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Tan X, Wu X, Han M, Wang L, Xu L, Li B, Yuan Y. Yeast autonomously replicating sequence (ARS): Identification, function, and modification. Eng Life Sci 2021. [DOI: 10.1002/elsc.202000085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xiao‐Yu Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Xiao‐Le Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Ming‐Zhe Han
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Li Xu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Bing‐Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
| | - Ying‐Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University Tianjin P. R. China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin P. R. China
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Barberis M. Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER. NPJ Syst Biol Appl 2021; 7:28. [PMID: 34117265 PMCID: PMC8196193 DOI: 10.1038/s41540-021-00187-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
In budding yeast, synchronization of waves of mitotic cyclins that activate the Cdk1 kinase occur through Forkhead transcription factors. These molecules act as controllers of their sequential order and may account for the separation in time of incompatible processes. Here, a Forkhead-mediated design principle underlying the quantitative model of Cdk control is proposed for budding yeast. This design rationalizes timing of cell division, through progressive and coordinated cyclin/Cdk-mediated phosphorylation of Forkhead, and autonomous cyclin/Cdk oscillations. A "clock unit" incorporating this design that regulates timing of cell division is proposed for both yeast and mammals, and has a DRIVER operating the incompatible processes that is instructed by multiple CLOCKS. TIMERS determine whether the clocks are active, whereas CONTROLLERS determine how quickly the clocks shall function depending on external MODULATORS. This "clock unit" may coordinate temporal waves of cyclin/Cdk concentration/activity in the eukaryotic cell cycle making the driver operate the incompatible processes, at separate times.
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Affiliation(s)
- Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.
- Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, UK.
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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Jin Y, Liang Z, Lou H. The Emerging Roles of Fox Family Transcription Factors in Chromosome Replication, Organization, and Genome Stability. Cells 2020; 9:cells9010258. [PMID: 31968679 PMCID: PMC7016735 DOI: 10.3390/cells9010258] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
The forkhead box (Fox) transcription factors (TFs) are widespread from yeast to humans. Their mutations and dysregulation have been linked to a broad spectrum of malignant neoplasias. They are known as critical players in DNA repair, metabolism, cell cycle control, differentiation, and aging. Recent studies, especially those from the simple model eukaryotes, revealed unexpected contributions of Fox TFs in chromosome replication and organization. More importantly, besides functioning as a canonical TF in cell signaling cascades and gene expression, Fox TFs can directly participate in DNA replication and determine the global replication timing program in a transcription-independent mechanism. Yeast Fox TFs preferentially recruit the limiting replication factors to a subset of early origins on chromosome arms. Attributed to their dimerization capability and distinct DNA binding modes, Fkh1 and Fkh2 also promote the origin clustering and assemblage of replication elements (replication factories). They can mediate long-range intrachromosomal and interchromosomal interactions and thus regulate the four-dimensional chromosome organization. The novel aspects of Fox TFs reviewed here expand their roles in maintaining genome integrity and coordinating the multiple essential chromosome events. These will inevitably be translated to our knowledge and new treatment strategies of Fox TF-associated human diseases including cancer.
