301
|
Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Grianti P, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS Biol 2011; 9:e1001086. [PMID: 21738444 PMCID: PMC3125158 DOI: 10.1371/journal.pbio.1001086] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 05/05/2011] [Indexed: 11/18/2022] Open
Abstract
The basic unit of genome packaging is the nucleosome, and nucleosomes have long been proposed to restrict DNA accessibility both to damage and to transcription. Nucleosome number in cells was considered fixed, but recently aging yeast and mammalian cells were shown to contain fewer nucleosomes. We show here that mammalian cells lacking High Mobility Group Box 1 protein (HMGB1) contain a reduced amount of core, linker, and variant histones, and a correspondingly reduced number of nucleosomes, possibly because HMGB1 facilitates nucleosome assembly. Yeast nhp6 mutants lacking Nhp6a and -b proteins, which are related to HMGB1, also have a reduced amount of histones and fewer nucleosomes. Nucleosome limitation in both mammalian and yeast cells increases the sensitivity of DNA to damage, increases transcription globally, and affects the relative expression of about 10% of genes. In yeast nhp6 cells the loss of more than one nucleosome in four does not affect the location of nucleosomes and their spacing, but nucleosomal occupancy. The decrease in nucleosomal occupancy is non-uniform and can be modelled assuming that different nucleosomal sites compete for available histones. Sites with a high propensity to occupation are almost always packaged into nucleosomes both in wild type and nucleosome-depleted cells; nucleosomes on sites with low propensity to occupation are disproportionately lost in nucleosome-depleted cells. We suggest that variation in nucleosome number, by affecting nucleosomal occupancy both genomewide and gene-specifically, constitutes a novel layer of epigenetic regulation.
Collapse
Affiliation(s)
| | - Assaf Weiner
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Francesca Di Felice
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | | | - Elisa Cesarini
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Riccardo L. Rossi
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | - Lorna Gregory
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dilair Baban
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Grazisa Rossetti
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | - Paolo Grianti
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Pagani
- Integrative Biology Program, Istituto Nazionale di Genetica Molecolare, Milan, Italy
| | | | - Jiannis Ragoussis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nir Friedman
- School of Computer Science and Engineering, Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
| | - Giorgio Camilloni
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
| | - Marco E. Bianchi
- San Raffaele University, Milan, Italy
- Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy
- * E-mail: (MEB); (AA)
| | - Alessandra Agresti
- Division of Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy
- * E-mail: (MEB); (AA)
| |
Collapse
|
302
|
Ferreira ME, Flaherty K, Prochasson P. The Saccharomyces cerevisiae histone chaperone Rtt106 mediates the cell cycle recruitment of SWI/SNF and RSC to the HIR-dependent histone genes. PLoS One 2011; 6:e21113. [PMID: 21698254 PMCID: PMC3115976 DOI: 10.1371/journal.pone.0021113] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/19/2011] [Indexed: 11/18/2022] Open
Abstract
Background In Saccharomyces cerevisiae, three out of the four histone gene pairs (HTA1-HTB1, HHT1-HHF1, and HHT2-HHF2) are regulated by the HIR co-repressor complex. The histone chaperone Rtt106 has recently been shown to be present at these histone gene loci throughout the cell cycle in a HIR- and Asf1-dependent manner and involved in their transcriptional repression. The SWI/SNF and RSC chromatin remodeling complexes are both recruited to the HIR-dependent histone genes; SWI/SNF is required for their activation in S phase, whereas RSC is implicated in their repression outside of S phase. Even though their presence at the histone genes is dependent on the HIR complex, their specific recruitment has not been well characterized. In this study we focused on characterizing the role played by the histone chaperone Rtt106 in the cell cycle-dependent recruitment of SWI/SNF and RSC complexes to the histone genes. Methodology/Principal Findings Using GST pull-down and co-immunoprecipitation assays, we showed that Rtt106 physically interacts with both the SWI/SNF and RSC complexes in vitro and in vivo. We then investigated the function of this interaction with respect to the recruitment of these complexes to HIR-dependent histone genes. Using chromatin immunoprecipitation assays (ChIP), we found that Rtt106 is important for the recruitment of both SWI/SNF and RSC complexes to the HIR-dependent histone genes. Furthermore, using synchronized cell cultures, we showed by ChIP assays that the Rtt106-dependent SWI/SNF recruitment to these histone gene loci is cell cycle regulated and restricted to late G1 phase just before the peak of histone gene expression in S phase. Conclusions/Significance Overall, these data strongly suggest that the interaction between the histone chaperone Rtt106 and both the SWI/SNF and RSC chromatin remodeling complexes is important for the cell cycle regulated recruitment of these two complexes to the HIR-dependent histone genes.
