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Distinct functions of three chromatin remodelers in activator binding and preinitiation complex assembly. PLoS Genet 2022; 18:e1010277. [PMID: 35793348 PMCID: PMC9292117 DOI: 10.1371/journal.pgen.1010277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 07/18/2022] [Accepted: 05/28/2022] [Indexed: 12/01/2022] Open
Abstract
The nucleosome remodeling complexes (CRs) SWI/SNF, RSC, and Ino80C cooperate in evicting or repositioning nucleosomes to produce nucleosome depleted regions (NDRs) at the promoters of many yeast genes induced by amino acid starvation. We analyzed mutants depleted of the catalytic subunits of these CRs for binding of transcriptional activator Gcn4 and recruitment of TATA-binding protein (TBP) during preinitiation complex (PIC) assembly. RSC and Ino80 were found to enhance Gcn4 binding to both UAS elements in NDRs upstream of promoters and to unconventional binding sites within nucleosome-occupied coding sequences; and SWI/SNF contributes to UAS binding when RSC is depleted. All three CRs are actively recruited by Gcn4 to most UAS elements and appear to enhance Gcn4 binding by reducing nucleosome occupancies at the binding motifs, indicating a positive regulatory loop. SWI/SNF acts unexpectedly in WT cells to prevent excessive Gcn4 binding at many UAS elements, indicating a dual mode of action that is modulated by the presence of RSC. RSC and SWI/SNF collaborate to enhance TBP recruitment at Gcn4 target genes, together with Ino80C, in a manner associated with nucleosome eviction at the TBP binding sites. Cooperation among the CRs in TBP recruitment is also evident at the highly transcribed ribosomal protein genes, while RSC and Ino80C act more broadly than SWI/SNF at the majority of other constitutively expressed genes to stimulate this step in PIC assembly. Our findings indicate a complex interplay among the CRs in evicting promoter nucleosomes to regulate activator binding and stimulate PIC assembly. ATP-dependent chromatin remodelers (CRs), including SWI/SNF and RSC in budding yeast, are thought to stimulate transcription by repositioning or evicting promoter nucleosomes, and we recently implicated the CR Ino80C in this process as well. The relative importance of these CRs in stimulating activator binding and recruitment of TATA-binding protein (TBP) to promoters is incompletely understood. Examining mutants depleted of the catalytic subunits of these CRs, we determined that RSC and Ino80C stimulate binding of transcription factor Gcn4 to nucleosome-depleted regions, or linkers between genic nucleosomes, at multiple target genes activated by Gcn4 in amino acid-starved cells, frequently via evicting nucleosomes from the Gcn4 binding motifs. At some genes, SWI/SNF functionally complements RSC, while opposing RSC at others to limit Gcn4 binding. The CRs in turn are recruited by Gcn4, consistent with a positive feedback loop that enhances Gcn4 binding. The three CRs also cooperate to enhance TBP recruitment, again involving nucleosome depletion, at both Gcn4 target and highly expressed ribosomal protein genes, whereas only RSC and Ino80C act broadly throughout the genome to enhance this key step in preinitiation complex assembly. Our findings illuminate functional cooperation among multiple CRs in regulating activator binding and promoter activation.
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2
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Rana A, Gupta N, Thakur A. Post-transcriptional and translational control of the morphology and virulence in human fungal pathogens. Mol Aspects Med 2021; 81:101017. [PMID: 34497025 DOI: 10.1016/j.mam.2021.101017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 08/13/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Host-pathogen interactions at the molecular level are the key to fungal pathogenesis. Fungal pathogens utilize several mechanisms such as adhesion, invasion, phenotype switching and metabolic adaptations, to survive in the host environment and respond. Post-transcriptional and translational regulations have emerged as key regulatory mechanisms ensuring the virulence and survival of fungal pathogens. Through these regulations, fungal pathogens effectively alter their protein pool, respond to various stress, and undergo morphogenesis, leading to efficient and comprehensive changes in fungal physiology. The regulation of virulence through post-transcriptional and translational regulatory mechanisms is mediated through mRNA elements (cis factors) or effector molecules (trans factors). The untranslated regions upstream and downstream of the mRNA, as well as various RNA-binding proteins involved in translation initiation or circularization of the mRNA, play pivotal roles in the regulation of morphology and virulence by influencing protein synthesis, protein isoforms, and mRNA stability. Therefore, post-transcriptional and translational mechanisms regulating the morphology, virulence and drug-resistance processes in fungal pathogens can be the target for new therapeutics. With improved "omics" technologies, these regulatory mechanisms are increasingly coming to the forefront of basic biology and drug discovery. This review aims to discuss various modes of post-transcriptional and translation regulations, and how these mechanisms exert influence in the virulence and morphogenesis of fungal pathogens.
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Affiliation(s)
- Aishwarya Rana
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Nidhi Gupta
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India
| | - Anil Thakur
- Regional Centre for Biotechnology, 3rd Milestone Gurgaon-Faridabad Expressway, Faridabad 121001, India.
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3
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Fultang N, Li X, Li T, Chen YH. Myeloid-Derived Suppressor Cell Differentiation in Cancer: Transcriptional Regulators and Enhanceosome-Mediated Mechanisms. Front Immunol 2021; 11:619253. [PMID: 33519825 PMCID: PMC7840597 DOI: 10.3389/fimmu.2020.619253] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/30/2020] [Indexed: 01/16/2023] Open
Abstract
Myeloid-derived Suppressor Cells (MDSCs) are a sub-population of leukocytes that are important for carcinogenesis and cancer immunotherapy. During carcinogenesis or severe infections, inflammatory mediators induce MDSCs via aberrant differentiation of myeloid precursors. Although several transcription factors, including C/EBPβ, STAT3, c-Rel, STAT5, and IRF8, have been reported to regulate MDSC differentiation, none of them are specifically expressed in MDSCs. How these lineage-non-specific transcription factors specify MDSC differentiation in a lineage-specific manner is unclear. The recent discovery of the c-Rel-C/EBPβ enhanceosome in MDSCs may help explain these context-dependent roles. In this review, we examine several transcriptional regulators of MDSC differentiation, and discuss the concept of non-modular regulation of MDSC signature gene expression by transcription factors such as c-Rel and C/EBPß.