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Hoggard TA, Chang F, Perry KR, Subramanian S, Kenworthy J, Chueng J, Shor E, Hyland EM, Boeke JD, Weinreich M, Fox CA. Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins. PLoS Genet 2018; 14:e1007418. [PMID: 29795547 PMCID: PMC5991416 DOI: 10.1371/journal.pgen.1007418] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/06/2018] [Accepted: 05/15/2018] [Indexed: 01/23/2023] Open
Abstract
Most active DNA replication origins are found within euchromatin, while origins within heterochromatin are often inactive or inhibited. In yeast, origin activity within heterochromatin is negatively controlled by the histone H4K16 deacetylase, Sir2, and at some heterochromatic loci also by the nucleosome binding protein, Sir3. The prevailing view has been that direct functions of Sir2 and Sir3 are confined to heterochromatin. However, growth defects in yeast mutants compromised for loading the MCM helicase, such as cdc6-4, are suppressed by deletion of either SIR2 or SIR3. While these and other observations indicate that SIR2,3 can have a negative impact on at least some euchromatic origins, the genomic scale of this effect was unknown. It was also unknown whether this suppression resulted from direct functions of Sir2,3 within euchromatin, or was an indirect effect of their previously established roles within heterochromatin. Using MCM ChIP-Seq, we show that a SIR2 deletion rescued MCM complex loading at ~80% of euchromatic origins in cdc6-4 cells. Therefore, Sir2 exhibited a pervasive effect at the majority of euchromatic origins. Using MNase-H4K16ac ChIP-Seq, we show that origin-adjacent nucleosomes were depleted for H4K16 acetylation in a SIR2-dependent manner in wild type (i.e. CDC6) cells. In addition, we present evidence that both Sir2 and Sir3 bound to nucleosomes adjacent to euchromatic origins. The relative levels of each of these molecular hallmarks of yeast heterochromatin–SIR2-dependent H4K16 hypoacetylation, Sir2, and Sir3 –correlated with how strongly a SIR2 deletion suppressed the MCM loading defect in cdc6-4 cells. Finally, a screen for histone H3 and H4 mutants that could suppress the cdc6-4 growth defect identified amino acids that map to a surface of the nucleosome important for Sir3 binding. We conclude that heterochromatin proteins directly modify the local chromatin environment of euchromatic DNA replication origins. When a cell divides, it must copy or “replicate” its DNA. DNA replication starts at chromosomal regions called origins when a collection of replication proteins gains local access to unwind the two DNA strands. Chromosomal DNA is packaged into a protein-DNA complex called chromatin and there are two major structurally and functionally distinct types. Euchromatin allows DNA replication proteins to access origin DNA, while heterochromatin inhibits their access. The prevalent view has been that the heterochromatin proteins required to inhibit origins are confined to heterochromatin. In this study, the conserved heterochromatin proteins, Sir2 and Sir3, were shown to both physically and functionally associate with the majority of origins in euchromatin. This observation raises important questions about the chromosomal targets of heterochromatin proteins, and how and why the majority of origins exist within a potentially repressive chromatin structure.
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Affiliation(s)
- Timothy A. Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, Madison, WI, United States of America
| | - FuJung Chang
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Kelsey Rae Perry
- Department of Biomolecular Chemistry, School of Medicine and Public Health, Madison, WI, United States of America
- Integrated Program in Biochemistry, School of Medicine and Public Health and College of Agricultural Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Sandya Subramanian
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Jessica Kenworthy
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Julie Chueng
- Integrated Program in Biochemistry, School of Medicine and Public Health and College of Agricultural Sciences, University of Wisconsin, Madison, WI, United States of America
| | - Erika Shor
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Edel M. Hyland
- School of Biological Sciences, Medical Biology Center, Queen’s University, Belfast, United Kingdom
| | - Jef D. Boeke
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics and NYU Langone Health, New York, NY, United States of America
| | - Michael Weinreich
- Laboratory of Genome Integrity and Tumorigenesis, Van Andel Research Institute, Grand Rapids, MI, United States of America
- * E-mail: (MW); (CAF)
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, Madison, WI, United States of America
- Integrated Program in Biochemistry, School of Medicine and Public Health and College of Agricultural Sciences, University of Wisconsin, Madison, WI, United States of America
- * E-mail: (MW); (CAF)
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Dummer AM, Su Z, Cherney R, Choi K, Denu J, Zhao X, Fox CA. Binding of the Fkh1 Forkhead Associated Domain to a Phosphopeptide within the Mph1 DNA Helicase Regulates Mating-Type Switching in Budding Yeast. PLoS Genet 2016; 12:e1006094. [PMID: 27257873 PMCID: PMC4892509 DOI: 10.1371/journal.pgen.1006094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/10/2016] [Indexed: 12/18/2022] Open
