scholarly journals Asymmetric Positioning of Nucleosomes and Directional Establishment of Transcriptionally Silent Chromatin by Saccharomyces cerevisiae Silencers

2006 ◽  
Vol 26 (20) ◽  
pp. 7806-7819 ◽  
Author(s):  
Yanfei Zou ◽  
Qun Yu ◽  
Xin Bi
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Origin Recognition Complex ◽  
Transcriptional Silencing ◽  
Nucleosome Positioning ◽  
Silent Chromatin ◽  
Genomic Context ◽  
Independent Manner ◽  
Sir Proteins ◽  
Sir Complex ◽  
Asymmetrically Distributed

ABSTRACT In Saccharomyces cerevisiae, silencers flanking the HML and HMR loci consist of various combinations of binding sites for Abf1p, Rap1p, and the origin recognition complex (ORC) that serve to recruit the Sir silencing complex, thereby initiating the establishment of transcriptionally silent chromatin. There have been seemingly conflicting reports concerning whether silencers function in an orientation-dependent or -independent manner, and what determines the directionality of a silencer has not been explored. We demonstrate that chromatin plays a key role in determining the potency and directionality of silencers. We show that nucleosomes are asymmetrically distributed around the HML-I or HMR-E silencer so that a nucleosome is positioned close to the Abf1p side but not the ORC side of the silencer. This coincides with preferential association of Sir proteins and transcriptional silencing on the Abf1p side of the silencer. Elimination of the asymmetry in nucleosome positioning at a silencer leads to comparable silencing on both sides. Asymmetric nucleosome positioning in the immediate vicinity of a silencer is independent of its orientation and genomic context, indicating that it is the inherent property of the silencer. Moreover, it is also independent of the Sir complex and thus precedes the formation of silent chromatin. Finally, we demonstrate that asymmetric positioning of nucleosomes and directional silencing by a silencer depend on ORC and Abf1p. We conclude that the HML-I and HMR-E silencers promote asymmetric positioning of nucleosomes, leading to unequal potentials of transcriptional silencing on their sides and, hence, directional silencing.

scholarly journals Reinventing Heterochromatin in Budding Yeasts: Sir2 and the Origin Recognition Complex Take Center Stage

2011 ◽  
Vol 10 (9) ◽  
pp. 1183-1192 ◽  
Author(s):  
Meleah A. Hickman ◽  
Cara A. Froyd ◽  
Laura N. Rusche
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Schizosaccharomyces Pombe ◽  
Mating Type ◽  
Origin Recognition Complex ◽  
Transcriptional Silencing ◽  
Gene Duplications ◽  
Heterochromatin Protein 1 ◽  
Heterochromatin Protein ◽  
Content Type ◽  
Sir Proteins

ABSTRACTThe transcriptional silencing of the cryptic mating-type loci inSaccharomyces cerevisiaeis one of the best-studied models of repressive heterochromatin. However, this type of heterochromatin, which is mediated by the Sir proteins, has a distinct molecular composition compared to the more ubiquitous type of heterochromatin found inSchizosaccharomyces pombe, other fungi, animals, and plants and characterized by the presence of HP1 (heterochromatin protein 1). This review discusses how the loss of important heterochromatin proteins, including HP1, in the budding yeast lineage presented an evolutionary opportunity for the development and diversification of alternative varieties of heterochromatin, in which the conserved deacetylase Sir2 and the replication protein Orc1 play key roles. In addition, we highlight how this diversification has been facilitated by gene duplications and has contributed to adaptations in lifestyle.

scholarly journals A Novel Form of Transcriptional Silencing by Sum1-1 Requires Hst1 and the Origin Recognition Complex

2001 ◽  
Vol 21 (10) ◽  
pp. 3514-3522 ◽  
Author(s):  
Ann Sutton ◽  
Ryan C. Heller ◽  
Joseph Landry ◽  
Jennifer S. Choy ◽  
Agnieszka Sirko ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Origin Recognition Complex ◽  
Chromatin Condensation ◽  
Transcriptional Silencing ◽  
The Novel ◽  
Dominant Mutation ◽  
Sir Proteins ◽  
Associated Proteins ◽  
Type Information ◽  
Origin Recognition

