Limits...
Proteomic and genomic characterization of chromatin complexes at a boundary.

Tackett AJ, Dilworth DJ, Davey MJ, O'Donnell M, Aitchison JD, Rout MP, Chait BT - J. Cell Biol. (2005)

Bottom Line: We have dissected specialized assemblies on the Saccharomyces cerevisiae genome that help define and preserve the boundaries that separate silent and active chromatin.The complexes consist of at least 15 chromatin-associated proteins, including DNA pol epsilon, the Isw2-Itc1 and Top2 chromatin remodeling proteins, the Sas3-Spt16 chromatin modifying complex, and Yta7, a bromodomain-containing AAA ATPase.We show that these complexes are important for the faithful maintenance of an established boundary, as disruption of the complexes results in specific, anomalous alterations of the silent and active epigenetic states.

View Article: PubMed Central - PubMed

Affiliation: Rockefeller University, New York, NY 10021, USA.

ABSTRACT
We have dissected specialized assemblies on the Saccharomyces cerevisiae genome that help define and preserve the boundaries that separate silent and active chromatin. These assemblies contain characteristic stretches of DNA that flank particular regions of silent chromatin, as well as five distinctively modified histones and a set of protein complexes. The complexes consist of at least 15 chromatin-associated proteins, including DNA pol epsilon, the Isw2-Itc1 and Top2 chromatin remodeling proteins, the Sas3-Spt16 chromatin modifying complex, and Yta7, a bromodomain-containing AAA ATPase. We show that these complexes are important for the faithful maintenance of an established boundary, as disruption of the complexes results in specific, anomalous alterations of the silent and active epigenetic states.

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A model for the roles of the Dpb4-associated complexes at a chromatin boundary. The mating genes at HMR are contained within a region flanked by Orc complexes and transcriptionally silenced through the binding of Sir proteins. The Dpb4-containing pol ɛ and chromatin modifying/remodeling complexes associate with boundary regions where they bind distinctively modified histones. The pol ɛ complex aids in duplication of the silent chromatin, whereas the Dpb4-chromatin remodeling complex preserves the boundaries. Precise protein positions and their oligomeric states have not been determined.
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fig8: A model for the roles of the Dpb4-associated complexes at a chromatin boundary. The mating genes at HMR are contained within a region flanked by Orc complexes and transcriptionally silenced through the binding of Sir proteins. The Dpb4-containing pol ɛ and chromatin modifying/remodeling complexes associate with boundary regions where they bind distinctively modified histones. The pol ɛ complex aids in duplication of the silent chromatin, whereas the Dpb4-chromatin remodeling complex preserves the boundaries. Precise protein positions and their oligomeric states have not been determined.

Mentions: Our findings support a multifunctional role for the Dpb4-containing pol ɛ and Dpb4-chromatin remodeling complexes at HMR (Fig. 8). We suggest that duplication of the silent state is aided by association of pol ɛ with the silent region during times of DNA replication (Fig. 7 A); alterations in the composition of pol ɛ, such as deletion of DPB3, result in mislocalization of the polymerase (Fig. 4 D) and inefficient replication of the silent state (Fig. 6, A and B). The duplication defect associated with removing Dpb3 from pol ɛ appears to be dependent on the amount of silent chromatin that needs to be duplicated. We speculate that normally partially mislocalized pol ɛ can still operate because WT levels of silent chromatin evidently do not overwhelm the polymerase. However, when the amount of silent chromatin is significantly increased by excess Sir3, the duplication capacity of the mislocalized polymerase becomes overwhelmed (Fig. 6, A and B). Correct propagation of the silent state also requires the maintenance of boundaries that separate transcriptionally active and silent chromatin. The chromatin remodeling complex, which remains associated with chromatin throughout the cell cycle (Fig. 7 B), appears to help maintain these boundary regions, preventing spreading of the silent state beyond the boundaries and into transcriptionally active regions (Fig. 6). Thus, the cell appears to use two functionally different systems, coordinated at similar locations, to provide for propagation and maintenance of silent chromatin. Moreover, these boundary complexes have dual “yin-yang” roles; they preserve both the silent state of the chromatin within the boundaries and the active state of the chromatin outside of the boundaries.


