SIR proteins create compact heterochromatin fibers

Heterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins—S...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2018-12, Vol.115 (49), p.12447-12452
Main Authors: Swygert, Sarah G., Senapati, Subhadip, Bolukbasi, Mehmet F., Wolfe, Scot A., Lindsay, Stuart, Peterson, Craig L.
Format: Article
Language:English
Subjects:
Atomic force microscopy
Biological Sciences
Chromatin
Conformation
Deacetylation
Dimers
Dynamic stability
Fibers
Gene Expression Regulation, Fungal
Genomics
Heterochromatin
Heterochromatin - physiology
Histone H4
Histones
Lysine
Microscopy
Molecular modelling
Nucleosomes
Protein Binding
Proteins
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae - metabolism
Sedimentation
Silent Information Regulator Proteins, Saccharomyces cerevisiae - metabolism
Stoichiometry
Trimers
Yeast
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Summary:Heterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins—Sir3, believed to be the primary structural component of SIR heterochromatin, and the Sir2–4 complex, responsible for the targeted recruitment of SIR proteins and the deacetylation of lysine 16 of histone H4. Previously, we found that Sir3 binds but does not compact nucleosomal arrays. Here we reconstitute chromatin fibers with the complete complement of SIR proteins and use sedimentation velocity, molecular modeling, and atomic force microscopy to characterize the stoichiometry and conformation of SIR chromatin fibers. In contrast to fibers with Sir3 alone, our results demonstrate that SIR arrays are highly compact. Strikingly, the condensed structure of SIR heterochromatin fibers requires both the integrity of H4K16 and an interaction between Sir3 and Sir4. We propose a model in which a dimer of Sir3 bridges and stabilizes two adjacent nucleosomes, while a Sir2–4 heterotetramer interacts with Sir3 associated with a nucleosomal trimer, driving fiber compaction.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1810647115