Abstract
The Saccharomyces cerevisiae Fkh1 protein has roles in cell-cycle regulated transcription as well as a transcription-independent role in recombination donor preference during mating-type switching. The conserved FHA domain of Fkh1 regulates donor preference by juxtaposing two distant regions on chromosome III to promote their recombination. A model posits that this Fkh1-mediated long-range chromosomal juxtaposition requires an interaction between the FHA domain and a partner protein(s), but to date no relevant partner has been described. In this study, we used structural modeling, 2-hybrid assays, and mutational analyses to show that the predicted phosphothreonine-binding FHA domain of Fkh1 interacted with multiple partner proteins. The Fkh1 FHA domain was important for its role in cell-cycle regulation, but no single interaction partner could account for this role. In contrast, Fkh1’s interaction with the Mph1 DNA repair helicase regulated donor preference during mating-type switching. Using 2-hybrid assays, co-immunoprecipitation, and fluorescence anisotropy, we mapped a discrete peptide within the regulatory Mph1 C-terminus required for this interaction and identified two threonines that were particularly important. In vitro binding experiments indicated that at least one of these threonines had to be phosphorylated for efficient Fkh1 binding. Substitution of these two threonines with alanines (mph1-2TA) specifically abolished the Fkh1-Mph1 interaction in vivo and altered donor preference during mating-type switching to the same degree as mph1Δ. Notably, the mph1-2TA allele maintained other functions of Mph1 in genome stability. Deletion of a second Fkh1-interacting protein encoded by YMR144W also resulted in a change in Fkh1-FHA-dependent donor preference. We have named this gene FDO1 for Forkhead one interacting protein involved in donor preference. We conclude that a phosphothreonine-mediated protein-protein interface between Fkh1-FHA and Mph1 contributes to a specific long-range chromosomal interaction required for mating-type switching, but that Fkh1-FHA must also interact with several other proteins to achieve full functionality in this process. Specific chromosomal interactions between distal regions of the genome allow for DNA transactions necessary for normal cell function, but the protein-protein interfaces that regulate such interactions remain largely unknown. The budding yeast Fkh1 protein uses its evolutionarily conserved phosphothreonine-binding FHA domain to regulate a long-range DNA transaction called mating-type switching that allows yeast cells to switch their sexual phenotype. In this study, another conserved nuclear protein, the Mph1 DNA repair helicase, was shown to interact directly with the FHA domain of Fkh1 to regulate mating-type switching. The Fkh1-Mph1 interaction required two phosphorylated threonines on Mph1 that were dispensable for many other Mph1-protein interactions and other Mph1 chromosomal functions. Thus a discrete protein-protein interface between two multifunctional chromosomal proteins helps define a long-range chromosomal interaction important for controlling cell behavior.
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Affiliation(s)
- Antoinette M. Dummer
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Zhangli Su
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rachel Cherney
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Koyi Choi
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - John Denu
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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6
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Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase. Genome Res 2016; 26:365-75. [PMID: 26728715 PMCID: PMC4772018 DOI: 10.1101/gr.196857.115] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/17/2015] [Indexed: 01/31/2023]
Abstract
The Saccharomyces cerevisiaeForkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering. We hypothesized that, as stimulators of early origin activation, Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide. Existing methods, however, are not well-suited to quantitative, genome-wide measurements of origin firing between strains and conditions. To overcome this limitation, we developed qBrdU-seq, a quantitative method for BrdU incorporation analysis of replication dynamics, and applied it to show that overexpression of Fkh1 and Fkh2 advances the initiation timing of many origins throughout the genome resulting in a higher total level of origin initiations in early S phase. The higher initiation rate is accompanied by slower replication fork progression, thereby maintaining a normal length of S phase without causing detectable Rad53 checkpoint kinase activation. The advancement of origin firing time, including that of origins in heterochromatic domains, was established in late G1 phase, indicating that origin timing can be reset subsequently to origin licensing. These results provide novel insights into the mechanisms of origin timing regulation by identifying Fkh1 and Fkh2 as rate-limiting factors for origin firing that determine the ability of replication origins to accrue limiting factors and have the potential to reprogram replication timing late in G1 phase.
