DOCSLIB.ORG

The Yeast Heterochromatin Protein Sir3 Experienced Functional Changes in the AAA+ Domain After Gene Duplication and Subfunctionalization

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Yeast Heterochromatin Protein Sir3 Experienced Functional Changes in the AAA+ Domain After Gene Duplication and Subfunctionalization Genetics: Early Online, published on August 21, 2017 as 10.1534/genetics.117.300180 The yeast heterochromatin protein Sir3 experienced functional changes in the AAA+ domain after gene duplication and subfunctionalization Ashleigh S. Hanner* and Laura N. Rusche*1 *Department of Biological Sciences, State University of New York at Buffalo, 14260 1 Copyright 2017. Short Title: Specialization of Sir3 AAA+ Domain Key Words: Gene Silencing, Escape from Adaptive Conflict (EAC), Gene Sharing Corresponding author: 1. Laura N. Rusche [email protected] 716‐645‐5198 109 Cooke Hall Buffalo, NY 14260 2 ABSTRACT A key unresolved issue in molecular evolution is how paralogs diverge after gene duplication. For multifunctional genes, duplication is often followed by subfunctionalization. Subsequently, new or optimized molecular properties may evolve once the protein is no longer constrained to achieve multiple functions. A potential example of this process is the evolution of the yeast heterochromatin protein Sir3, which arose by duplication from the conserved DNA replication protein Orc1. We previously found that Sir3 subfunctionalized after duplication. In this study, we investigated whether Sir3 evolved new or optimized properties after subfunctionalization. This possibility is supported by our observation that non‐duplicated Orc1/Sir3 proteins from three species were unable to complement a sir3Δ mutation in Saccharomyces cerevisiae. To identify regions of Sir3 that may have evolved new properties, we created chimeric proteins of ScSir3 and non‐duplicated Orc1 from Kluyveromyces lactis. We identified the AAA+ base subdomain of KlOrc1 as insufficient for heterochromatin formation in S. cerevisiae. In Orc1, this subdomain is intimately associated with other ORC subunits, enabling ATP hydrolysis. In Sir3, this subdomain binds Sir4 and perhaps nucleosomes. Our data are inconsistent with the insufficiency of KlOrc1 resulting from its ATPase activity or an inability to bind ScSir4. Thus, once Sir3 was no longer constrained to assemble into the ORC complex, its heterochromatin‐forming potential evolved through changes in the AAA+ base subdomain. 3 INTRODUCTION Gene duplication is a fundamental mechanism through which genetic diversity increases. A common outcome of gene duplication is subfunctionalization, in which the functions of an ancestral gene are partitioned between the duplicates. Several theoretical models describe subfunctionalization and differ with respect to whether new or specialized functions emerge after subfunctionalization. Models including Duplication‐Degeneration‐ Complementation (DDC) (Force et al., 1999) and Constructive Neutral Evolution (Stoltzfus, 1999) describe a situation in which no new function arises. In this scenario, the duplicate genes acquire complementary inactivating mutations, such that they each perform a subset of the ancestral functions. Other models, such as Escape from Adaptive Conflict (EAC) (Hittinger and Carroll, 2007) and Gene Sharing (Hughes, 1994) describe a situation in which new or enhanced function does arise. In this scenario, the ancestral gene cannot optimize any one of its functions without disrupting the others. However, after duplication and subfunctionalization, the duplicate genes escape this conflict and can acquire optimizing mutations. To gain insight into gene fate after subfunctionalization, we have examined the yeast genes ORC1 and SIR3, a duplicate pair that arose during a whole‐genome duplication and for which there is extensive functional and structural information. Orc1 is a conserved eukaryotic protein required for DNA replication. It is the largest subunit of the Origin Recognition Complex (ORC), which binds to and identifies origins of replication throughout the genome (Li and Stillman, 2012). In Saccharomyces cerevisiae, ORC also serves as a silencer‐binding protein, which recruits the SIR complex (Silent Information Regulator) to the silenced cryptic mating‐type loci, HMRa and HMLα. In particular, the Orc1 4 subunit binds to Sir1 (Triolo and Sternglanz, 1996), which in turn recruits other Sir