Histone Acetylation, Not Stoichiometry, Regulates Linker Histone Binding in Saccharomyces cerevisiae

Abstract Chromosome structure at the multi-nucleosomal level has remained ambiguous in spite of its central role in epigenetic regulation and genome dynamics. Recent investigations of chromatin architecture portray diverse modes of interaction within and between nucleosome chains, but how this is realized at the atomic level is unclear. Here we present near-atomic resolution crystal structures of nucleosome fibres that assemble from cohesive-ended dinucleosomes with and without linker histone. As opposed to adopting folded helical ‘30 nm’ structures, the fibres instead assume open zigzag conformations that are interdigitated with one another. Zigzag conformations obviate extreme bending of the linker DNA, while linker DNA size (nucleosome repeat length) dictates fibre configuration and thus fibre–fibre packing, which is supported by variable linker histone binding. This suggests that nucleosome chains have a predisposition to interdigitate with specific characteristics under condensing conditions, which rationalizes observations of local chromosome architecture and the general heterogeneity of chromatin structure.

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Genome-Wide Relationships between TAF1 and Histone Acetyltransferases in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.26.7.2791-2802.2006 ◽

2006 ◽

Vol 26 (7) ◽

pp. 2791-2802 ◽

Cited By ~ 36

Author(s):

Melissa Durant ◽

B. Franklin Pugh

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Histone Acetylation ◽

Rna Polymerase Ii ◽

Histone Acetyltransferases ◽

Histone H4 ◽

Promoter Regions ◽

Genome Wide ◽

Acetylated Histone H4

ABSTRACT Histone acetylation regulates gene expression, yet the functional contributions of the numerous histone acetyltransferases (HATs) to gene expression and their relationships with each other remain largely unexplored. The central role of the putative HAT-containing TAF1 subunit of TFIID in gene expression raises the fundamental question as to what extent, if any, TAF1 contributes to acetylation in vivo and to what extent it is redundant with other HATs. Our findings herein do not support the basic tenet that TAF1 is a major HAT in Saccharomyces cerevisiae, nor do we find that TAF1 is functionally redundant with other HATs, including Gcn5, Elp3, Hat1, Hpa2, Sas3, and Esa1, which is in contrast to previous conclusions regarding Gcn5. Our findings do reveal that of these HATs, only Gcn5 and Esa1 contribute substantially to gene expression genome wide. Interestingly, histone acetylation at promoter regions throughout the genome does not require TAF1 or RNA polymerase II, indicating that most acetylation is likely to precede transcription and not depend upon it. TAF1 function has been linked to Bdf1, which binds TFIID and acetylated histone H4 tails, but no linkage between TAF1 and the H4 HAT Esa1 has been established. Here, we present evidence for such a linkage through Bdf1.

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Evolutionary Conservation Levels of Subunits of Histone-Modifying Protein Complexes in Fungi

Comparative and Functional Genomics ◽

10.1155/2009/379317 ◽

2009 ◽

Vol 2009 ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

Hiromi Nishida

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone Acetylation ◽

Histone Methylation ◽

Protein Complex ◽

Histone Acetyltransferase ◽

Protein Complexes ◽

Evolutionary Conservation ◽

Catalytic Subunits ◽

Evolutionary Lineage ◽

Conservation Level

Eukaryotes possess a variety of histone-modifying protein complexes. Generally, a histone-modifying protein complex consists of multiple subunits, that is, a catalytic subunit and the associated subunits. In this study, I analyzed 62 and 48 subunits of the histone-modifying protein complexes ofSaccharomyces cerevisiaeandSchizosaccharomyces pombe, respectively. The evolutionary conservation levels of the 110 subunits were measured. The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes. Thus, in the fungal histone acetylation and deacetylation systems, the catalytic subunits of histone-modifying protein complexes are conserved and the associated subunits are evolutionary lineage-specific. In contrast, in the fungal histone methylation system, both the catalytic and the associated subunits are evolutionary lineage-specific.

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‐The Influence of Histone Variant H2A.Z and Linker Histone H1 on Saccharomyces cerevisiae Meiosis

The FASEB Journal ◽

10.1096/fasebj.2020.34.s1.06049 ◽

2020 ◽

Vol 34 (S1) ◽

pp. 1-1

Author(s):

Lorencia Chigweshe ◽

Amy MacQueen ◽

Scott Holmes

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone H1 ◽

Linker Histone ◽

Histone Variant ◽

Linker Histone H1

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Structure of the human histone chaperone FACT Spt16 N-terminal domain

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x15024565 ◽

2016 ◽

Vol 72 (2) ◽

pp. 121-128 ◽

Cited By ~ 8

Author(s):

G. Marcianò ◽

D. T. Huang

Keyword(s):

Crystal Structure ◽

Saccharomyces Cerevisiae ◽

Complex Surface ◽

Histone Chaperone ◽

Titration Calorimetry ◽

Nucleosome Assembly ◽

Surface Residue ◽

Histone Binding ◽

Terminal Domain ◽

Heterodimeric Complex

The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of human Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of theSaccharomyces cerevisiaeandSchizosaccharomyces pombeSpt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding.

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Promoter Occupancy Is a Major Determinant of Chromatin Remodeling Enzyme Requirements

Molecular and Cellular Biology ◽

10.1128/mcb.25.7.2698-2707.2005 ◽

2005 ◽

Vol 25 (7) ◽

pp. 2698-2707 ◽

Cited By ~ 35

Author(s):

Archana Dhasarathy ◽

Michael P. Kladde

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone Acetylation ◽

Binding Site ◽

Chromatin Remodeling ◽

Chromatin Immunoprecipitation ◽

Site Occupancy ◽

Major Determinant ◽

Activator Concentration ◽

Promoter Occupancy

ABSTRACT Chromatin creates transcriptional barriers that are overcome by coactivator activities such as histone acetylation by Gcn5 and ATP-dependent chromatin remodeling by SWI/SNF. Factors defining the differential coactivator requirements in the transactivation of various promoters remain elusive. Induction of the Saccharomyces cerevisiae PHO5 promoter does not require Gcn5 or SWI/SNF under fully inducing conditions of no phosphate. We show that PHO5 activation is highly dependent on both coactivators at intermediate phosphate concentrations, conditions that reduce the nuclear concentration of the Pho4 transactivator and severely diminish its association with PHO5 in the absence of Gcn5 or SWI/SNF. Conversely, physiological increases in Pho4 nuclear concentration and binding at PHO5 suppress the need for both Gcn5 and SWI/SNF, suggesting that coactivator redundancy is established at high Pho4 binding site occupancy. Consistent with this, we demonstrate, using chromatin immunoprecipitation, that Gcn5 and SWI/SNF are directly recruited to PHO5 and other strongly transcribed promoters, including GAL1-10, RPL19B, RPS22B, PYK1, and EFT2, which do not require either coactivator for expression. These results show that activator concentration and binding site occupancy play crucial roles in defining the extent to which transcription requires individual chromatin remodeling enzymes. In addition, Gcn5 and SWI/SNF associate with many more genomic targets than previously appreciated.

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