Collapse
Affiliation(s)
- Monica E. Ferreira
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Kacie Flaherty
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Philippe Prochasson
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
| |
Collapse
|
303
|
Rossmann MP, Luo W, Tsaponina O, Chabes A, Stillman B. A common telomeric gene silencing assay is affected by nucleotide metabolism. Mol Cell 2011; 42:127-36. [PMID: 21474074 DOI: 10.1016/j.molcel.2011.03.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 12/21/2010] [Accepted: 02/16/2011] [Indexed: 01/06/2023]
Abstract
Telomere-associated position-effect variegation (TPEV) in budding yeast has been used as a model for understanding epigenetic inheritance and gene silencing. A widely used assay to identify mutants with improper TPEV employs the URA3 gene at the telomere of chromosome VII-L that can be counterselected with 5-fluoroorotic acid (5-FOA). 5-FOA resistance has been inferred to represent lack of transcription of URA3 and therefore to represent heterochromatin-induced gene silencing. For two genes implicated in telomere silencing, POL30 and DOT1, we show that the URA3 telomere reporter assay does not reflect their role in heterochromatin formation. Rather, an imbalance in ribonucleotide reductase (RNR), which is induced by 5-FOA, and the specific promoter of URA3 fused to ADH4 at telomere VII-L are jointly responsible for the variegated phenotype. We conclude that metabolic changes caused by the drug employed and certain mutants being studied are incompatible with the use of certain prototrophic markers for TPEV.
Collapse
|
304
|
Avvakumov N, Nourani A, Côté J. Histone chaperones: modulators of chromatin marks. Mol Cell 2011; 41:502-14. [PMID: 21362547 DOI: 10.1016/j.molcel.2011.02.013] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/26/2011] [Accepted: 02/09/2011] [Indexed: 10/18/2022]
Abstract
The many factors that control chromatin biology play key roles in essential nuclear functions like transcription, DNA damage response and repair, recombination, and replication and are critical for proper cell-cycle progression, stem cell renewal, differentiation, and development. These players belong to four broad classes: histone modifiers, chromatin remodelers, histone variants, and histone chaperones. A large number of studies have established the existence of an intricate functional crosstalk between the different factors, not only within a single class but also between different classes. In light of this, while many recent reviews have focused on structure and functions of histone chaperones, the current text highlights novel and striking links that have been established between these proteins and posttranslational modifications of histones and discusses the functional consequences of this crosstalk. These findings feed a current hot question of how cell memory may be maintained through epigenetic mechanisms involving histone chaperones.
Collapse
Affiliation(s)
- Nikita Avvakumov
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), 9 McMahon Street, Quebec City, Quebec G1R 2J6, Canada
| | | | | |
Collapse
|
305
|
Musgrove EA, Sutherland RL. RB in breast cancer: differential effects in estrogen receptor-positive and estrogen receptor-negative disease. Cell Cycle 2011; 9:4607. [PMID: 21260944 DOI: 10.4161/cc.9.23.13889] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
306
|
Hachinohe M, Hanaoka F, Masumoto H. Hst3 and Hst4 histone deacetylases regulate replicative lifespan by preventing genome instability in Saccharomyces cerevisiae. Genes Cells 2011; 16:467-77. [PMID: 21401809 DOI: 10.1111/j.1365-2443.2011.01493.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The acetylation of histone H3 on lysine 56 (H3-K56) occurs during S phase and contributes to the processes of DNA damage repair and histone gene transcription. Hst3 and Hst4 have been implicated in the removal of histone H3-K56 acetylation in Saccharomyces cerevisiae. Here, we show that Hst3 and Hst4 regulate the replicative lifespan of S. cerevisiae mother cells. An hst3Δ hst4Δ double-mutant strain, in which acetylation of histone H3-K56 persists throughout the genome during the cell cycle, exhibits genomic instability, which is manifested by a loss of heterozygosity with cell aging. Furthermore, we show that in the absence of other proteins Hst3 and Hst4 can deacetylate nucleosomal histone H3-K56 in a nicotinamide adenine dinucleotide(NAD)(+) -dependent manner. Our results suggest that Hst3 and Hst4 regulate replicative lifespan through their ability to deacetylate histone H3-K56 to minimize genomic instability.