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Abstract
While large portions of the mammalian genome are known to replicate sequentially in a distinct, tissue-specific order, recent studies suggest that the inactive X chromosome is duplicated rapidly via random, synchronous DNA synthesis at numerous adjacent regions. The rapid duplication of the inactive X chromosome was observed in high-resolution studies visualizing DNA replication patterns in the nucleus, and by allele-specific DNA sequencing studies measuring the extent of DNA synthesis. These studies conclude that inactive X chromosomes complete replication earlier than previously thought and suggest that the strict order of DNA replication detected in the majority of genomic regions is not preserved in non-transcribed, "silent" chromatin. These observations alter current concepts about the regulation of DNA replication in non-transcribed portions of the genome in general and in the inactive X-chromosome in particular.
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Affiliation(s)
- Mirit I Aladjem
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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Ostrow AZ, Nellimoottil T, Knott SRV, Fox CA, Tavaré S, Aparicio OM. Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics. PLoS One 2014; 9:e87647. [PMID: 24504085 PMCID: PMC3913637 DOI: 10.1371/journal.pone.0087647] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/26/2013] [Indexed: 11/30/2022] Open
Abstract
Forkhead box (FOX) transcription factors regulate a wide variety of cellular functions in higher eukaryotes, including cell cycle control and developmental regulation. In Saccharomyces cerevisiae, Forkhead proteins Fkh1 and Fkh2 perform analogous functions, regulating genes involved in cell cycle control, while also regulating mating-type silencing and switching involved in gamete development. Recently, we revealed a novel role for Fkh1 and Fkh2 in the regulation of replication origin initiation timing, which, like donor preference in mating-type switching, appears to involve long-range chromosomal interactions, suggesting roles for Fkh1 and Fkh2 in chromatin architecture and organization. To elucidate how Fkh1 and Fkh2 regulate their target DNA elements and potentially regulate the spatial organization of the genome, we undertook a genome-wide analysis of Fkh1 and Fkh2 chromatin binding by ChIP-chip using tiling DNA microarrays. Our results confirm and extend previous findings showing that Fkh1 and Fkh2 control the expression of cell cycle-regulated genes. In addition, the data reveal hundreds of novel loci that bind Fkh1 only and exhibit a distinct chromatin structure from loci that bind both Fkh1 and Fkh2. The findings also show that Fkh1 plays the predominant role in the regulation of a subset of replication origins that initiate replication early, and that Fkh1/2 binding to these loci is cell cycle-regulated. Finally, we demonstrate that Fkh1 and Fkh2 bind proximally to a variety of genetic elements, including centromeres and Pol III-transcribed snoRNAs and tRNAs, greatly expanding their potential repertoire of functional targets, consistent with their recently suggested role in mediating the spatial organization of the genome.