ABSTRACT In the yeast Saccharomyces cerevisiae, a and α mating-type information is stored in transcriptionally silenced cassettes called HML and HMR. Silencing of these loci, maintained by the formation of a specialized type of heterochromatin, requires trans-acting proteins andcis-acting elements. Proteins required for silencing include the Sir2 NAD+-dependent deacetylase, Sir3, and Sir4. Factors that bind to the cis elements atHMR and HML and that are important for silencing include the origin recognition complex (ORC). Mutations of any of these Sir proteins or combinations of cis elements result in loss of silencing. SUM1-1 was previously identified as a dominant mutation that restores silencing toHMR in the absence of either the Sir proteins or some of the cis elements. We have investigated the novel mechanism whereby Sum1-1 causes Sir-independent silencing at HMR and present the following findings: Sum1-1 requires the Sir2 homolog, Hst1, for silencing and most probably requires the NAD+-dependent deacetylase activity of this protein. Sum1-1 interacts strongly with ORC, and this strong interaction is dependent on HMR DNA. Furthermore, ORC is required for Sum1-1-mediated silencing atHMR. These observations lead to a model for Sum1-1 silencing of HMR in which Sum1-1 is recruited toHMR by binding to ORC. Sum1-1, in turn, recruits Hst1. Hst1 then deacetylates histones or other chromatin-associated proteins to cause chromatin condensation and transcriptional silencing.

scholarly journals Sum1p, the Origin Recognition Complex, and the Spreading of a Promoter-Specific Repressor in Saccharomyces cerevisiae

2005 ◽  
Vol 25 (14) ◽  
pp. 5920-5932 ◽  
Author(s):  
Patrick J. Lynch ◽  
Hunter B. Fraser ◽  
Elena Sevastopoulos ◽  
Jasper Rine ◽  
Laura N. Rusche
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Origin Recognition Complex ◽  
Single Amino Acid ◽  
Wild Type ◽  
Genomic Context ◽  
Functional Connection ◽  
Histone Tails ◽  
Repressive Chromatin ◽  
Single Amino Acid Change ◽  
Origin Recognition

ABSTRACT In Saccharomyces cerevisiae, Sum1p is a promoter-specific repressor. A single amino acid change generates the mutant Sum1-1p, which causes regional silencing at new loci where wild-type Sum1p does not act. Thus, Sum1-1p is a model for understanding how the spreading of repressive chromatin is regulated. When wild-type Sum1p was targeted to a locus where mutant Sum1-1p spreads, wild-type Sum1p did not spread as efficiently as mutant Sum1-1p did, despite being in the same genomic context. Thus, the SUM1-1 mutation altered the ability of the protein to spread. The spreading of Sum1-1p required both an enzymatically active deacetylase, Hst1p, and the N-terminal tail of histone H4, consistent with the spreading of Sum1-1p involving sequential modification of and binding to histone tails, as observed for other silencing proteins. Furthermore, deletion of the N-terminal tail of H4 caused Sum1-1p to return to loci where wild-type Sum1p acts, consistent with the SUM1-1 mutation increasing the affinity of the protein for H4 tails. These results imply that the spreading of repressive chromatin proteins is regulated by their affinities for histone tails. Finally, this study uncovered a functional connection between wild-type Sum1p and the origin recognition complex, and this relationship also contributes to mutant Sum1-1p localization.

scholarly journals The Origin Recognition Complex and Sir4 Protein Recruit Sir1p to Yeast Silent Chromatin through Independent Interactions Requiring a Common Sir1p Domain

2004 ◽  
Vol 24 (2) ◽  
pp. 774-786 ◽  
Author(s):  
Melissa E. Bose ◽  
Kristopher H. McConnell ◽  
Kelly A. Gardner-Aukema ◽  
Ulrika Müller ◽  
Michael Weinreich ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Origin Recognition Complex ◽  
Amino Acid Substitutions ◽  
Silent Chromatin ◽  
Type Locus ◽  
Defective Region ◽  
And Function ◽  
Necessary And Sufficient ◽  
Discrete Domain ◽  
Origin Recognition