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Affiliation(s)
- Norman Fultang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | | | | | - Youhai H. Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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4
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Erkine AM. 'Nonlinear' Biochemistry of Nucleosome Detergents. Trends Biochem Sci 2018; 43:951-959. [PMID: 30297207 DOI: 10.1016/j.tibs.2018.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/21/2022]
Abstract
The transcriptional activation domains (TADs) are critical for life, yet intrinsically disordered polypeptides with no specific consensus sequence, interacting with multiple targets via low-specificity fuzzy contacts. The recent integration of machine learning approaches in biochemistry allows analysis of large experimental datasets of functional TADs as a whole and clear observation of TAD features. The emerging picture describes TADs as sequences without consensus but with a variety of detergent-like mini-motifs enriched in negatively charged and aromatic amino acids. Comparison of the canonical direct coactivator recruitment model and a new model describing TADs as nucleosome detergents that trigger chromatin remodeling during gene activation helps solve a fundamental enigma of molecular biology spanning 30 years.
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Yu X, Meng X, Liu Y, Li N, Zhang A, Wang TJ, Jiang L, Pang J, Zhao X, Qi X, Zhang M, Wang S, Liu B, Xu ZY. The chromatin remodeler ZmCHB101 impacts expression of osmotic stress-responsive genes in maize. PLANT MOLECULAR BIOLOGY 2018; 97:451-465. [PMID: 29956114 DOI: 10.1007/s11103-018-0751-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/18/2018] [Indexed: 05/16/2023]
Abstract
The maize chromatin remodeler ZmCHB101 plays an essential role in the osmotic stress response. ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Drought and osmotic stresses are recurring conditions that severely constrain crop production. Evidence accumulated in the model plant Arabidopsis thaliana suggests that core components of SWI/SNF chromatin remodeling complexes play essential roles in abiotic stress responses. However, how maize SWI/SNF chromatin remodeling complexes function in osmotic and drought stress responses remains unknown. Here we show that ZmCHB101, a homolog of A. thaliana SWI3D in maize, plays essential roles in osmotic and dehydration stress responses. ZmCHB101-RNA interference (RNAi) transgenic plants displayed osmotic, salt and drought stress-sensitive phenotypes. Genome-wide RNA-sequencing analysis revealed that ZmCHB101 impacts the transcriptional expression landscape of osmotic stress-responsive genes. Intriguingly, ZmCHB101 controls nucleosome densities around transcription start sites of essential stress-responsive genes. Furthermore, we identified that ZmCHB101 associates with RNA polymerase II (RNAPII) in vivo and is a prerequisite for the proper occupancy of RNAPII on the proximal regions of transcription start sites of stress-response genes. Taken together, our findings suggest that ZmCHB101 affects gene expression by remodeling chromatin states and controls RNAPII occupancies in maize under osmotic stress.
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Affiliation(s)
- Xiaoming Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
- Department of Bioengineering, Jilin Agricultural Science and Technology College, Jilin, People's Republic of China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Jinsong Pang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Xinxin Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Meishan Zhang
- Department of Agronomy, Jilin Agricultural University, Changchun, People's Republic of China
| | - Shucai Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China.
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Rawal Y, Chereji RV, Valabhoju V, Qiu H, Ocampo J, Clark DJ, Hinnebusch AG. Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5' Promoters in Yeast. Mol Cell 2018; 70:297-311.e4. [PMID: 29628310 PMCID: PMC6133248 DOI: 10.1016/j.molcel.2018.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/16/2018] [Accepted: 03/02/2018] [Indexed: 01/07/2023]
Abstract
Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ∼30% of Gcn4-binding motifs. Surprisingly, only ∼40% of the bound sites are in promoters, of which only ∼60% activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining ∼300 Gcn4-bound sites are within coding sequences (CDSs), with ∼75 representing the only bound sites near Gcn4-induced genes. Many such unconventional sites map between divergent antisense and sub-genic sense transcripts induced within CDSs adjacent to induced TBP peaks, consistent with Gcn4 activation of cryptic bidirectional internal promoters. Mutational analysis confirms that Gcn4 sites within CDSs can activate sub-genic and full-length transcripts from the same or adjacent genes, showing that functional Gcn4 binding is not confined to promoters. Our results show that internal promoters can be regulated by an activator that functions at conventional 5'-positioned promoters.
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Affiliation(s)
- Yashpal Rawal
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Vishalini Valabhoju
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Hongfang Qiu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Josefina Ocampo
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
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7
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Dahiya R, Natarajan K. Mutational analysis of TAF6 revealed the essential requirement of the histone-fold domain and the HEAT repeat domain for transcriptional activation. FEBS J 2018; 285:1491-1510. [PMID: 29485702 DOI: 10.1111/febs.14423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 12/31/2022]
Abstract
TAF6, bearing the histone H4-like histone-fold domain (HFD), is a subunit of the core TAF module in TFIID and SAGA transcriptional regulatory complexes. We isolated and characterized several yeast TAF6 mutants bearing amino acid substitutions in the HFD, the middle region or the HEAT repeat domain. The TAF6 mutants were highly defective for transcriptional activation by the Gcn4 and Gal4 activators. CHIP assays showed that the TAF6-HFD and the TAF6-HEAT domain mutations independently abrogated the promoter occupancy of TFIID and SAGA complex in vivo. We employed genetic and biochemical assays to identify the relative contributions of the TAF6 HFD and HEAT domains. First, the temperature-sensitive phenotype of the HEAT domain mutant was suppressed by overexpression of the core TAF subunits TAF9 and TAF12, as well as TBP. The HFD mutant defect, however, was suppressed by TAF5 but not by TAF9, TAF12 or TBP. Second, the HEAT mutant but not the HFD mutant was defective for growth in the presence of transcription elongation inhibitors. Third, coimmunoprecipitation assays using yeast cell extracts indicated that the specific TAF6 HEAT domain residues are critical for the interaction of core TAF subunits with the SAGA complex but not with TFIID. The specific HFD residues in TAF6, although required for heterodimerization between TAF6 and TAF9 recombinant proteins, were dispensable for association of the core TAF subunits with TFIID and SAGA in yeast cell extracts. Taken together, the results of our studies have uncovered the non-overlapping requirement of the evolutionarily conserved HEAT domain and the HFD in TAF6 for transcriptional activation.