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Affiliation(s)
- A. Zachary Ostrow
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Tittu Nellimoottil
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Simon R. V. Knott
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, Wisconsin, United States of America
| | - Simon Tavaré
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Oscar M. Aparicio
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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9
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Linke C, Klipp E, Lehrach H, Barberis M, Krobitsch S. Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions. Front Physiol 2013; 4:173. [PMID: 23874301 PMCID: PMC3709100 DOI: 10.3389/fphys.2013.00173] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 06/20/2013] [Indexed: 01/22/2023] Open
Abstract
The Forkhead (Fkh) box family of transcription factors is evolutionary conserved from yeast to higher eukaryotes and its members are involved in many physiological processes including metabolism, DNA repair, cell cycle, stress resistance, apoptosis, and aging. In budding yeast, four Fkh transcription factors were identified, namely Fkh1, Fkh2, Fhl1, and Hcm1, which are implicated in chromatin silencing, cell cycle regulation, and stress response. These factors impinge transcriptional regulation during cell cycle progression, and histone deacetylases (HDACs) play an essential role in this process, e.g., the nuclear localization of Hcm1 depends on Sir2 activity, whereas Sin3/Rpd3 silence cell cycle specific gene transcription in G2/M phase. However, a direct involvement of Sir2 in Fkh1/Fkh2-dependent regulation of target genes is at present unknown. Here, we show that Fkh1 and Fkh2 associate with Sir2 in G1 and M phase, and that Fkh1/Fkh2-mediated activation of reporter genes is antagonized by Sir2. We further report that Sir2 overexpression strongly affects cell growth in an Fkh1/Fkh2-dependent manner. In addition, Sir2 regulates the expression of the mitotic cyclin Clb2 through Fkh1/Fkh2-mediated binding to the CLB2 promoter in G1 and M phase. We finally demonstrate that Sir2 is also enriched at the CLB2 promoter under stress conditions, and that the nuclear localization of Sir2 is dependent on Fkh1 and Fkh2. Taken together, our results show a functional interplay between Fkh1/Fkh2 and Sir2 suggesting a novel mechanism of cell cycle repression. Thus, in budding yeast, not only the regulation of G2/M gene expression but also the protective response against stress could be directly coordinated by Fkh1 and Fkh2.
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Affiliation(s)
- Christian Linke
- Otto Warburg Laboratory, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics Berlin, Germany ; Department of Biology, Chemistry and Pharmacy, Free University Berlin Berlin, Germany
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Functions of protosilencers in the formation and maintenance of heterochromatin in Saccharomyces cerevisiae. PLoS One 2012; 7:e37092. [PMID: 22615905 PMCID: PMC3355138 DOI: 10.1371/journal.pone.0037092] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 04/17/2012] [Indexed: 11/19/2022] Open
Abstract
In Saccharomyces cerevisiae, transcriptionally silent heterochromatin at HML and HMR loci is established by silencers that recruit SIR complex and promote its propagation along chromatin. Silencers consist of various combinations of two or three binding sites for origin recognition complex (ORC), Abf1 and Rap1. A single ORC, Abf1 or Rap1 site cannot promote silencing, but can enhance silencing by a distant silencer, and is called a protosilencer. The mechanism of protosilencer function is not known. We examine the functions of ORC, Abf1 and Rap1 sites as components of the HMR-E silencer, and as protosilencers. We find that the Rap1 site makes a larger and unique contribution to HMR-E function compared to ORC and Abf1 sites. On the other hand, Rap1 site does not act as a protosilencer to assist HML-E silencer in forming heterochromatin, whereas ORC and Abf1 sites do. Therefore, different mechanisms may be involved in the roles of Rap1 site as a component of HMR-E and as a protosilencer. Heterochromatin formed by ORC or Abf1 site in collaboration with HML-E is not as stable as that formed by HMR-E and HML-E, but increasing the copy number of Abf1 site enhances heterochromatin stability. ORC and Abf1 sites acting as protosilencers do not modulate chromatin structure in the absence of SIR complex, which argues against the hypothesis that protosilencers serve to create a chromatin structure favorable for SIR complex propagation. We also investigate the function of ARS1 containing an ORC site and an Abf1 site as a protosilencer. We find that ARS1 inserted at HML enhances heterochromatin stability, and promotes de novo formation of a chromatin structure that partially resembles heterochromatin in an S phase dependent manner. Taken together, our results indicate that protosilencers aid in the formation and maintenance of heterochromatin structure.
