An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae

Abstract Fourteen novel single-amino-acid substitution mutations in histone H3 that disrupt telomeric silencing in Saccharomyces cerevisiae were identified, 10 of which are clustered within the α1 helix and L1 loop of the essential histone fold. Several of these mutations cause derepression of silent mating locus HML, and an additional subset cause partial loss of basal repression at the GAL1 promoter. Our results identify a new domain within the essential core of histone H3 that is required for heterochromatin-mediated silencing.

Download Full-text

Histone H3 transcription in Saccharomyces cerevisiae is controlled by multiple cell cycle activation sites and a constitutive negative regulatory element

Molecular and Cellular Biology ◽

10.1128/mcb.12.12.5455-5463.1992 ◽

1992 ◽

Vol 12 (12) ◽

pp. 5455-5463 ◽

Cited By ~ 1

Author(s):

K B Freeman ◽

L R Karns ◽

K A Lutz ◽

M M Smith

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Cycle ◽

Cell Division ◽

Transcriptional Activation ◽

Regulatory Element ◽

Histone H3 ◽

Regulatory Elements ◽

Cell Division Cycle ◽

Cell Cycle Activation ◽

Multiple Cell

The promoters of the Saccharomyces cerevisiae histone H3 and H4 genes were examined for cis-acting DNA sequence elements regulating transcription and cell division cycle control. Deletion and linker disruption mutations identified two classes of regulatory elements: multiple cell cycle activation (CCA) sites and a negative regulatory site (NRS). Duplicate 19-bp CCA sites are present in both the copy I and copy II histone H3-H4 promoters arranged as inverted repeats separated by 45 and 68 bp. The CCA sites are both necessary and sufficient to activate transcription under cell division cycle control. A single CCA site provides cell cycle control but is a weak transcriptional activator, while an inverted repeat comprising two CCA sites provides both strong transcriptional activation and cell division cycle control. The NRS was identified in the copy I histone H3-H4 promoter. Deletion or disruption of the NRS increased the level of the histone H3 promoter activity but did not alter the cell division cycle periodicity of transcription. When the CCA sites were deleted from the histone promoter, the NRS element was unable to confer cell division cycle control on the remaining basal level of transcription. When the NRS element was inserted into the promoter of a foreign reporter gene, transcription was constitutively repressed and did not acquire cell cycle regulation.

Download Full-text

Saccharomyces cerevisiae ubiquitin-like protein Rub1 conjugates to cullin proteins Rtt101 and Cul3 in vivo

Biochemical Journal ◽

10.1042/bj20030755 ◽

2004 ◽

Vol 377 (2) ◽

pp. 459-467 ◽

Cited By ~ 17

Author(s):

Jose M. LAPLAZA ◽

Magnolia BOSTICK ◽

Derek T. SCHOLES ◽

M. Joan CURCIO ◽

Judy CALLIS

Keyword(s):

Saccharomyces Cerevisiae ◽

Protein A ◽

Fold Increase ◽

Lysine Residue ◽

Reading Frame ◽

E3 Ligases ◽

C Terminus ◽

Dependent Modification ◽

F Box Protein

In Saccharomyces cerevisiae, the ubiquitin-like protein Rub1p (related to ubiquitin 1 protein) covalently attaches to the cullin protein Cdc53p (cell division cycle 53 protein), a subunit of a class of ubiquitin E3 ligases named SCF (Skp1–Cdc53–F-box protein) complex. We identified Rtt101p (regulator of Ty transposition 101 protein, where Ty stands for transposon of yeast), initially found during a screen for proteins to confer retrotransposition suppression, and Cul3p (cullin 3 protein), a protein encoded by the previously uncharacterized open reading frame YGR003w, as two new in vivo targets for Rub1p conjugation. These proteins show significant identity with Cdc53p and, therefore, are cullin proteins. Modification of Cul3p is eliminated by deletion of the Rub1p pathway through disruption of either RUB1 or its activating enzyme ENR2/ULA1. The same disruptions in the Rub pathway decreased the percentage of total Rtt101p that is modified from approx. 60 to 30%. This suggests that Rtt101p has an additional RUB1- and ENR2-independent modification. All modified forms of Rtt101p and Cul3p were lost when a single lysine residue in a conserved region near the C-terminus was replaced by an arginine residue. These results suggest that this lysine residue is the site of Rub1p-dependent and -independent modifications in Rtt101p and of Rub1p-dependent modification in Cul3p. An rtt101Δ strain was hypersensitive to thiabendazole, isopropyl (N-3-chlorophenyl) carbamate and methyl methanesulphonate, but rub1Δ strains were not. Whereas rtt101Δ strains exhibited a 14-fold increase in Ty1 transposition, isogenic rub1Δ strains did not show statistically significant increases. Rtt101K791Rp, which cannot be modified, complemented for Rtt101p function in a transposition assay. Altogether, these results suggest that neither the RUB1-dependent nor the RUB1-independent form of Rtt101p is required for Rtt101p function. The identification of additional Rub1p targets in S. cerevisiae suggests an expanded role for Rub in this organism.

