations and can have different outcomes (see text). 1) Competition within heterochromatin regions creates a semi-stable epigenetic state. 2) Competition at the interface between euchromatin and heterochromatin prevents local spreading of the Sir complex, thereby on the one hand avoiding ectopic silencing of regions adjacent to heterochromatin and on the other hand ensuring availability of limiting silencing proteins for the endogenous heterochromatic regions. 3) Competition throughout euchromatin prevents non-specific binding of the Sir2/3/4 complex to bulk chromatin, thereby enhancing targeting of Sir proteins to endogenous heterochromatic regions to ensure sufficient spreading of the Sir complex. By these mechanisms, the function of a euchromatic histone modification in gene silencing depends on the relative contribution that it makes to each of these mechanisms and to what extend the negative and positive functions counteract each other.
Mentions: Heterochromatin in yeast is characterized by the absence of post-translational modifications of histone proteins and biochemical and genetic studies indicate that binding of Sir proteins to nucleosomes is negatively affected by histone methylation and acetylation. Therefore, heterochromatin formation and spreading seems to be determined by a competition between binding of the Sir complex and action of euchromatic histone modifying enzymes. Competition between histone modifiers and the Sir proteins can in principle affect heterochromatin at three distinct genomic or chromatin locations (Figure 7). First, histone modifiers can compete with Sir proteins within heterochromatin domains. By doing so they are expected to destabilize heterochromatin domains. Indeed, when Sas2 or Dot1 are overexpressed and lead to increased global histone acetylation and methylation, respectively, Sir protein binding and silencing at telomeres is reduced [5,17,28,81]. Furthermore, the presence of Sas2 and Dot1 in yeast cells delays the onset of silencing at a previously active locus [82]. Second, modifying enzymes can deposit an anti-silencing mark at the interface between euchromatin and heterochromatin and thereby form a boundary. By this mechanism, loss of a histone modifying enzyme is expected to lead to increased spreading of heterochromatin into adjacent regions. When excessive spreading occurs of the limiting Sir proteins this may be accompanied by reduced Sir protein binding and impaired silencing of the distal wild-type silenced loci, as has been observed for strains lacking SAS2, BDF1 or GCN5+ELP3 [21,22,75,83]. Third, histone modifications throughout euchromatin can prevent non-specific binding of Sir proteins, which increases the availability of the limiting Sir proteins for heterochromatic regions [19]. By this model, loss of a modifying enzyme is expected to reduce targeting of Sir proteins to heterochromatic areas as well as their flanking regions, as has been described for DOT1 and SET1. In cells lacking Dot1 or Set1, Sir proteins do not spread excessively but become redistributed throughout the genome [5,25,26]. Also by this model, higher levels of a global and limiting histone modification are expected to improve targeting, silencing, and ectopic spreading of Sir proteins, in which case the degree of spreading will depend on how the increased mark affects competition within heterochromatin and at the boundary.

Bottom Line: Thus, Dot1 affects silencing by indirect mechanisms and does not act by the recruitment model commonly proposed for histone modifications.Our study shows that multiple histone modifications associated with euchromatin positively modulate the function of heterochromatin by distinct mechanisms.We discuss how euchromatic histone modifiers can make negative as well as positive contributions to gene silencing by competing with heterochromatin proteins within heterochromatin, within euchromatin, and at the boundary between euchromatin and heterochromatin.

View Article: PubMed Central - HTML - PubMed

Affiliation: Fred van Leeuwen, Division of Gene Regulation B4, Netherlands Cancer Institute, The Netherlands. k.verzijlbergen@nki.nl

ABSTRACT

Background: Methylation of lysine 79 on histone H3 by Dot1 is required for maintenance of heterochromatin structure in yeast and humans. However, this histone modification occurs predominantly in euchromatin. Thus, Dot1 affects silencing by indirect mechanisms and does not act by the recruitment model commonly proposed for histone modifications. To better understand the role of H3K79 methylation gene silencing, we investigated the silencing function of Dot1 by genetic suppressor and enhancer analysis and examined the relationship between Dot1 and other global euchromatic histone modifiers.

Result: We determined that loss of H3K79 methylation results in a partial silencing defect that could be bypassed by conditions that promote targeting of Sir proteins to heterochromatin. Furthermore, the silencing defect in strains lacking Dot1 was dependent on methylation of H3K4 by Set1 and histone acetylation by Gcn5, Elp3, and Sas2 in euchromatin. Our study shows that multiple histone modifications associated with euchromatin positively modulate the function of heterochromatin by distinct mechanisms. Genetic interactions between Set1 and Set2 suggested that the H3K36 methyltransferase Set2, unlike most other euchromatic modifiers, negatively affects gene silencing.

Conclusion: Our genetic dissection of Dot1's role in silencing in budding yeast showed that heterochromatin formation is modulated by multiple euchromatic histone modifiers that act by non-overlapping mechanisms. We discuss how euchromatic histone modifiers can make negative as well as positive contributions to gene silencing by competing with heterochromatin proteins within heterochromatin, within euchromatin, and at the boundary between euchromatin and heterochromatin.

Show MeSH
Related in: MedlinePlus