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11
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Knott SRV, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavaré S, Aparicio OM. Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Cell 2012; 148:99-111. [PMID: 22265405 DOI: 10.1016/j.cell.2011.12.012] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 10/11/2011] [Accepted: 12/09/2011] [Indexed: 12/28/2022]
Abstract
The replication of eukaryotic chromosomes is organized temporally and spatially within the nucleus through epigenetic regulation of replication origin function. The characteristic initiation timing of specific origins is thought to reflect their chromatin environment or sub-nuclear positioning, however the mechanism remains obscure. Here we show that the yeast Forkhead transcription factors, Fkh1 and Fkh2, are global determinants of replication origin timing. Forkhead regulation of origin timing is independent of local levels or changes of transcription. Instead, we show that Fkh1 and Fkh2 are required for the clustering of early origins and their association with the key initiation factor Cdc45 in G1 phase, suggesting that Fkh1 and Fkh2 selectively recruit origins to emergent replication factories. Fkh1 and Fkh2 bind Fkh-activated origins, and interact physically with ORC, providing a plausible mechanism to cluster origins. These findings add a new dimension to our understanding of the epigenetic basis for differential origin regulation and its connection to chromosomal domain organization.
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Affiliation(s)
- Simon R V Knott
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA
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12
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The chromatin backdrop of DNA replication: lessons from genetics and genome-scale analyses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:794-801. [PMID: 22342530 DOI: 10.1016/j.bbagrm.2012.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/27/2012] [Accepted: 01/31/2012] [Indexed: 01/04/2023]
Abstract
The entire cellular genome must replicate during each cell cycle, but it is yet unclear how replication proceeds along with chromatin condensation and remodeling while ensuring the fidelity of the replicated genome. Mapping replication initiation sites can provide clues for the coordination of DNA replication and transcription on a whole-genome scale. Here we discuss recent insights obtained from genome-scale analyses of replication initiation sites and transcription in mammalian cells and ask how transcription and chromatin modifications affect the frequency of replication initiation events. We also discuss DNA sequences, such as insulators and replicators, which modulate replication and transcription of target genes, and use genome-wide maps of replication initiation sites to evaluate possible commonalities between replicators and chromatin insulators. This article is part of a Special Issue entitled: Chromatin in time and space.
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Palmitoylation controls the dynamics of budding-yeast heterochromatin via the telomere-binding protein Rif1. Proc Natl Acad Sci U S A 2011; 108:14572-7. [PMID: 21844336 DOI: 10.1073/pnas.1105262108] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The posttranslational addition of palmitate to cysteines occurs ubiquitously in eukaryotic cells, where it functions in anchoring target proteins to membranes and in vesicular trafficking. Here we show that the Saccharomyces cerevisiae palmitoyltransferase Pfa4 enhanced heterochromatin formation at the cryptic mating-type loci HMR and HML via Rif1, a telomere regulatory protein. Acylated Rif1 was detected in extracts from wild-type but not pfa4Δ mutant cells. In a pfa4Δ mutant, Rif1-GFP dispersed away from foci positioned at the nuclear periphery into the nucleoplasm. Sir3-GFP distribution was also perturbed, indicating a change in the nuclear dynamics of heterochromatin proteins. Genetic analyses indicated that PFA4 functioned upstream of RIF1. Surprisingly, the pfa4Δ mutation had only mild effects on telomeric regulation, suggesting Rif1's roles at HM loci and telomeres were more complexly related than previously thought. These data supported a model in which Pfa4-dependent palmitoylation of Rif1 anchored it to the inner nuclear membrane, influencing its role in heterochromatin dynamics.