proteins to establish a domain of repressive or “silenced” chromatin. The paralog of Orc1, Sir3, is also involved in silenced chromatin formation but has a different role. Sir3 binds to deacetylated nucleosomes (Hecht et al., 1995; Onishi et al., 2007), enabling the spreading of the SIR complex along a chromosome (Hoppe et al., 2002; Luo et al., 2002; Rusche et al., 2002). SIR‐mediated silencing occurs at the cryptic mating‐type loci, whose repression maintains haploid cell identity, and at telomeres, where this chromatin is thought to stabilize the ends of chromosomes. Orc1 and Sir3 retain homology along their entire lengths and have three major structural domains (Figure 1). The AAA+ domain is a hallmark of the AAA+ superfamily, whose members couple ATP hydrolysis to structural rearrangements of proteins. In this family, ATP binding and hydrolysis requires amino acids from two interacting AAA+ domains. Although both Orc1 and Sir3 contain an AAA+ domain, Sir3 lacks key amino acids required to bind ATP and has no detectable ATPase activity (Bell et al., 1995). Instead, the AAA+‐like domain in Sir3 interacts with Sir4 (Chang et al., 2003; Ehrentraut et al., 2011; King et al., 2006) and is also proposed to bind histones (Altaf et al., 2007; Ehrentraut et al., 2011; Hecht et al., 1995). A second domain is a winged helix domain, whose ancestral function is to bind DNA (Gaudier et al., 2007). However, the winged helix domains of both Sir3 and Orc1 in S. cerevisiae lack this activity and instead are involved in homo‐dimerization (Oppikofer et al., 2013). The third domain is the N‐ terminal bromo‐adjacent homology (BAH) domain. The BAH domains of both Orc1 and Sir3 bind to nucleosomes (Armache et al., 2011; Onishi et al., 2007; Zhang et al., 2015). The BAH domain of ScOrc1 also binds to Sir1 (Hou et al., 2005; Triolo and Sternglanz, 1996). In addition to these 5 three structural domains, there is a rapidly evolving linker that separates the BAH domain from the AAA+ domain. Prior work indicates that Orc1 and Sir3 subfunctionalized after duplication (Hickman and Rusche, 2010; van Hoof, 2005). In particular, the non‐duplicated Orc1 from Kluyveromyces lactis, which serves as a proxy for the ancestral non‐duplicated protein, has both replication and silencing functions. KlOrc1 is required for transcriptional repression at heterochromatic loci, and its nucleosome‐binding BAH domain is required for spreading across these loci (Hickman and Rusche, 2010), as seen for ScSir3. Another indication that the ancestral protein had a silencing function is that the non‐duplicated ORC1 gene from Lachancea kluyverii weakly complements a sir3Δ mutation in S. cerevisiae (van Hoof, 2005). These results imply that Orc1 was involved in heterochromatin formation before the gene duplication and therefore that subfunctionalization occurred after duplication. Despite the role of KlOrc1 in forming heterochromatin in its native context, we found that when KlOrc1 is expressed in a S. cerevisiae sir3Δ strain, heterochromatin formation does not occur. This inability of KlOrc1 to complement a sir3Δ mutation suggests that Sir3 acquired new or optimized molecular properties after duplication. If so, Sir3 could be an example of the type of evolutionary change described by the EAC and gene sharing models. To examine this possibility, we identified the sections of KlOrc1 that are insufficient for heterochromatin formation by creating chimeric proteins composed of ScSir3 and KlOrc1. We discovered that the primary insufficiency lies in the AAA+ base subdomain. This portion of Sir3 interacts with Sir4. However, our data are inconsistent with the insufficiency of the KlOrc1 base subdomain resulting from a failure to interact with ScSir4. Moreover, our data do not support the 6 possibility that the presumed ability of KlOrc1 to bind ATP interferes with heterochromatin formation in S. cerevisiae. Therefore, the AAA+ base subdomain may have acquired new or optimized molecular properties after duplication. 