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Affiliation(s)
- Rashmi Dahiya
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Krishnamurthy Natarajan
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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8
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Eychenne T, Werner M, Soutourina J. Toward understanding of the mechanisms of Mediator function in vivo: Focus on the preinitiation complex assembly. Transcription 2017; 8:328-342. [PMID: 28841352 DOI: 10.1080/21541264.2017.1329000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mediator is a multisubunit complex conserved in eukaryotes that plays an essential coregulator role in RNA polymerase (Pol) II transcription. Despite intensive studies of the Mediator complex, the molecular mechanisms of its function in vivo remain to be fully defined. In this review, we will discuss the different aspects of Mediator function starting with its interactions with specific transcription factors, its recruitment to chromatin and how, as a coregulator, it contributes to the assembly of transcription machinery components within the preinitiation complex (PIC) in vivo and beyond the PIC formation.
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Affiliation(s)
- Thomas Eychenne
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France.,b Institut Pasteur, (Epi)genomics of Animal Development Unit , Development and Stem Cell Biology Department, CNRS UMR3778 , Paris , France
| | - Michel Werner
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
| | - Julie Soutourina
- a Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, CEA, CNRS , Univ. Paris Sud, University Paris Saclay , Gif-sur-Yvette , France
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9
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Bae NS, Seberg AP, Carroll LP, Swanson MJ. Identification of Genes in Saccharomyces cerevisiae that Are Haploinsufficient for Overcoming Amino Acid Starvation. G3 (BETHESDA, MD.) 2017; 7:1061-1084. [PMID: 28209762 PMCID: PMC5386856 DOI: 10.1534/g3.116.037416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/11/2017] [Indexed: 12/17/2022]
Abstract
The yeast Saccharomyces cerevisiae responds to amino acid deprivation by activating a pathway conserved in eukaryotes to overcome the starvation stress. We have screened the entire yeast heterozygous deletion collection to identify strains haploinsufficient for growth in the presence of sulfometuron methyl, which causes starvation for isoleucine and valine. We have discovered that cells devoid of MET15 are sensitive to sulfometuron methyl, and loss of heterozygosity at the MET15 locus can complicate screening the heterozygous deletion collection. We identified 138 cases of loss of heterozygosity in this screen. After eliminating the issues of the MET15 loss of heterozygosity, strains isolated from the collection were retested on sulfometuron methyl. To determine the general effect of the mutations for a starvation response, SMM-sensitive strains were tested for the ability to grow in the presence of canavanine, which induces arginine starvation, and strains that were MET15 were also tested for growth in the presence of ethionine, which causes methionine starvation. Many of the genes identified in our study were not previously identified as starvation-responsive genes, including a number of essential genes that are not easily screened in a systematic way. The genes identified span a broad range of biological functions, including many involved in some level of gene expression. Several unnamed proteins have also been identified, giving a clue as to possible functions of the encoded proteins.
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Affiliation(s)
- Nancy S Bae
- Department of Biochemistry, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona 85308
| | - Andrew P Seberg
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Leslie P Carroll
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, Georgia 31207
| | - Mark J Swanson
- Department of Biochemistry, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona 85308
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, Georgia 31207
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10
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Erkina TY, Erkine AM. Nucleosome distortion as a possible mechanism of transcription activation domain function. Epigenetics Chromatin 2016; 9:40. [PMID: 27679670 PMCID: PMC5029090 DOI: 10.1186/s13072-016-0092-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022] Open
Abstract
After more than three decades since the discovery of transcription activation domains (ADs) in gene-specific activators, the mechanism of their function remains enigmatic. The widely accepted model of direct recruitment by ADs of co-activators and basal transcriptional machinery components, however, is not always compatible with the short size yet very high degree of sequence randomness and intrinsic structural disorder of natural and synthetic ADs. In this review, we formulate the basis for an alternative and complementary model, whereby sequence randomness and intrinsic structural disorder of ADs are necessary for transient distorting interactions with promoter nucleosomes, triggering promoter nucleosome translocation and subsequently gene activation.
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Affiliation(s)
- Tamara Y Erkina
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN 46208 USA
| | - Alexandre M Erkine
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University, Indianapolis, IN 46208 USA
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Abstract
In this mini-review, we summarize our current knowledge about the cross-talk between the different levels of gene expression. We introduce the Ccr4 (carbon catabolite repressed 4)–Not (negative on TATA-less) complex as a candidate to be a master regulator that orchestrates between the different levels of gene expression. An integrated view of the findings about the Ccr4–Not complex suggests that it is involved in gene expression co-ordination. Since the discovery of the Not proteins in a selection for transcription regulators in yeast [Collart and Struhl (1994) Genes Dev. 8, 525–537], the Ccr4–Not complex has been connected to every step of the mRNA lifecycle. Moreover, it has been found to be relevant for appropriate protein folding and quaternary protein structure by being involved in co-translational protein complex assembly.
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12
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Qiu H, Chereji RV, Hu C, Cole HA, Rawal Y, Clark DJ, Hinnebusch AG. Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation. Genome Res 2015; 26:211-25. [PMID: 26602697 PMCID: PMC4728374 DOI: 10.1101/gr.196337.115] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/18/2015] [Indexed: 12/27/2022]
Abstract
Chaperones, nucleosome remodeling complexes, and histone acetyltransferases have been implicated in nucleosome disassembly at promoters of particular yeast genes, but whether these cofactors function ubiquitously, as well as the impact of nucleosome eviction on transcription genome-wide, is poorly understood. We used chromatin immunoprecipitation of histone H3 and RNA polymerase II (Pol II) in mutants lacking single or multiple cofactors to address these issues for about 200 genes belonging to the Gcn4 transcriptome, of which about 70 exhibit marked reductions in H3 promoter occupancy on induction by amino acid starvation. Examining four target genes in a panel of mutants indicated that SWI/SNF, Gcn5, the Hsp70 cochaperone Ydj1, and chromatin-associated factor Yta7 are required downstream from Gcn4 binding, whereas Asf1/Rtt109, Nap1, RSC, and H2AZ are dispensable for robust H3 eviction in otherwise wild-type cells. Using ChIP-seq to interrogate all 70 exemplar genes in single, double, and triple mutants implicated Gcn5, Snf2, and Ydj1 in H3 eviction at most, but not all, Gcn4 target promoters, with Gcn5 generally playing the greatest role and Ydj1 the least. Remarkably, these three cofactors cooperate similarly in H3 eviction at virtually all yeast promoters. Defective H3 eviction in cofactor mutants was coupled with reduced Pol II occupancies for the Gcn4 transcriptome and the most highly expressed uninduced genes, but the relative Pol II levels at most genes were unaffected or even elevated. These findings indicate that nucleosome eviction is crucial for robust transcription of highly expressed genes but that other steps in gene activation are more rate-limiting for most other yeast genes.