Proteomic and genomic characterization of chromatin complexes at a boundary.

Tackett AJ, Dilworth DJ, Davey MJ, O'Donnell M, Aitchison JD, Rout MP, Chait BT - J. Cell Biol. (2005)

A model for the roles of the Dpb4-associated complexes at a chromatin boundary. The mating genes at HMR are contained within a region flanked by Orc complexes and transcriptionally silenced through the binding of Sir proteins. The Dpb4-containing pol ɛ and chromatin modifying/remodeling complexes associate with boundary regions where they bind distinctively modified histones. The pol ɛ complex aids in duplication of the silent chromatin, whereas the Dpb4-chromatin remodeling complex preserves the boundaries. Precise protein positions and their oligomeric states have not been determined.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2171912&req=5

fig8: A model for the roles of the Dpb4-associated complexes at a chromatin boundary. The mating genes at HMR are contained within a region flanked by Orc complexes and transcriptionally silenced through the binding of Sir proteins. The Dpb4-containing pol ɛ and chromatin modifying/remodeling complexes associate with boundary regions where they bind distinctively modified histones. The pol ɛ complex aids in duplication of the silent chromatin, whereas the Dpb4-chromatin remodeling complex preserves the boundaries. Precise protein positions and their oligomeric states have not been determined.
Mentions: Our findings support a multifunctional role for the Dpb4-containing pol ɛ and Dpb4-chromatin remodeling complexes at HMR (Fig. 8). We suggest that duplication of the silent state is aided by association of pol ɛ with the silent region during times of DNA replication (Fig. 7 A); alterations in the composition of pol ɛ, such as deletion of DPB3, result in mislocalization of the polymerase (Fig. 4 D) and inefficient replication of the silent state (Fig. 6, A and B). The duplication defect associated with removing Dpb3 from pol ɛ appears to be dependent on the amount of silent chromatin that needs to be duplicated. We speculate that normally partially mislocalized pol ɛ can still operate because WT levels of silent chromatin evidently do not overwhelm the polymerase. However, when the amount of silent chromatin is significantly increased by excess Sir3, the duplication capacity of the mislocalized polymerase becomes overwhelmed (Fig. 6, A and B). Correct propagation of the silent state also requires the maintenance of boundaries that separate transcriptionally active and silent chromatin. The chromatin remodeling complex, which remains associated with chromatin throughout the cell cycle (Fig. 7 B), appears to help maintain these boundary regions, preventing spreading of the silent state beyond the boundaries and into transcriptionally active regions (Fig. 6). Thus, the cell appears to use two functionally different systems, coordinated at similar locations, to provide for propagation and maintenance of silent chromatin. Moreover, these boundary complexes have dual “yin-yang” roles; they preserve both the silent state of the chromatin within the boundaries and the active state of the chromatin outside of the boundaries.

Bottom Line: We have dissected specialized assemblies on the Saccharomyces cerevisiae genome that help define and preserve the boundaries that separate silent and active chromatin.The complexes consist of at least 15 chromatin-associated proteins, including DNA pol epsilon, the Isw2-Itc1 and Top2 chromatin remodeling proteins, the Sas3-Spt16 chromatin modifying complex, and Yta7, a bromodomain-containing AAA ATPase.We show that these complexes are important for the faithful maintenance of an established boundary, as disruption of the complexes results in specific, anomalous alterations of the silent and active epigenetic states.

View Article: PubMed Central - PubMed

Affiliation: Rockefeller University, New York, NY 10021, USA.

ABSTRACT
We have dissected specialized assemblies on the Saccharomyces cerevisiae genome that help define and preserve the boundaries that separate silent and active chromatin. These assemblies contain characteristic stretches of DNA that flank particular regions of silent chromatin, as well as five distinctively modified histones and a set of protein complexes. The complexes consist of at least 15 chromatin-associated proteins, including DNA pol epsilon, the Isw2-Itc1 and Top2 chromatin remodeling proteins, the Sas3-Spt16 chromatin modifying complex, and Yta7, a bromodomain-containing AAA ATPase. We show that these complexes are important for the faithful maintenance of an established boundary, as disruption of the complexes results in specific, anomalous alterations of the silent and active epigenetic states.

Show MeSH
Related in: MedlinePlus