7 MATERIALS AND METHODS Yeast strain construction and growth The yeast strains used in this study (Table 1) were derived from W303‐1a. Yeast were grown in YM (0.67% yeast nitrogen base without amino acids, 2% glucose) or CSM‐Trp (YM supplemented with a mixture of amino acids and other nutrients but lacking tryptophan (MPBio 4512‐522)). Yeast transformation was performed using lithium acetate and PEG (Schiestl and Gietz, 1989). Cells were harvested at an OD600 around 1, washed twice with TEL (10 mM tris, pH 7.5; 1 mM EDTA; 100 mM LiOAc), and resuspended in 10 μl TEL/ OD cells. For transformation, 100 μl of cells were added to 0.1 µg plasmid DNA or 0.1 μg of linear DNA plus 30 µg sheared salmon sperm DNA. To express KlSir4‐HA or ScSir4‐HA in S. cerevisiae, we first generated tagging cassettes on plasmids and then used these cassettes to transform strain LRY1098. Plasmid pLR588 contains the ScSIR4 gene with a C‐terminal HA tag and downstream HIS3 marker. The original source for the 3xHA tag was pMPY‐3XHA (Schneider et al., 1995). This plasmid was altered by site‐directed mutagenesis to add a stop codon immediately after the HA tag (…DVPDYAA stop), yielding pLR522. Next, HIS3 from pRS403 (Sikorski and Hieter, 1989) was ligated into the SphI and XmaI sites of pLR522 in place of URA3, generating pLR541. The original source for the ScSIR4 gene was pJR2027 (gift from Jasper Rine), based on vector pRS315. The 3x‐HA tag plus HIS3 marker
Load more

Recommended publications
  • Jasper D. Rine, Phd FASEB Board of Directors
    Jasper D. Rine, PhD FASEB Board of Directors Research Interests The research in my lab is centered on the epigenetic mechanisms by which the information in a genome is expressed in a manner that is stable and heritable through cell division. This issue has led us to discoveries on how specialized domains of chromatin structure are established, maintained, and inherited. Our studies use the yeast Saccharomyces cerevisiae and the powerful genetic, genomic, and proteomic approaches that are so facile in this organism to study the nature of the chromatin in specialized domains of the yeast genome, how it is assembled and modified, and how these modifications affect its expression, replication, and repair. Recently, the lab has started a new emphasis focused on exploring the functional consequences of human genetic and epigenetic variation with the goal of understanding and reducing the incidence of two of the most common birth defects, and the mechanism of particular driver mutations in human cancer. Current Projects The most prominent epigenetic mechanism in Saccharomyces involves the silencing of genes controlling cell type. The a and alpha cell types of yeast are controlled by transposable genes that are alleles of the mating type locus (MAT). These alleles are complex blocks of DNA encoding regulatory proteins whose synthesis controls the expression of genes that specify the identity of different cell types of yeast. In addition to MAT, the a and alpha genes are also located at two additional loci, known as HML and HMR, where they are transcriptionally silenced. Transcriptional silencing requires a complex series of interactions between proteins, regulatory sites, and origins of replication that result in the establishment of inactive chromatin in these regions.
    [Show full text]
  • Telomeric Heterochromatin Boundaries Require Nua4-Dependent Acetylation of Histone Variant H2A.Z in Saccharomyces Cerevisiae
    Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae Joshua E. Babiarz, Jeffrey E. Halley, and Jasper Rine1 Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3202, USA SWR1-Com, which is responsible for depositing H2A.Z into chromatin, shares four subunits with the NuA4 histone acetyltransferase complex. This overlap in composition led us to test whether H2A.Z was a substrate of NuA4 in vitro and in vivo. The N-terminal tail of H2A.Z was acetylated in vivo at multiple sites by a combination of NuA4 and SAGA. H2A.Z acetylation was also dependent on SWR1-Com, causing H2A.Z to be efficiently acetylated only when incorporated in chromatin. Unacetylatable H2A.Z mutants were, like wild-type H2A.Z, enriched at heterochromatin boundaries, but were unable to block spreading of heterochromatin. A mutant version of H2A.Z that could not be acetylated, in combination with a mutation in a nonessential gene in the NuA4 complex, caused a pronounced decrease in growth rate. This H2A.Z mutation was lethal in combination with a mutant version of histone H4 that could not be acetylated by NuA4. Taken together, these results show a role for H2A.Z acetylation in restricting silent chromatin, and reveal that acetylation of H2A.Z and H4 can contribute to a common function essential to life. [Keywords: Silencing; SIR proteins; histone code; HTZ1] Supplemental material is available at http://www.genesdev.org.