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Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, Weinreich M, Eaton ML, MacAlpine DM, Fox CA. The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev 2010; 24:1418-33. [PMID: 20595233 PMCID: PMC2895200 DOI: 10.1101/gad.1906410] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 05/11/2010] [Indexed: 12/15/2022]
Abstract
The origin recognition complex (ORC) binds to the specific positions on chromosomes that serve as DNA replication origins. Although ORC is conserved from yeast to humans, the DNA sequence elements that specify ORC binding are not. In particular, metazoan ORC shows no obvious DNA sequence specificity, whereas yeast ORC binds to a specific DNA sequence within all yeast origins. Thus, whereas chromatin must play an important role in metazoan ORC's ability to recognize origins, it is unclear whether chromatin plays a role in yeast ORC's recognition of origins. This study focused on the role of the conserved N-terminal bromo-adjacent homology domain of yeast Orc1 (Orc1BAH). Recent studies indicate that BAH domains are chromatin-binding modules. We show that the Orc1BAH domain was necessary for ORC's stable association with yeast chromosomes, and was physiologically relevant to DNA replication in vivo. This replication role was separable from the Orc1BAH domain's previously defined role in transcriptional silencing. Genome-wide analyses of ORC binding in ORC1 and orc1bahDelta cells revealed that the Orc1BAH domain contributed to ORC's association with most yeast origins, including a class of origins highly dependent on the Orc1BAH domain for ORC association (orc1bahDelta-sensitive origins). Orc1bahDelta-sensitive origins required the Orc1BAH domain for normal activity on chromosomes and plasmids, and were associated with a distinct local nucleosome structure. These data provide molecular insights into how the Orc1BAH domain contributes to ORC's selection of replication origins, as well as new tools for examining conserved mechanisms governing ORC's selection of origins within eukaryotic chromosomes.
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Affiliation(s)
- Philipp Müller
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sookhee Park
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Erika Shor
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dana J. Huebert
- Program in Cellular and Molecular Biology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Christopher L. Warren
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aseem Z. Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael Weinreich
- Laboratory for Chromosome Replication, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Matthew L. Eaton
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David M. MacAlpine
- Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Catherine A. Fox
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Program in Cellular and Molecular Biology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Swamy KBS, Cho CY, Chiang S, Tsai ZTY, Tsai HK. Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Res 2010; 37:6991-7001. [PMID: 19767613 PMCID: PMC2790881 DOI: 10.1093/nar/gkp743] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific binding sites (TFBSs) in gene promoters. TFBS motifs may contain one or more variable positions. Although the prevailing assumption is that nucleotide variants at such positions are functionally equivalent, there is increasing evidence that such variants play a role in regulation of gene expression. In this article, we propose a method for studying the relationship between the expression of target genes and nucleotide variants in TFBS motifs at a genome-wide scale in Saccharomyces cerevisiae, especially the combinatorial effects of variants at two positions. Our analysis shows that nucleotide variations in more than one-third of variable positions and in 20% of dependent position pairs are highly correlated to gene expression. We define such positions as 'functional'. However, some positions are only functional as dependent pairs, but not individually. In addition, a significant proportion of the functional positions have been well conserved across all yeast-related species studied. We also find that some positions require the presence of co-occurring TFs, while others maintain their functionality in the absence of a co-occurring TF. Our analysis supports the importance of nucleotide variants at variable positions of TFBSs in gene regulation.
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Affiliation(s)
- Krishna B S Swamy
- Institute of Information Science, National Yang-Ming University, Taiwan
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16
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Rehman MA, Yankulov K. The dual role of autonomously replicating sequences as origins of replication and as silencers. Curr Genet 2009; 55:357-63. [PMID: 19633981 DOI: 10.1007/s00294-009-0265-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/10/2009] [Accepted: 07/11/2009] [Indexed: 10/20/2022]
Abstract
Autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae have been extensively characterized as both origins of DNA replication and as chromatin repressors/silencers. It has been conclusively shown that the origin and the silencer activities of ARS are substantially, but not entirely interchangeable and that they are modulated by position effects and chromatin environment. It remains unclear how these two quite divergent functions of ARS co-exist. This perspective focuses on recent advances, which have shown that slight differences in ARSs can modulate their affinity for origin recognition complex and their activity as silencers or origins.