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Affiliation(s)
- Hongfang Qiu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Răzvan V Chereji
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Cuihua Hu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Hope A Cole
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yashpal Rawal
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David J Clark
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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13
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Moraga F, Aquea F. Composition of the SAGA complex in plants and its role in controlling gene expression in response to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2015; 6:865. [PMID: 26528322 PMCID: PMC4604261 DOI: 10.3389/fpls.2015.00865] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/30/2015] [Indexed: 05/07/2023]
Abstract
Protein complexes involved in epigenetic regulation of transcription have evolved as molecular strategies to face environmental stress in plants. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is a transcriptional co-activator complex that regulates numerous cellular processes through the coordination of multiple post-translational histone modifications, including acetylation, deubiquitination, and chromatin recognition. The diverse functions of the SAGA complex involve distinct modules that are highly conserved between yeast, flies, and mammals. In this review, the composition of the SAGA complex in plants is described and its role in gene expression regulation under stress conditions summarized. Some of these proteins are likely involved in the regulation of the inducible expression of genes under light, cold, drought, salt, and iron stress, although the functions of several of its components remain unknown.
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Affiliation(s)
- Felipe Moraga
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
| | - Felipe Aquea
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
- Center for Applied Ecology and SustainabilitySantiago, Chile
- *Correspondence: Felipe Aquea
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14
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Fromm M, Avramova Z. ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes? CURRENT OPINION IN PLANT BIOLOGY 2014; 21:75-82. [PMID: 25047977 DOI: 10.1016/j.pbi.2014.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/26/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or 'registers', activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity about the role of H3K4me3 as an activating mark is due to the unknown duality of the ATX1/AtCOMPASS to facilitate PIC assembly and to generate H3K4me3, which is essential for activating transcriptional elongation.
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Affiliation(s)
- Michael Fromm
- Department of Agronomy and Plant Science Innovation, UNL, Lincoln, NE 68588-6008, USA
| | - Zoya Avramova
- School of Biological Science, UNL, Lincoln, NE 68588-6008, USA.
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15
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Rawal Y, Qiu H, Hinnebusch AG. Accumulation of a threonine biosynthetic intermediate attenuates general amino acid control by accelerating degradation of Gcn4 via Pho85 and Cdk8. PLoS Genet 2014; 10:e1004534. [PMID: 25079372 PMCID: PMC4117449 DOI: 10.1371/journal.pgen.1004534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 06/11/2014] [Indexed: 11/19/2022] Open
Abstract
Gcn4 is a master transcriptional regulator of amino acid and vitamin biosynthetic enzymes subject to the general amino acid control (GAAC), whose expression is upregulated in response to amino acid starvation in Saccharomyces cerevisiae. We found that accumulation of the threonine pathway intermediate β-aspartate semialdehyde (ASA), substrate of homoserine dehydrogenase (Hom6), attenuates the GAAC transcriptional response by accelerating degradation of Gcn4, already an exceedingly unstable protein, in cells starved for isoleucine and valine. The reduction in Gcn4 abundance on ASA accumulation requires Cdk8/Srb10 and Pho85, cyclin-dependent kinases (CDKs) known to mediate rapid turnover of Gcn4 by the proteasome via phosphorylation of the Gcn4 activation domain under nonstarvation conditions. Interestingly, rescue of Gcn4 abundance in hom6 cells by elimination of SRB10 is not accompanied by recovery of transcriptional activation, while equivalent rescue of UAS-bound Gcn4 in hom6 pho85 cells restores greater than wild-type activation of Gcn4 target genes. These and other findings suggest that the two CDKs target different populations of Gcn4 on ASA accumulation, with Srb10 clearing mostly inactive Gcn4 molecules at the promoter that are enriched for sumoylation of the activation domain, and Pho85 clearing molecules unbound to the UAS that include both fully functional and inactive Gcn4 species. Transcriptional activator Gcn4 maintains amino acid homeostasis in budding yeast by inducing multiple amino acid biosynthetic pathways in response to starvation for any amino acid—the general amino acid control. Gcn4 abundance is tightly regulated by the interplay between an intricate translational control mechanism, which induces Gcn4 synthesis in starved cells, and a pathway of phosphorylation and ubiquitylation that mediates its rapid degradation by the proteasome. Here, we discovered that accumulation of a threonine biosynthetic pathway intermediate, β-aspartate semialdehyde (ASA), in hom6Δ mutant cells impairs general amino acid control in cells starved for isoleucine and valine by accelerating the already rapid degradation of Gcn4, in a manner requiring its phosphorylation by cyclin-dependent kinases Cdk8/Srb10 and Pho85. Interestingly, our results unveil a division of labor between these two kinases wherein Srb10 primarily targets inactive Gcn4 molecules—presumably damaged under conditions of ASA excess—while Pho85 clears a greater proportion of functional Gcn4 species from the cell. The ability of ASA to inhibit transcriptional induction of threonine pathway enzymes by Gcn4, dampening ASA accumulation and its toxic effects on cell physiology, should be adaptive in the wild when yeast encounters natural antibiotics that target Hom6 enzymatic activity.