    [Show full text]
  • Histone H3 N-Terminus Regulates Higher Order Structure of Yeast
    Histone H3 N-terminus regulates higher order INAUGURAL ARTICLE structure of yeast heterochromatin Adam S. Sperling and Michael Grunstein1 Department of Biological Chemistry, Geffen School of Medicine, and the Molecular Biology Institute, University of California, Los Angeles, CA 90095 This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected in 2008. Contributed by Michael Grunstein, June 20, 2009 (sent for review June 5, 2009) In budding yeast, telomeres and the mating type (HM) loci are acetylates H4 K16 in adjacent euchromatin, thus preventing the found in a heterochromatin-like silent structure initiated by Rap1 promiscuous spread of Sir3 and the rest of the Sir protein complex and extended by the interaction of Silencing Information Regulator (13, 14). Heterochromatin is further tethered to the nuclear pe- (Sir) proteins with histones. Binding data demonstrate that both riphery by yKu70/80 telomeric DNA binding proteins and Sir4, a the H3 and H4 N-terminal domains required for silencing in vivo subcellular localization that can influence silencing (15, 16). interact directly with Sir3 and Sir4 in vitro. The role of H4 lysine 16 Although there is a fairly good understanding of the role of the deacetylation is well established in Sir3 protein recruitment; how- H4 N terminus in the formation of heterochromatin the role of ever, that of the H3 N-terminal tail has remained unclear. To H3 has been much less clear. Like H4 K16, the H3 N terminus characterize the role of H3 in silent chromatin formation and and K56 in the core of H3 are deacetylated by Sir2 in vitro (6, compare it to H4 we have generated comprehensive high resolu- 17).
    [Show full text]
  • Sir3-Independent Binding of a Sir2/Sir4 Complex to Silencers and Role for Sir2-Dependent Deacetylation Georg J
    MOLECULAR AND CELLULAR BIOLOGY, June 2002, p. 4167–4180 Vol. 22, No. 12 0270-7306/02/$04.00ϩ0 DOI: 10.1128/MCB.22.12.4167–4180.2002 Copyright © 2002, American Society for Microbiology. All Rights Reserved. Steps in Assembly of Silent Chromatin in Yeast: Sir3-Independent Binding of a Sir2/Sir4 Complex to Silencers and Role for Sir2-Dependent Deacetylation Georg J. Hoppe,1† Jason C. Tanny,1 Adam D. Rudner,1 Scott A. Gerber,1,2 Sherwin Danaie,1 Steven P. Gygi,1,2 and Danesh Moazed1* Department of Cell Biology1 and Taplin Biological Mass Spectrometry Facility,2 Harvard Medical School, Boston, Massachusetts 02115 Received 17 January 2002/Returned for modification 25 February 2002/Accepted 10 March 2002 Transcriptional silencing at the budding yeast silent mating type (HM) loci and telomeric DNA regions requires Sir2, a conserved NAD-dependent histone deacetylase, Sir3, Sir4, histones H3 and H4, and several DNA-binding proteins. Silencing at the yeast ribosomal DNA (rDNA) repeats requires a complex containing Sir2, Net1, and Cdc14. Here we show that the native Sir2/Sir4 complex is composed solely of Sir2 and Sir4 and Downloaded from that native Sir3 is not associated with other proteins. We further show that the initial binding of the Sir2/Sir4 complex to DNA sites that nucleate silencing, accompanied by partial Sir2-dependent histone deacetylation, occurs independently of Sir3 and is likely to be the first step in assembly of silent chromatin at the HM loci and telomeres. The enzymatic activity of Sir2 is not required for this initial binding, but is required for the association of silencing proteins with regions distal from nucleation sites.
    [Show full text]
  • A Green Link to RNA Silencing
    Oncogene (2007) 26, 5477–5488 & 2007 Nature Publishing Group All rights reserved 0950-9232/07 $30.00 www.nature.com/onc REVIEW Arabidopsis histone deacetylase 6: a green link to RNA silencing W Aufsatz, T Stoiber, B Rakic and K Naumann Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria Epigenetic reprogramming is at the base of cancer together result in a transcriptionally repressive chroma- initiation and progression. Generally, genome-wide tin state and silencing of gene expression. Usually, both reduction in cytosine methylation contrasts with the alleles of a tumor suppressor gene have to be defective hypermethylation of control regions of functionally well- or inactivated for the full expression of a transformed established tumor suppressor genes and many other genes phenotype. Thus, epigenetic silencing of one tumor whose role in cancer biology is not yet clear. While insight suppressor allele does not result in disease, but predis- into mechanisms that induce aberrant cytosine methyla- poses cells to undergo malignant growth that occurs if tion in cancer cells is just beginning to emerge, the the second allele is disabled by mutation, chromosome initiating signals for analogous promoter methylation in rearrangements resulting in loss of heterozygosity or, plants are well documented. In Arabidopsis, the silencing again, by transcriptional gene silencing via epigenetic of promoters requires components of the RNA inter- mechanisms. The list of cancer-related genes that are ference machinery and promoter double-stranded RNA affected by aberrant de novo methylation in cancer (dsRNA) to induce a repressive chromatin state that is patients is growing steadily and may already outnumber characterized by cytosine methylation and histone deace- reported mutation events at those genes (Jones and tylation catalysed by the RPD3-type histone deacetylase Baylin, 2002).