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Affiliation(s)
- Muhammad Attiq Rehman
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Phylogenetic conservation and homology modeling help reveal a novel domain within the budding yeast heterochromatin protein Sir1. Mol Cell Biol 2008; 29:687-702. [PMID: 19029247 DOI: 10.1128/mcb.00202-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The yeast Sir1 protein's ability to bind and silence the cryptic mating-type locus HMRa requires a protein-protein interaction between Sir1 and the origin recognition complex (ORC). A domain within the C-terminal half of Sir1, the Sir1 ORC interaction region (Sir1OIR), and the conserved bromo-adjacent homology (BAH) domain within Orc1, the largest subunit of ORC, mediate this interaction. The structure of the Sir1OIR-Orc1BAH complex is known. Sir1OIR and Orc1BAH interacted with a high affinity in vitro, but the Sir1OIR did not inhibit Sir1-dependent silencing when overproduced in vivo, suggesting that other regions of Sir1 helped it bind HMRa. Comparisons of diverged Sir1 proteins revealed two highly conserved regions, N1 and N2, within Sir1's poorly characterized N-terminal half. An N-terminal portion of Sir1 (residues 27 to 149 [Sir1(27-149)]) is similar in sequence to the Sir1OIR; homology modeling predicted a structure for Sir1(27-149) in which N1 formed a submodule similar to the known Orc1BAH-interacting surface on Sir1. Consistent with these findings, two-hybrid assays indicated that the Sir1 N terminus could interact with BAH domains. Amino acid substitutions within or near N1 or N2 reduced full-length Sir1's ability to bind and silence HMRa and to interact with Orc1BAH in a two-hybrid assay. Purified recombinant Sir1 formed a large protease-resistant structure within which the Sir1OIR domain was protected, and Orc1BAH bound Sir1OIR more efficiently than full-length Sir1 in vitro. Thus, the Sir1 N terminus exhibited both positive and negative roles in the formation of a Sir1-ORC silencing complex. This functional duality might contribute to Sir1's selectivity for silencer-bound ORCs in vivo.
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18
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Abstract
Sir1 establishes transcriptional silencing at the cryptic mating-type loci HMR and HML (HM loci) by recruiting the three other Sir proteins, Sir2, -3, and -4, that function directly in silenced chromatin. However, SIR1-independent mechanisms also contribute to recruiting the Sir2-4 proteins to the HM loci. A screen to elucidate SIR1-independent mechanisms that establish HMR silencing identified a mutation in YKU80. The role for Ku in silencing both HMR and HML was masked by SIR1. Ku's role in silencing the HM loci was distinct from its shared role with the nuclear architecture protein Esc1 in tethering the HM loci and telomeres to the nuclear periphery. The ability of high-copy SIR4 to rescue HMR silencing defects in sir1Delta cells required Ku, and chromatin immunoprecipitation (ChIP) experiments provided evidence that Ku contributed to Sir4's physical association with the HM loci in vivo. Additional ChIP experiments provided evidence that Ku functioned directly at the HM loci. Thus Ku and Sir1 had overlapping roles in silencing the HM loci.
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Analysis of chromosome III replicators reveals an unusual structure for the ARS318 silencer origin and a conserved WTW sequence within the origin recognition complex binding site. Mol Cell Biol 2008; 28:5071-81. [PMID: 18573888 DOI: 10.1128/mcb.00206-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae chromosome III encodes 11 autonomously replicating sequence (ARS) elements that function as chromosomal replicators. The essential 11-bp ARS consensus sequence (ACS) that binds the origin recognition complex (ORC) has been experimentally defined for most of these replicators but not for ARS318 (HMR-I), which is one of the HMR silencers. In this study, we performed a comprehensive linker scan analysis of ARS318. Unexpectedly, this replicator depends on a 9/11-bp match to the ACS that positions the ORC binding site only 6 bp away from an Abf1p binding site. Although a largely inactive replicator on the chromosome, ARS318 becomes active if the nearby HMR-E silencer is deleted. We also performed a multiple sequence alignment of confirmed replicators on chromosomes III, VI, and VII. This analysis revealed a highly conserved WTW motif 17 to 19 bp from the ACS that is functionally important and is apparent in the 228 phylogenetically conserved ARS elements among the six sensu stricto Saccharomyces species.
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