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Affiliation(s)
- Yashpal Rawal
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hongfang Qiu
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan G. Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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16
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Ansari SA, Paul E, Sommer S, Lieleg C, He Q, Daly AZ, Rode KA, Barber WT, Ellis LC, LaPorta E, Orzechowski AM, Taylor E, Reeb T, Wong J, Korber P, Morse RH. Mediator, TATA-binding protein, and RNA polymerase II contribute to low histone occupancy at active gene promoters in yeast. J Biol Chem 2014; 289:14981-95. [PMID: 24727477 DOI: 10.1074/jbc.m113.529354] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Transcription by RNA polymerase II (Pol II) in eukaryotes requires the Mediator complex, and often involves chromatin remodeling and histone eviction at active promoters. Here we address the role of Mediator in recruitment of the Swi/Snf chromatin remodeling complex and its role, along with components of the preinitiation complex (PIC), in histone eviction at inducible and constitutively active promoters in the budding yeast Saccharomyces cerevisiae. We show that recruitment of the Swi/Snf chromatin remodeling complex to the induced CHA1 promoter, as well as its association with several constitutively active promoters, depends on the Mediator complex but is independent of Mediator at the induced MET2 and MET6 genes. Although transcriptional activation and histone eviction at CHA1 depends on Swi/Snf, Swi/Snf recruitment is not sufficient for histone eviction at the induced CHA1 promoter. Loss of Swi/Snf activity does not affect histone occupancy of several constitutively active promoters; in contrast, higher histone occupancy is seen at these promoters in Mediator and PIC component mutants. We propose that an initial activator-dependent, nucleosome remodeling step allows PIC components to outcompete histones for occupancy of promoter sequences. We also observe reduced promoter association of Mediator and TATA-binding protein in a Pol II (rpb1-1) mutant, indicating mutually cooperative binding of these components of the transcription machinery and indicating that it is the PIC as a whole whose binding results in stable histone eviction.
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Affiliation(s)
- Suraiya A Ansari
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Emily Paul
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Sebastian Sommer
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Corinna Lieleg
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Qiye He
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
| | - Alexandre Z Daly
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Kara A Rode
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Wesley T Barber
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Laura C Ellis
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Erika LaPorta
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
| | - Amanda M Orzechowski
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Emily Taylor
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Tanner Reeb
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Jason Wong
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509
| | - Philipp Korber
- the Adolf-Butenandt-Institut, Universität München, 80336 Munich, Germany
| | - Randall H Morse
- From the Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, the Department of Biomedical Science, University at Albany School of Public Health, Albany, New York 12201-0509, and
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17
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The TAF9 C-terminal conserved region domain is required for SAGA and TFIID promoter occupancy to promote transcriptional activation. Mol Cell Biol 2014; 34:1547-63. [PMID: 24550006 DOI: 10.1128/mcb.01060-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A common function of the TFIID and SAGA complexes, which are recruited by transcriptional activators, is to deliver TBP to promoters to stimulate transcription. Neither the relative contributions of the five shared TBP-associated factor (TAF) subunits in TFIID and SAGA nor the requirement for different domains in shared TAFs for transcriptional activation is well understood. In this study, we uncovered the essential requirement for the highly conserved C-terminal region (CRD) of Taf9, a shared TAF, for transcriptional activation in yeast. Transcriptome profiling performed under Gcn4-activating conditions showed that the Taf9 CRD is required for induced expression of ∼9% of the yeast genome. The CRD was not essential for the Taf9-Taf6 interaction, TFIID or SAGA integrity, or Gcn4 interaction with SAGA in cell extracts. Microarray profiling of a SAGA mutant (spt20Δ) yielded a common set of genes induced by Spt20 and the Taf9 CRD. Chromatin immunoprecipitation (ChIP) assays showed that, although the Taf9 CRD mutation did not impair Gcn4 occupancy, the occupancies of TFIID, SAGA, and the preinitiation complex were severely impaired at several promoters. These results suggest a crucial role for the Taf9 CRD in genome-wide transcription and highlight the importance of conserved domains, other than histone fold domains, as a common determinant for TFIID and SAGA functions.
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Panepinto JC, Heinz E, Traven A. The cellular roles of Ccr4-NOT in model and pathogenic fungi-implications for fungal virulence. Front Genet 2013; 4:302. [PMID: 24391665 PMCID: PMC3868889 DOI: 10.3389/fgene.2013.00302] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/09/2013] [Indexed: 11/13/2022] Open
Abstract
The fungal Ccr4-NOT complex has been implicated in orchestrating gene expression networks that impact on pathways key for virulence in pathogenic species. The activity of Ccr4-NOT regulates cell wall integrity, antifungal drug susceptibility, adaptation to host temperature, and the developmental switches that enable the formation of pathogenic structures, such as filamentous hyphae. Moreover, Ccr4-NOT impacts on DNA repair pathways and genome stability, opening the possibility that this gene regulator could control adaptive responses in pathogens that are driven by chromosomal alterations. Here we provide a synthesis of the cellular roles of the fungal Ccr4-NOT, focusing on pathways important for virulence toward animals. Our review is based on studies in models yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and two species that cause serious human infections, Candida albicans and Cryptococcus neoformans. We hypothesize that the activity of Ccr4-NOT could be targeted for future antifungal drug discovery, a proposition supported by the fact that inactivation of the genes encoding subunits of Ccr4-NOT in C. albicans and C. neoformans reduces virulence in the mouse infection model. We performed bioinformatics analysis to identify similarities and differences between Ccr4-NOT subunits in fungi and animals, and discuss this knowledge in the context of future antifungal strategies.
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Affiliation(s)
- John C Panepinto
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York Buffalo, NY, USA
| | - Eva Heinz
- Department of Microbiology, Monash University Clayton, VIC, Australia ; Victorian Bioinformatics Consortium, School of Biomedical Sciences, Monash University Clayton, VIC, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology, Monash University Clayton, VIC, Australia
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19
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Kamata K, Goswami G, Kashio S, Urano T, Nakagawa R, Uchida H, Oki M. The N-terminus and Tudor domains of Sgf29 are important for its heterochromatin boundary formation function. ACTA ACUST UNITED AC 2013; 155:159-71. [DOI: 10.1093/jb/mvt108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Ansari SA, Morse RH. Mechanisms of Mediator complex action in transcriptional activation. Cell Mol Life Sci 2013; 70:2743-56. [PMID: 23361037 PMCID: PMC11113466 DOI: 10.1007/s00018-013-1265-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 12/14/2022]
Abstract
Mediator is a large multisubunit complex that plays a central role in the regulation of RNA Pol II transcribed genes. Conserved in overall structure and function among eukaryotes, Mediator comprises 25-30 protein subunits that reside in four distinct modules, termed head, middle, tail, and CDK8/kinase. Different subunits of Mediator contact other transcriptional regulators including activators, co-activators, general transcription factors, subunits of RNA Pol II, and specifically modified histones, leading to the regulated expression of target genes. This review is focused on the interactions of specific Mediator subunits with diverse transcription regulators and how those interactions contribute to Mediator function in transcriptional activation.