    [Show full text]
  • Mechanism for Epigenetic Variegation of Gene Expression at Yeast Telomeric Heterochromatin
    Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Mechanism for epigenetic variegation of gene expression at yeast telomeric heterochromatin Tasuku Kitada,1,2 Benjamin G. Kuryan,1,2 Nancy Nga Huynh Tran,1,2 Chunying Song,1,2 Yong Xue,1,2 Michael Carey,1,2 and Michael Grunstein1,2,3 1Department of Biological Chemistry, David Geffen School of Medicine, 2the Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA Yeast contains heterochromatin at telomeres and the silent mating-type loci (HML/HMR). Genes positioned within the telomeric heterochromatin of Saccharomyces cerevisiae switch stochastically between epigenetically bistable ON and OFF expression states. Important aspects of the mechanism of variegated gene expression, including the chromatin structure of the natural ON state and the mechanism by which it is maintained, are unknown. To address this issue, we developed approaches to select cells in the ON and OFF states. We found by chromatin immunoprecipitation (ChIP) that natural ON telomeres are associated with Rap1 binding and, surprisingly, also contain known characteristics of OFF telomeres, including significant amounts of Sir3 and H4K16 deacetylated nucleosomes. Moreover, we found that H3K79 methylation (H3K79me), H3K4me, and H3K36me, which are depleted from OFF telomeres, are enriched at ON telomeres. We demonstrate in vitro that H3K79me, but not H3K4me or H3K36me, disrupts transcriptional silencing. Importantly, H3K79me does not significantly reduce Sir complex binding in vivo or in vitro. Finally, we show that maintenance of H3K79me at ON telomeres is dependent on transcription. Therefore, although Sir proteins are required for silencing, we propose that epigenetic variegation of telomeric gene expression is due to the bistable enrichment/depletion of H3K79me and not the fluctuation in the amount of Sir protein binding to nucleosomes.
    [Show full text]
  • Genome-Wide, As Opposed to Local, Antisilencing Is Mediated Redundantly by the Euchromatic Factors Set1 and H2A.Z
    Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z Shivkumar Venkatasubrahmanyam*, William W. Hwang*, Marc D. Meneghini*, Amy Hin Yan Tong†, and Hiten D. Madhani*‡ *Department of Biochemistry and Biophysics, University of California, 600 16th Street, MC 2200, San Francisco, CA 94158; and †Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON, Canada M5G 1L6 Edited by Keith R. Yamamoto, University of California, San Francisco, CA, and approved August 24, 2007 (received for review January 31, 2007) In Saccharomyces cerevisiae, several nonessential mechanisms in- that these antisilencing factors have redundant roles. Presum- cluding histone variant H2A.Z deposition and transcription- ably, if local spread of Sir proteins resulted in the silencing of associated histone H3 methylation antagonize the local spread of even a single essential gene or sufficiently reduced transcription Sir-dependent silent chromatin into adjacent euchromatic regions. of multiple essential genes, then loss of H2A.Z, Sas2, or Dot1 However, it is unclear how and where these factors cooperate. To should be lethal. However, htz1⌬, sas2⌬, and dot1⌬ cells are probe this question, we performed systematic genetic array viable and have only a mild growth defect (2, 10, 11). In this screens for gene deletions that cause a synthetic growth defect in article, we describe our analysis of double-mutant phenotypes, an htz1⌬ mutant but not in an htz1⌬ sir3⌬ double mutant. Of the which has revealed a genome-wide, as opposed to local, antisi- four genes identified, three, SET1, SWD1, and SWD3, encode lencing function that is shared by H2A.Z and the histone components of the Set1 complex, which catalyzes the methylation methyltransferase Set1.