Download Full-text

Dispersed Mutations in Histone H3 That Affect Transcriptional Repression and Chromatin Structure of the CHA1 Promoter in Saccharomyces cerevisiae

Eukaryotic Cell ◽

10.1128/ec.00233-08 ◽

2008 ◽

Vol 7 (10) ◽

pp. 1649-1660 ◽

Cited By ~ 7

Author(s):

Qiye He ◽

Cailin Yu ◽

Randall H. Morse

Keyword(s):

Saccharomyces Cerevisiae ◽

Chromatin Structure ◽

Transcriptional Repression ◽

Histone H3 ◽

Temperature Sensitive ◽

Active Chromatin ◽

Temperature Sensitive Mutants ◽

Nucleosome Structure ◽

Lysine Residues ◽

Chromatin Configuration

ABSTRACT The histone H3 amino terminus, but not that of H4, is required to prevent the constitutively bound activator Cha4 from remodeling chromatin and activating transcription at the CHA1 gene in Saccharomyces cerevisiae. Here we show that neither the modifiable lysine residues nor any specific region of the H3 tail is required for repression of CHA1. We then screened for histone H3 mutations that cause derepression of the uninduced CHA1 promoter and identified six mutants, three of which are also temperature-sensitive mutants and four of which exhibit a sin − phenotype. Histone mutant levels were similar to that of wild-type H3, and the mutations did not cause gross alterations in nucleosome structure. One specific and strongly derepressing mutation, H3 A111G, was examined in depth and found to cause a constitutively active chromatin configuration at the uninduced CHA1 promoter as well as at the ADH2 promoter. Transcriptional derepression and altered chromatin structure of the CHA1 promoter depend on the activator Cha4. These results indicate that modest perturbations in distinct regions of the nucleosome can substantially affect the repressive function of chromatin, allowing activation in the absence of a normal inducing signal (at CHA1) or of Swi/Snf (resulting in a sin − phenotype).

Download Full-text

Analysis of Saccharomyces cerevisiae histone H3 mutants reveals the role of the αN helix in nucleosome function

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2008.07.084 ◽

2008 ◽

Vol 374 (3) ◽

pp. 543-548 ◽

Cited By ~ 5

Author(s):

Ja-Hwan Seol ◽

Hye-Jin Kim ◽

Ja-Kyung Yoo ◽

Hyun-Ju Park ◽

Eun-Jung Cho

Keyword(s):

Saccharomyces Cerevisiae ◽

Histone H3

Download Full-text

Global Replication-Independent Histone H4 Exchange in Budding Yeast

Eukaryotic Cell ◽

10.1128/ec.00202-06 ◽

2006 ◽

Vol 5 (10) ◽

pp. 1780-1787 ◽

Cited By ~ 19

Author(s):

Jeffrey Linger ◽

Jessica K. Tyler

Keyword(s):

Saccharomyces Cerevisiae ◽

Cell Cycle ◽

Dna Replication ◽

Budding Yeast ◽

Histone H3 ◽

Eukaryotic Genome ◽

Histone H4 ◽

Histone Proteins ◽

Dynamic Exchange ◽

Histone Exchange

ABSTRACT The eukaryotic genome is packaged together with histone proteins into chromatin following DNA replication. Recent studies have shown that histones can also be assembled into chromatin independently of DNA replication and that this dynamic exchange of histones may be biased toward sites undergoing transcription. Here we show that epitope-tagged histone H4 can be incorporated into nucleosomes throughout the budding yeast (Saccharomyces cerevisiae) genome regardless of the phase of the cell cycle, the transcriptional status, or silencing of the region. Direct comparisons reveal that the amount of histone incorporation that occurs in G1-arrested cells is similar to that occurring in cells undergoing DNA replication. Additionally, we show that this histone incorporation is not dependent on the histone H3/H4 chaperones CAF-1, Asf1, and Hir1 individually. This study demonstrates that DNA replication and transcription are not necessary prerequisites for histone exchange in budding yeast, indicating that chromatin is more dynamic than previously thought.

Download Full-text

Mutational Analysis of the Sir3 BAH Domain Reveals Multiple Points of Interaction with Nucleosomes

Molecular and Cellular Biology ◽

10.1128/mcb.01682-08 ◽

2009 ◽

Vol 29 (10) ◽

pp. 2532-2545 ◽

Cited By ~ 29

Author(s):

Vinaya Sampath ◽

Peihua Yuan ◽

Isabel X. Wang ◽

Evelyn Prugar ◽

Fred van Leeuwen ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Mutational Analysis ◽

Histone H3 ◽

Transcriptional Silencing ◽

In Vitro Experiments ◽

Multiple Points ◽

Alanine Residue ◽

Bah Domain ◽

Multiple Domains

ABSTRACT Sir3, a component of the transcriptional silencing complex in the yeast Saccharomyces cerevisiae, has an N-terminal BAH domain that is crucial for the protein's silencing function. Previous work has shown that the N-terminal alanine residue of Sir3 (Ala2) and its acetylation play an important role in silencing. Here we show that the silencing defects of Sir3 Ala2 mutants can be suppressed by mutations in histones H3 and H4, specifically, by H3 D77N and H4 H75Y mutations. Additionally, a mutational analysis demonstrates that three separate regions of the Sir3 BAH domain are important for its role in silencing. Many of these BAH mutations also can be suppressed by the H3 D77N and H4 H75Y mutations. In agreement with the results of others, in vitro experiments show that the Sir3 BAH domain can interact with partially purified nucleosomes. The silencing-defective BAH mutants are defective for this interaction. These results, together with the previously characterized interaction between the C-terminal region of Sir3 and the histone H3/H4 tails, suggest that Sir3 utilizes multiple domains to interact with nucleosomes.

Download Full-text