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Affiliation(s)
- Suraiya A. Ansari
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
| | - Randall H. Morse
- Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12201–0509 USA
- Department of Biomedical Science, University at Albany School of Public Health, Albany, NY USA
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21
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Correct assembly of RNA polymerase II depends on the foot domain and is required for multiple steps of transcription in Saccharomyces cerevisiae. Mol Cell Biol 2013; 33:3611-26. [PMID: 23836886 DOI: 10.1128/mcb.00262-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recent papers have provided insight into the cytoplasmic assembly of RNA polymerase II (RNA pol II) and its transport to the nucleus. However, little is known about the mechanisms governing its nuclear assembly, stability, degradation, and recycling. We demonstrate that the foot of RNA pol II is crucial for the assembly and stability of the complex, by ensuring the correct association of Rpb1 with Rpb6 and of the dimer Rpb4-Rpb7 (Rpb4/7). Mutations at the foot affect the assembly and stability of the enzyme, a defect that is offset by RPB6 overexpression, in coordination with Rpb1 degradation by an Asr1-independent mechanism. Correct assembly is a prerequisite for the proper maintenance of several transcription steps. In fact, assembly defects alter transcriptional activity and the amount of enzyme associated with the genes, affect C-terminal domain (CTD) phosphorylation, interfere with the mRNA-capping machinery, and possibly increase the amount of stalled RNA pol II. In addition, our data show that TATA-binding protein (TBP) occupancy does not correlate with RNA pol II occupancy or transcriptional activity, suggesting a functional relationship between assembly, Mediator, and preinitiation complex (PIC) stability. Finally, our data help clarify the mechanisms governing the assembly and stability of RNA pol II.
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22
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Endo H, Nakabayashi Y, Kawashima S, Enomoto T, Seki M, Horikoshi M. Nucleosome surface containing nucleosomal DNA entry/exit site regulates H3-K36me3 via association with RNA polymerase II and Set2. Genes Cells 2013; 17:65-81. [PMID: 22212475 DOI: 10.1111/j.1365-2443.2011.01573.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A nucleosome is composed of intrinsically disordered histone tails and a structured nucleosome core surrounded by DNA. A variety of modifiable residues on the intrinsically disordered histone tails have been identified in the last decade. Mapping of the functional residues on the structured nucleosome core surface was recently initiated by global analysis of a comprehensive histone point mutant library (histone-GLibrary). It stands to reason that a functional relationship exists between modifiable residues on the intrinsically disordered histone tails and functional residues on the structured nucleosome core; however, this matter has been poorly explored. During transcription elongation, trimethylation of histone H3 at lysine 36 (H3-K36me3) is mediated by histone methyltransferase Set2, which binds to RNA polymerase II. Here, we used a histone-GLibrary that encompasses the nucleosomal DNA entry/exit site to show that six residues (H2A-G107, H2A-I112, H2A-L117, H3-T45, H3-R49 and H3-R52) form a surface on the structured nucleosome core and regulate H3-K36me3. Trimethylation at H3-K4 introduced by histone methyltransferase Set1 was not affected by the mutation of any of the six residues. Chromatin immunoprecipitation analysis showed that most of these residues are critical for the chromatin association of RNA polymerase II and Set2, suggesting that these components regulate H3-K36me3 through functional interactions with the structured nucleosome core surface.
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Affiliation(s)
- Hirohito Endo
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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23
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Abstract
There is increasing evidence that certain Vacuolar protein sorting (Vps) proteins, factors that mediate vesicular protein trafficking, have additional roles in regulating transcription factors at the endosome. We found that yeast mutants lacking the phosphatidylinositol 3-phosphate [PI(3)P] kinase Vps34 or its associated protein kinase Vps15 display multiple phenotypes indicating impaired transcription elongation. These phenotypes include reduced mRNA production from long or G+C-rich coding sequences (CDS) without affecting the associated GAL1 promoter activity, and a reduced rate of RNA polymerase II (Pol II) progression through lacZ CDS in vivo. Consistent with reported genetic interactions with mutations affecting the histone acetyltransferase complex NuA4, vps15Δ and vps34Δ mutations reduce NuA4 occupancy in certain transcribed CDS. vps15Δ and vps34Δ mutants also exhibit impaired localization of the induced GAL1 gene to the nuclear periphery. We found unexpectedly that, similar to known transcription elongation factors, these and several other Vps factors can be cross-linked to the CDS of genes induced by Gcn4 or Gal4 in a manner dependent on transcriptional induction and stimulated by Cdk7/Kin28-dependent phosphorylation of the Pol II C-terminal domain (CTD). We also observed colocalization of a fraction of Vps15-GFP and Vps34-GFP with nuclear pores at nucleus-vacuole (NV) junctions in live cells. These findings suggest that Vps factors enhance the efficiency of transcription elongation in a manner involving their physical proximity to nuclear pores and transcribed chromatin.