    [Show full text]
  • Transcriptional Silencing and Longevity Protein Sir2 Is an NAD-Dependent
    letters to nature injection of UAS±Nkd constructs; and K. Cadigan and D. Bilder for stained material. W.Z. rise to two peaks (3 and 5), which were analysed by mass and J.M. were supported by postdoctoral training grants from the NIH and by the Howard spectroscopy (Fig. 1b; and Supplementary Information) and corre- Hughes Medical Institute (HHMI). K.A.W. was supported by an HHMI postdoctoral fellowship for physicians and a NIH K-08 Award. P.K. and M.P.S. are Investigators of the spond to a monomeric (relative molecular mass (Mr) 2370) and a HHMI. dimeric (Mr 4740) peptide, the latter probably due to oxidation of the peptide at the carboxyl cysteine residue. The same species were Correspondence and requests for materials should be addressed to M.P.S. (e-mail: [email protected]). The Drosophila nkd cDNA has been deposited with observed in reactions with a control bacterial preparation (`pET' in GenBank (accession no. AF213376). Fig. 1a) in the presence of NAD. The addition of NAD to the reaction containing Sir2 gave rise to three additional peaks (1, 2 and 4) and an alteration in peak 3, which were also analysed by mass spectroscopy (Fig. 1c±f; and Supple- mentary Information). These peaks did not correspond to ADP- ................................................................. ribosylated species, but, rather, to deacetylated species of peptide (Fig. 1g). Peak 4 corresponded to the singly deacetylated dimer Transcriptional silencing and (Mr 4698); peak 3 also contained the doubly deacetylated dimer (Mr 4656); peak 2 corresponded to the triply deacetylated dimer (Mr 4614), longevity protein Sir2 is an and peak 1 to the singly deacetylated monomer (Mr 2328).
    [Show full text]
  • Telomere Position Effect: Silencing Near the End
    10_Telomeres_p_261_316.qxd 1/16/07 11:24 AM Page 261 10 Telomere Position Effect: Silencing Near the End Michelle A. Mondoux and Virginia A. Zakian Department of Molecular Biology, Lewis Thomas Laboratories Princeton University Princeton, New Jersey 08544-1014 HETEROCHROMATIC SILENCING IS DISTINCT FROM TRANSCRIPTIONAL GENE REPRESSION The organization of genomes into heterochromatic and euchromatic regions is a global method of gene regulation, in contrast to single-gene transcriptional control. Originally defined cytologically in higher organisms as dark-staining chromatin, heterochromatin is now characterized by a collection of molecular markers including repetitive DNA, regular nucleo- some spacing, low gene density, late S phase replication, and histone tail modifications including hypoacetylation (for review, see Henikoff 2000; Richards and Elgin 2002). Heterochromatin is often found at centromeric and telomeric loci, and active genes that are translocated to heterochromatin are heritably silenced, often in a mosaic or variegated pattern from cell to cell. This variegation is thought to reflect a stochastic heterochromatin assembly at a formerly euchromatic locus. Termed “facultative heterochro- matin,” these genes are silent in only a subset of the cells, as opposed to “constitutive heterochromatin,” where silencing is stable in all cells (for review, see Richards and Elgin 2002). Heterochromatic transcriptional silencing is distinct from transcrip- tional repression seen at individual promoters that occurs at particular times in the cell cycle or during organismal development. Unlike the mechanisms of repression at specific promoters, heterochromatic silencing is generally promoter-nonspecific, such that almost all promoters are silenced by heterochromatin. Heterochromatin constitutes a repressive environment for gene expression over a large distance, in contrast to Telomeres, 2nd Ed.
    [Show full text]
  • Lysine Methylation Within the Globular Domain of Histone H3 by Dot1 Is Important for Telomeric Silencing and Sir Protein Association
    Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association Huck Hui Ng,1 Qin Feng,2 Hengbin Wang,2 Hediye Erdjument-Bromage,3 Paul Tempst,3 Yi Zhang,2,5 and Kevin Struhl1,4 1Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; 2Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; 3Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA The amino-terminal histone tails are subject to covalent post-translational modifications such as acetylation, methylation, and phosphorylation. In the histone code hypothesis, these exposed and unstructured histone tails are accessible to a repertoire of regulatory factors that specifically recognize the various modified histones, thereby generating altered chromatin structures that mediate specific biological responses. Here, we report that lysine (Lys) 79 of histone H3, which resides in the globular domain, is methylated in eukaryotic organisms. In the yeast Saccharomyces cerevisiae, Lys 79 of histone H3 is methylated by Dot1, a protein shown previously to play a role in telomeric silencing. Mutations of Lys 79 of histone H3 and mutations that abolish the catalytic activity of Dot1 impair telomeric silencing, suggesting that Dot1 mediates telomeric silencing largely through methylation of Lys 79. This defect in telomeric silencing might reflect an interaction between Sir proteins and Lys 79, because dot1 and Lys 79 mutations weaken the interaction of Sir2and Sir3 with the telomeric region in vivo. Our results indicate that histone modifications in the core globular domain have important biological functions.