Collapse
Affiliation(s)
- Mayumi Hachinohe
- Graduate School of Life and Environmental Sciences, Initiative for the Promotion of Young Scientists' Independent Research, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | | | | |
Collapse
|
307
|
Mao C, Brown CR, Griesenbeck J, Boeger H. Occlusion of regulatory sequences by promoter nucleosomes in vivo. PLoS One 2011; 6:e17521. [PMID: 21408617 PMCID: PMC3048331 DOI: 10.1371/journal.pone.0017521] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 02/03/2011] [Indexed: 01/30/2023] Open
Abstract
Nucleosomes are believed to inhibit DNA binding by transcription factors. Theoretical attempts to understand the significance of nucleosomes in gene expression and regulation are based upon this assumption. However, nucleosomal inhibition of transcription factor binding to DNA is not complete. Rather, access to nucleosomal DNA depends on a number of factors, including the stereochemistry of transcription factor-DNA interaction, the in vivo kinetics of thermal fluctuations in nucleosome structure, and the intracellular concentration of the transcription factor. In vitro binding studies must therefore be complemented with in vivo measurements. The inducible PHO5 promoter of yeast has played a prominent role in this discussion. It bears two binding sites for the transcriptional activator Pho4, which at the repressed promoter are positioned within a nucleosome and in the linker region between two nucleosomes, respectively. Earlier studies suggested that the nucleosomal binding site is inaccessible to Pho4 binding in the absence of chromatin remodeling. However, this notion has been challenged by several recent reports. We therefore have reanalyzed transcription factor binding to the PHO5 promoter in vivo, using ‘chromatin endogenous cleavage’ (ChEC). Our results unambiguously demonstrate that nucleosomes effectively interfere with the binding of Pho4 and other critical transcription factors to regulatory sequences of the PHO5 promoter. Our data furthermore suggest that Pho4 recruits the TATA box binding protein to the PHO5 promoter.
Collapse
Affiliation(s)
- Changhui Mao
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Christopher R. Brown
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Joachim Griesenbeck
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| |
Collapse
|
308
|
Tone up your chromatin and stay young. J Biosci 2011; 36:5-11. [DOI: 10.1007/s12038-011-9013-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
309
|
Abstract
This annual review focuses on invertebrate model organisms, which continue to yield fundamental new insights into mechanisms of aging. This year, the budding yeast has been used to understand how asymmetrical partitioning of cellular constituents at cell division can produce a rejuvenated offspring from an aging parent. Blocking of sensation of carbon dioxide is shown to extend fly lifespan and to mediate the lifespan-shortening effect of sensory exposure to fermenting yeast. A new study of daf-16, the key forkhead transcription factor that mediates extension of lifespan by mutants in the insulin-signalling pathway in Caenorhabditis elegans, demonstrates that expression of tissue-specific isoforms with different patterns of response to upstream signalling mediates the highly pleiotropic effects of the pathway on lifespan and other traits. A new approach to manipulating mitochondrial activity in Drosophila, by introducing the yeast NADH-ubiquinone oxidoreductase, shows promise for understanding the role of mitochondrial reactive oxygen species in aging. An exciting new study of yeast and mammalian cells implicates deterioration of the nuclear pore, and consequent leakage of cytoplasmic components into the nucleus, as an important cause of aging in postmitotic tissues. Loss of, or damage to, chromosome-associated histones is also implicated in the determination of lifespan in yeast, worms and fruit flies. The relationship between functional aging, susceptibility to aging-related disease and lifespan itself are explored in two studies in C. elegans, the first examining the role of dietary restriction and reduced insulin signalling in cognitive decline and the second profiling aggregation of the proteome during aging. The invertebrates continue to be a power house of discovery for future work in mammals.
Collapse
Affiliation(s)
- Linda Partridge
- Max Planck Institute for Biology of Ageing, Gleueler Strasse 55a, 50931 Köln, Germany.
| |
Collapse
|
310
|
Abstract
Changes in chromatin structure are a conserved hallmark of ageing, and the mechanism driving these changes, as well as their functional significance, are heavily investigated. Loss of core histones is now observed in aged cells and may contribute to this phenomenon. Histone loss is coupled to cell division and seems to be triggered by telomeric DNA damage.
Collapse
|
311
|
Kaufman PD. Toxicity and lifespan extension: complex outcomes of histone overexpression in budding yeast. Cell Cycle 2010; 9:4611-2. [PMID: 21260949 PMCID: PMC3685622 DOI: 10.4161/cc.9.23.13931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
312
|
Abstract
In this issue of Molecular Cell, Feser et al. (2010) show that aging yeast lose chromatin-associated histones and, furthermore, that correcting this deficiency robustly enhances replicative life span, indicating that loss of normal chromatin packing contributes to the aging process.
Collapse
Affiliation(s)
- Mark A McCormick
- Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | | |
Collapse
|