ABSTRACT Sir1p is one of four SIR (silent information regulator) proteins required for silencing the cryptic mating-type locus HMR a in the budding yeast Saccharomyces cerevisiae. A Sir1p interaction with Orc1p, the largest subunit of the origin recognition complex (ORC), is critical for Sir1p's ability to bind HMR a and function in the formation of silent chromatin. Here we show that a discrete domain within Sir1p, the ORC interaction region (OIR), was necessary and sufficient for a Sir1p-ORC interaction. The OIR contains the originally defined silencer recognition-defective region as well as additional amino acids. In addition, a Sir1p-Sir4p interaction required a larger region of Sir1p that included the OIR. Amino acid substitutions causing defects in either a Sir1p-Orc1p or a Sir1p-Sir4p interaction reduced HMR a silencing and Sir1p binding to HMR a in chromatin. These data support a model in which Sir1p's association with HMR a is mediated by separable Sir1p-ORC and Sir1p-Sir4p interactions requiring a common Sir1p domain, and they indicate that a Sir1p-ORC interaction is restricted to silencers, at least in part, through interactions with Sir4p.

scholarly journals SUM1-1, a dominant suppressor of SIR mutations in Saccharomyces cerevisiae, increases transcriptional silencing at telomeres and HM mating-type loci and decreases chromosome stability.

1996 ◽  
Vol 16 (8) ◽  
pp. 4281-4294 ◽  
Author(s):  
M H Chi ◽  
D Shore
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Transcriptional Silencing ◽  
Chromosome Loss ◽  
Yeast Saccharomyces Cerevisiae ◽  
Sir Proteins ◽  
Telomere Binding Protein ◽  
Single Allele ◽  
Dominant Suppressor

Transcriptional silencing in the yeast Saccharomyces cerevisiae occurs at HML and HMR mating-type loci and telomeres and requires the products of the silent information regulator (SIR) genes. Recent evidence suggests that the silencer- and telomere-binding protein Rap1p initiates silencing by recruiting a complex of Sir proteins to the chromosome, where they act in some way to modify chromatin structure or accessibility. A single allele of the SUM1gene (SUM1-1) which restores silencing at HM loci in strains mutant for any of the four SIR genes was identified a number of years ago. However, conflicting genetic results and the lack of other alleles of SUM1 made it difficult to surmise the wild-type function of SUM1 or the manner in which the SUM1-1 mutation restores silencing in sir mutant strains. Here we report the cloning and characterization of the SUM1 gene and the SUM1-1 mutant allele. Our results indicate that SUM1-1 is an unusual altered-function mutation that can bypass the need for SIR function in HM silencing and increase repression at telomeres. A sum1 deletion mutation has only minor effects on silencing in SIR strains and does not restore silencing in sir mutants. In addition to its effect on transcriptional silencing, the SUM1-1 mutation (but not a sum1 deletion) increases the rate of chromosome loss and cell death. We suggest several speculative models for the action of SUM1-1 in silencing based on these and other data.

scholarly journals Sir3-Nucleosome Interactions in Spreading of Silent Chromatin in Saccharomyces cerevisiae

2008 ◽  
Vol 28 (22) ◽  
pp. 6903-6918 ◽  
Author(s):  
Johannes R. Buchberger ◽  
Megumi Onishi ◽  
Geng Li ◽  
Jan Seebacher ◽  
Adam D. Rudner ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Binding Activity ◽  
Chromatin Fiber ◽  
Silent Chromatin ◽  
Histone H4 ◽  
Histone Binding ◽  
Aaa Atpase ◽  
Binding Domains ◽  
Sir Complex