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Ding Y, Ndamukong I, Xu Z, Lapko H, Fromm M, Avramova Z. ATX1-generated H3K4me3 is required for efficient elongation of transcription, not initiation, at ATX1-regulated genes. PLoS Genet 2012; 8:e1003111. [PMID: 23284292 PMCID: PMC3527332 DOI: 10.1371/journal.pgen.1003111] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 10/08/2012] [Indexed: 01/26/2023] Open
Abstract
Tri-methylated H3 lysine 4 (H3K4me3) is associated with transcriptionally active genes, but its function in the transcription process is still unclear. Point mutations in the catalytic domain of ATX1 (ARABIDOPSIS TRITHORAX1), a H3K4 methyltransferase, and RNAi knockdowns of subunits of the AtCOMPASS–like (Arabidopsis Complex Proteins Associated with Set) were used to address this question. We demonstrate that both ATX1 and AtCOMPASS–like are required for high level accumulation of TBP (TATA-binding protein) and Pol II at promoters and that this requirement is independent of the catalytic histone modifying activity. However, the catalytic function is critically required for transcription as H3K4me3 levels determine the efficiency of transcription elongation. The roles of H3K4me3, ATX1, and AtCOMPASS–like may be of a general relevance for transcription of Trithorax-activated eukaryotic genes. We provide a definitive answer to the question regarding the role of histone H3 lysine 4 tri-methylation marks in the transcription of two ATX1-regulated genes. Despite the proven correlation between the gene transcriptional activity and the level of H3K4me3 modification on the nucleosomes, whether H3K4me3 contributes to, or simply “registers,” active transcription has remained unclear. Another broader-relevance question is whether histone-modifying proteins are required for recruitment of the general transcription machinery, thus playing roles beyond their catalytic activity. Using a combination of gene deletion and specific point mutation analyses, we untangle overlapping effects and reveal that H3K4me3 is not required for TBP/Pol II recruitment to promoters but is critical as an activating mark for transcription elongation. The existing hitherto ambiguity about the role of H3K4me3 as an activating mark has been largely due to the unknown duality of the ATX1/AtCOMPASS functions: facilitating PIC assembly and producing H3K4me3 as an activating mark for transcription elongation.
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Affiliation(s)
- Yong Ding
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
| | - Ivan Ndamukong
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Zaoshi Xu
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
| | - Hanna Lapko
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
| | - Michael Fromm
- University of Nebraska Center for Biotechnology, Lincoln, Nebraska, United States of America
- Center for Plant Science Innovation, Lincoln, Nebraska, United States of America
- * E-mail: (MF); (ZA)
| | - Zoya Avramova
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (MF); (ZA)
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Abstract
The purpose of this review is to provide an analysis of the latest developments on the functions of the carbon catabolite-repression 4-Not (Ccr4-Not) complex in regulating eukaryotic gene expression. Ccr4-Not is a nine-subunit protein complex that is conserved in sequence and function throughout the eukaryotic kingdom. Although Ccr4-Not has been studied since the 1980s, our understanding of what it does is constantly evolving. Once thought to solely regulate transcription, it is now clear that it has much broader roles in gene regulation, such as in mRNA decay and quality control, RNA export, translational repression and protein ubiquitylation. The mechanism of actions for each of its functions is still being debated. Some of the difficulty in drawing a clear picture is that it has been implicated in so many processes that regulate mRNAs and proteins in both the cytoplasm and the nucleus. We will describe what is known about the Ccr4-Not complex in yeast and other eukaryotes in an effort to synthesize a unified model for how this complex coordinates multiple steps in gene regulation and provide insights into what questions will be most exciting to answer in the future.
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Affiliation(s)
- Jason E. Miller
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Center for RNA Molecular Biology, Penn State University, University Park, PA 16802
| | - Joseph C. Reese
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Center for RNA Molecular Biology, Penn State University, University Park, PA 16802
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26
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Abstract
All RNA species in yeast cells are subject to turnover. Work over the past 20 years has defined degradation mechanisms for messenger RNAs, transfer RNAs, ribosomal RNAs, and noncoding RNAs. In addition, numerous quality control mechanisms that target aberrant RNAs have been identified. Generally, each decay mechanism contains factors that funnel RNA substrates to abundant exo- and/or endonucleases. Key issues for future work include determining the mechanisms that control the specificity of RNA degradation and how RNA degradation processes interact with translation, RNA transport, and other cellular processes.
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Affiliation(s)
- Roy Parker
- Department of Molecular and Cellular Biology, University of Arizona and Howard Hughes Medical Institute, Tucson, AZ 85721, USA.
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Brannan K, Kim H, Erickson B, Glover-Cutter K, Kim S, Fong N, Kiemele L, Hansen K, Davis R, Lykke-Andersen J, Bentley DL. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol Cell 2012; 46:311-24. [PMID: 22483619 DOI: 10.1016/j.molcel.2012.03.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/27/2011] [Accepted: 03/08/2012] [Indexed: 02/07/2023]
Abstract
We report a function of human mRNA decapping factors in control of transcription by RNA polymerase II. Decapping proteins Edc3, Dcp1a, and Dcp2 and the termination factor TTF2 coimmunoprecipitate with Xrn2, the nuclear 5'-3' exonuclease "torpedo" that facilitates transcription termination at the 3' ends of genes. Dcp1a, Xrn2, and TTF2 localize near transcription start sites (TSSs) by ChIP-seq. At genes with 5' peaks of paused pol II, knockdown of decapping or termination factors Xrn2 and TTF2 shifted polymerase away from the TSS toward upstream and downstream distal positions. This redistribution of pol II is similar in magnitude to that caused by depletion of the elongation factor Spt5. We propose that coupled decapping of nascent transcripts and premature termination by the "torpedo" mechanism is a widespread mechanism that limits bidirectional pol II elongation. Regulated cotranscriptional decapping near promoter-proximal pause sites followed by premature termination could control productive pol II elongation.
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Affiliation(s)
- Kris Brannan
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
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28
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Rosonina E, Duncan SM, Manley JL. Sumoylation of transcription factor Gcn4 facilitates its Srb10-mediated clearance from promoters in yeast. Genes Dev 2012; 26:350-5. [PMID: 22345516 DOI: 10.1101/gad.184689.111] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The small ubiquitin-related modifier (SUMO) is a conserved factor that post-translationally regulates proteins involved in many cellular processes, including gene transcription. We previously demonstrated that promoter-bound factors become sumoylated during activation of inducible genes in yeast, but the identity of these factors, and the role of sumoylation in their function, was unknown. Here we show that the transcriptional activator Gcn4 is sumoylated on two specific lysine residues and in a manner that depends on its ability to bind DNA, indicating that sumoylation occurs after Gcn4 binding to target promoters. Importantly, this functions to facilitate the subsequent removal of the activator from these promoters after recruitment of RNA polymerase II, which can prevent inappropriate transcription of target genes. Furthermore, we show that clearance of sumoylated Gcn4 requires the protein kinase and Mediator complex subunit Srb10, linking activator removal with target gene transcription. Our study demonstrates an unexpected role for protein sumoylation in the process of transcriptional activation.
