Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres

Sarah G. Swygert; Benjamin J. Manning; Subhadip Senapati; Parminder Kaur; Stuart Lindsay; Borries Demeler; Craig L. Peterson

doi:10.1038/ncomms5751

Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres

Sarah G. Swygert
, Benjamin J. Manning
, Subhadip Senapati
, Parminder Kaur
, Stuart Lindsay
, Borries Demeler
, Craig L. Peterson

Chemistry and Biochemistry

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

Heterochromatin is a repressive chromatin compartment essential for maintaining genomic integrity. A hallmark of heterochromatin is the presence of specialized nonhistone proteins that alter chromatin structure to inhibit transcription and recombination. It is generally assumed that heterochromatin is highly condensed. However, surprisingly little is known about the structure of heterochromatin or its dynamics in solution. In budding yeast, formation of heterochromatin at telomeres and the homothallic silent mating type loci require the Sir3 protein. Here, we use a combination of sedimentation velocity, atomic force microscopy and nucleosomal array capture to characterize the stoichiometry and conformation of Sir3 nucleosomal arrays. The results indicate that Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome. We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres. We suggest that heterochromatin proteins promote silencing by 'coating' nucleosomal arrays, stabilizing interactions between nucleosomal histones and DNA.

Original language	English
Article number	4751
Journal	Nature Communications
Volume	5
DOIs	https://doi.org/10.1038/ncomms5751
State	Published - Aug 28 2014

Funding

We thank Kimberly Crowley for assistance with SV-AUC studies, and other members of the Peterson laboratory for helpful discussions. The Sir3 BAH D205N expression construct was a generous gift from Rolf Sternglanz and Robert Kingston. This work was supported by grants from the NIH to C.L.P. (GM54096) and from the NCI to S.L. (U54 CA143862). We also acknowledge grants to B.D. from the National Science Foundation (NSF-DAC-1339649) for supporting the UltraScan XSEDE Science Gateway integration, and NSF Teragrid TG-MCB070039 for supporting the cycles used for calculations.

Funder number
NSF-DAC-1339649, TG-MCB070039
GM54096
U54CA143862

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10.1038/ncomms5751

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title = "Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres",

abstract = "Heterochromatin is a repressive chromatin compartment essential for maintaining genomic integrity. A hallmark of heterochromatin is the presence of specialized nonhistone proteins that alter chromatin structure to inhibit transcription and recombination. It is generally assumed that heterochromatin is highly condensed. However, surprisingly little is known about the structure of heterochromatin or its dynamics in solution. In budding yeast, formation of heterochromatin at telomeres and the homothallic silent mating type loci require the Sir3 protein. Here, we use a combination of sedimentation velocity, atomic force microscopy and nucleosomal array capture to characterize the stoichiometry and conformation of Sir3 nucleosomal arrays. The results indicate that Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome. We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres. We suggest that heterochromatin proteins promote silencing by 'coating' nucleosomal arrays, stabilizing interactions between nucleosomal histones and DNA.",

author = "Swygert, \{Sarah G.\} and Manning, \{Benjamin J.\} and Subhadip Senapati and Parminder Kaur and Stuart Lindsay and Borries Demeler and Peterson, \{Craig L.\}",

note = "Funding Information: We thank Kimberly Crowley for assistance with SV-AUC studies, and other members of the Peterson laboratory for helpful discussions. The Sir3 BAH D205N expression construct was a generous gift from Rolf Sternglanz and Robert Kingston. This work was supported by grants from the NIH to C.L.P. (GM54096) and from the NCI to S.L. (U54 CA143862). We also acknowledge grants to B.D. from the National Science Foundation (NSF-DAC-1339649) for supporting the UltraScan XSEDE Science Gateway integration, and NSF Teragrid TG-MCB070039 for supporting the cycles used for calculations.",

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doi = "10.1038/ncomms5751",

language = "English",

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AU - Swygert, Sarah G.

AU - Manning, Benjamin J.

AU - Senapati, Subhadip

AU - Kaur, Parminder

AU - Lindsay, Stuart

AU - Demeler, Borries

AU - Peterson, Craig L.

N1 - Funding Information: We thank Kimberly Crowley for assistance with SV-AUC studies, and other members of the Peterson laboratory for helpful discussions. The Sir3 BAH D205N expression construct was a generous gift from Rolf Sternglanz and Robert Kingston. This work was supported by grants from the NIH to C.L.P. (GM54096) and from the NCI to S.L. (U54 CA143862). We also acknowledge grants to B.D. from the National Science Foundation (NSF-DAC-1339649) for supporting the UltraScan XSEDE Science Gateway integration, and NSF Teragrid TG-MCB070039 for supporting the cycles used for calculations.

PY - 2014/8/28

Y1 - 2014/8/28

N2 - Heterochromatin is a repressive chromatin compartment essential for maintaining genomic integrity. A hallmark of heterochromatin is the presence of specialized nonhistone proteins that alter chromatin structure to inhibit transcription and recombination. It is generally assumed that heterochromatin is highly condensed. However, surprisingly little is known about the structure of heterochromatin or its dynamics in solution. In budding yeast, formation of heterochromatin at telomeres and the homothallic silent mating type loci require the Sir3 protein. Here, we use a combination of sedimentation velocity, atomic force microscopy and nucleosomal array capture to characterize the stoichiometry and conformation of Sir3 nucleosomal arrays. The results indicate that Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome. We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres. We suggest that heterochromatin proteins promote silencing by 'coating' nucleosomal arrays, stabilizing interactions between nucleosomal histones and DNA.

AB - Heterochromatin is a repressive chromatin compartment essential for maintaining genomic integrity. A hallmark of heterochromatin is the presence of specialized nonhistone proteins that alter chromatin structure to inhibit transcription and recombination. It is generally assumed that heterochromatin is highly condensed. However, surprisingly little is known about the structure of heterochromatin or its dynamics in solution. In budding yeast, formation of heterochromatin at telomeres and the homothallic silent mating type loci require the Sir3 protein. Here, we use a combination of sedimentation velocity, atomic force microscopy and nucleosomal array capture to characterize the stoichiometry and conformation of Sir3 nucleosomal arrays. The results indicate that Sir3 interacts with nucleosomal arrays with a stoichiometry of two Sir3 monomers per nucleosome. We also find that Sir3 fibres are less compact than canonical magnesium-induced 30 nm fibres. We suggest that heterochromatin proteins promote silencing by 'coating' nucleosomal arrays, stabilizing interactions between nucleosomal histones and DNA.

UR - https://www.scopus.com/pages/publications/84907320786

U2 - 10.1038/ncomms5751

DO - 10.1038/ncomms5751

M3 - Article

C2 - 25163529

AN - SCOPUS:84907320786

SN - 2041-1723

VL - 5

JO - Nature Communications

JF - Nature Communications

M1 - 4751

ER -

Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres

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