    [Show full text]
  • Modulations of SIR-Nucleosome Interactions of Reconstructed Yeast Silent Pre-Heterochromatin by O-Acetyl-ADP-Ribose and Magnesium
    M BoC | BRIEF REPORT Modulations of SIR-nucleosome interactions of reconstructed yeast silent pre-heterochromatin by O-acetyl-ADP-ribose and magnesium Shu-Yun Tunga, Sue-Hong Wangb, Sue-Ping Leea, Shu-Ping Tsaia, Hsiao-Hsuian Shenc, Feng-Jung Chenc, Yu-Yi Wuc, Sheng-Pin Hsiaoc, and Gunn-Guang Lioua,c,d,* aInstitute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan; bDepartment of Biomedical Sciences, Chung Shan Medical University, Taichung 402, Taiwan; cInstitute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan; dGuang EM Laboratory, New Taipei 242, Taiwan ABSTRACT Yeast silent heterochromatin provides an excellent model with which to study Monitoring Editor epigenetic inheritance. Previously we developed an in vitro assembly system to demonstrate Karsten Weis the formation of filament structures with requirements that mirror yeast epigenetic gene si- ETH Zurich lencing in vivo. However, the properties of these filaments were not investigated in detail. Received: Jun 6, 2016 Here we show that the assembly system requires Sir2, Sir3, Sir4, nucleosomes, and O-acetyl- Revised: Nov 22, 2016 ADP-ribose. We also demonstrate that all Sir proteins and nucleosomes are components of Accepted: Nov 29, 2016 these filaments to prove that they are SIR-nucleosome filaments. Furthermore, we show that the individual localization patterns of Sir proteins on the SIR-nucleosome filament reflect those patterns on telomeres in vivo. In addition, we reveal that magnesium exists in the SIR- nucleosome filament, with a role similar to that for chromatin condensation. These results suggest that a small number of proteins and molecules are sufficient to mediate the forma- tion of a minimal yeast silent pre-heterochromatin in vitro.
    [Show full text]
  • The SIR2 Gene Family, Conserved from Bacteria to Humans, Functions in Silencing, Cell Cycle Progiression, and Chromosome Stability
    Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progiression, and chromosome stability Carrie Baker Brachmann, Joyce M. herm man,' Scott E. Devine, Elizabeth E. Cameron, Lorraine pillus,' and Jef D. Boeke Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205; 'Department of Molecular, Cellular and Developmental Biology, Porter Biosciences, University of Colorado, CB347, Boulder, Colorado 80309 USA Genomic silencing is a fundamental mechanism of transcriptional regulation, yet little is known about conserved mechanisms of silencing. We report here the discovery of four Saccharomyces cerevisiae homologs of the SIR2 silencing gene (HSTs), as well as conservation of this gene family from bacteria to mammals. At least three HST genes can function in silencing; HSTl overexpression restores transcriptional silencing to a sir2 mutant and hst3 hst4 double mutants are defective in telomeric silencing. In addition, HST3 and HST4 together contribute to proper cell cycle progression, radiation resistance, and genomic stability, establishing new connections between silencing and these fundamental cellular processes. [Key Words: HST genes; Saccharomyces cerevisiae; telomeric silencing; homologous recombination; chromosome segregation] Received September 13, 1995; revised version accepted October 13, 1995. Transcriptional inactivation of large genomic regions, or (Gottschling 1992; Singh and Klar 1992; Wright et al. silencing, is an important and highly conserved mecha- 1992; Loo and Rine 1994), supporting the idea that si- nism of gene regulation. This regonal, gene nonspecific lencing is associated with altered chromatin structure. form of repression is often associated with local alter- Although cis-regulatory elements differ between the HM ations in chromatin structure.
    [Show full text]