ABSTRACT Silent chromatin in Saccharomyces cerevisiae is established in a stepwise process involving the SIR complex, comprised of the histone deacetylase Sir2 and the structural components Sir3 and Sir4. The Sir3 protein, which is the primary histone-binding component of the SIR complex, forms oligomers in vitro and has been proposed to mediate the spreading of the SIR complex along the chromatin fiber. In order to analyze the role of Sir3 in the spreading of the SIR complex, we performed a targeted genetic screen for alleles of SIR3 that dominantly disrupt silencing. Most mutations mapped to a single surface in the conserved N-terminal BAH domain, while one, L738P, localized to the AAA ATPase-like domain within the C-terminal half of Sir3. The BAH point mutants, but not the L738P mutant, disrupted the interaction between Sir3 and nucleosomes. In contrast, Sir3-L738P bound the N-terminal tail of histone H4 more strongly than wild-type Sir3, indicating that misregulation of the Sir3 C-terminal histone-binding activity also disrupted spreading. Our results underscore the importance of proper interactions between Sir3 and the nucleosome in silent chromatin assembly. We propose a model for the spreading of the SIR complex along the chromatin fiber through the two distinct histone-binding domains in Sir3.

scholarly journals A Role for the Replication Proteins PCNA, RF-C, Polymerase ε and Cdc45 in Transcriptional Silencing in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1171-1182
Author(s):  
Ann E Ehrenhofer-Murray ◽  
Rohinton T Kamakaka ◽  
Jasper Rine
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Origin Recognition Complex ◽  
Transcriptional Silencing ◽  
Replication Timing ◽  
Replication Proteins ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cycle Progression

Abstract Transcriptional silencing in the budding yeast Saccharomyces cerevisiae may be linked to DNA replication and cell cycle progression. In this study, we have surveyed the effect of 41 mutations in genes with a role in replication, the cell cycle, and DNA repair on silencing at HMR. Mutations in PCNA (POL30), RF-C (CDC44), polymerase ε (POL2, DPB2, DPB11), and CDC45 were found to restore silencing at a mutant HMR silencer allele that was still a chromosomal origin of replication. Replication timing experiments indicated that the mutant HMR locus was replicated late in S-phase, at the same time as wild-type HMR. Restoration of silencing by PCNA and CDC45 mutations required the origin recognition complex binding site of the HMR-E silencer. Several models for the precise role of these replication proteins in silencing are discussed.

scholarly journals Tolerance of Sir1p/Origin Recognition Complex-Dependent Silencing for Enhanced Origin Firing at HMRa

2006 ◽  
Vol 26 (5) ◽  
pp. 1955-1966 ◽  
Author(s):  
Kristopher H. McConnell ◽  
Philipp Müller ◽  
Catherine A. Fox
Keyword(s):  
Origin Recognition Complex ◽  
Substantial Reduction ◽  
Replication Timing ◽  
S Phase ◽  
Replication Initiation ◽  
Silent Chromatin ◽  
Replication Origins ◽  
Origin Firing ◽  
Sir Proteins ◽  
Origin Recognition

ABSTRACT The HMR-E silencer is a DNA element that directs the formation of silent chromatin at the HMR a locus in Saccharomyces cerevisiae. Sir1p is one of four Sir proteins required for silent chromatin formation at HMR a. Sir1p functions by binding the origin recognition complex (ORC), which binds to HMR-E, and recruiting the other Sir proteins (Sir2p to -4p). ORCs also bind to hundreds of nonsilencer positions distributed throughout the genome, marking them as replication origins, the sites for replication initiation. HMR-E also acts as a replication origin, but compared to many origins in the genome, it fires extremely inefficiently and late during S phase. One postulate to explain this observation is that ORC's role in origin firing is incompatible with its role in binding Sir1p and/or the formation of silent chromatin. Here we examined a mutant HMR-E silencer and fusions between robust replication origins and HMR-E for HMR a silencing, origin firing, and replication timing. Origin firing within HMR a and from the HMR-E silencer itself could be significantly enhanced, and the timing of HMR a replication during an otherwise normal S phase advanced, without a substantial reduction in SIR1-dependent silencing. However, although the robust origin/silencer fusions silenced HMR a quite well, they were measurably less effective than a comparable silencer containing HMR-E's native ORC binding site.

Sign in / Sign up

Export Citation Format

Share Document