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Affiliation(s)
- Emanuel Rosonina
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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29
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Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 2012; 189:705-36. [PMID: 22084422 DOI: 10.1534/genetics.111.127019] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Here we review recent advances in understanding the regulation of mRNA synthesis in Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been conserved in all eukaryotes, and budding yeast has been at the forefront in the discovery and dissection of these conserved mechanisms. Topics covered include upstream activation sequence and promoter structure, transcription factor classification, and examples of regulated transcription factor activity. We also examine advances in understanding the RNA polymerase II transcription machinery, conserved coactivator complexes, transcription activation domains, and the cooperation of these factors in gene regulatory mechanisms.
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Paf1 restricts Gcn4 occupancy and antisense transcription at the ARG1 promoter. Mol Cell Biol 2012; 32:1150-63. [PMID: 22252319 DOI: 10.1128/mcb.06262-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conserved Paf1 complex negatively regulates the expression of numerous genes, yet the mechanisms by which it represses gene expression are not well understood. In this study, we use the ARG1 gene as a model to investigate the repressive functions of the Paf1 complex in Saccharomyces cerevisiae. Our results indicate that Paf1 mediates repression of the ARG1 gene independently of the gene-specific repressor, ArgR/Mcm1. Rather, by promoting histone H2B lysine 123 ubiquitylation, Paf1 represses the ARG1 gene by negatively affecting Gcn4 occupancy at the promoter. Consistent with this observation, Gcn5 and its acetylation sites on histone H3 are required for full ARG1 derepression in paf1Δ cells, and the repressive effect of Paf1 is largely maintained when the ARG1 promoter directs transcription of a heterologous coding region. Derepression of the ARG1 gene in paf1Δ cells is accompanied by small changes in nucleosome occupancy, although these changes are subtle in comparison to those that accompany gene activation through amino acid starvation. Additionally, conditions that stimulate ARG1 transcription, including PAF1 deletion, lead to increased antisense transcription across the ARG1 promoter. This promoter-associated antisense transcription positively correlates with ARG1 sense transcription. Finally, our results indicate that Paf1 represses other genes through mechanisms similar to those used at the ARG1 gene.
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Shukla A, Lahudkar S, Durairaj G, Bhaumik SR. Sgf29p facilitates the recruitment of TATA box binding protein but does not alter SAGA's global structural integrity in vivo. Biochemistry 2012; 51:706-14. [PMID: 22224423 DOI: 10.1021/bi201708z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although Sgf29p has been biochemically implicated as a component of SAGA (Spt-Ada-Gcn5 acetyltransferase), its precise mechanism of action in transcription is not clearly understood in vivo. Here, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation (ChIP) assay in conjunction with transcriptional and mutational analyses, we show that Sgf29p along with other SAGA components is recruited to the upstream activating sequence (UAS) of a SAGA-regulated gene, GAL1, in an activation domain-dependent manner. However, Sgf29p does not alter the recruitment of Spt20p that maintains the overall structural and functional integrity of SAGA. The recruitment of other SAGA components such as TAF10p, TAF12p, and Ubp8p to the GAL1 UAS is also not altered in the absence of Sgf29p. Interestingly, we find that the recruitment of TBP (TATA box binding protein that nucleates the assembly of general transcription factors to form the preinitiation complex for transcriptional initiation) to the core promoter of GAL1 is weakened in Δsgf29. Likewise, Sgf29p also enhances the recruitment of TBP to other SAGA-regulated promoters. Such weakening of recruitment of TBP to these promoters subsequently decreases the level of transcription. Taken together, these results support the idea that SAGA-associated Sgf29p facilitates the recruitment of TBP (and hence transcription) without altering the global structural integrity of SAGA in vivo.
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Affiliation(s)
- Abhijit Shukla
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901, United States
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Sun WJ, Zhou X, Zheng JH, Lu MD, Nie JY, Yang XJ, Zheng ZQ. Histone acetyltransferases and deacetylases: molecular and clinical implications to gastrointestinal carcinogenesis. Acta Biochim Biophys Sin (Shanghai) 2012; 44:80-91. [PMID: 22194016 DOI: 10.1093/abbs/gmr113] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Histone acetyltransferases and deacetylases are two groups of enzymes whose opposing activities govern the dynamic levels of reversible acetylation on specific lysine residues of histones and many other proteins. Gastrointestinal (GI) carcinogenesis is a major cause of morbidity and mortality worldwide. In addition to genetic and environmental factors, the role of epigenetic abnormalities such as aberrant histone acetylation has been recognized to be pivotal in regulating benign tumorigenesis and eventual malignant transformation. Here we provide an overview of histone acetylation, list the major groups of histone acetyltransferases and deacetylases, and cover in relatively more details the recent studies that suggest the links of these enzymes to GI carcinogenesis. As potential novel therapeutics for GI and other cancers, histone deacetylase inhibitors are also discussed.
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Affiliation(s)
- Wei-Jian Sun
- The 2nd Affiliated Hospital, Wenzhou Medical College, China
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Collart MA, Panasenko OO. The Ccr4--not complex. Gene 2011; 492:42-53. [PMID: 22027279 DOI: 10.1016/j.gene.2011.09.033] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/06/2011] [Accepted: 09/29/2011] [Indexed: 12/11/2022]
Abstract
The Ccr4-Not complex is a unique, essential and conserved multi-subunit complex that acts at the level of many different cellular functions to regulate gene expression. Two enzymatic activities, namely ubiquitination and deadenylation, are provided by different subunits of the complex. However, studies over the last decade have demonstrated a tantalizing multi-functionality of this complex that extends well beyond its identified enzymatic activities. Most of our initial knowledge about the Ccr4-Not complex stemmed from studies in yeast, but an increasing number of reports on this complex in other species are emerging. In this review we will discuss the structure and composition of the complex, and describe the different cellular functions with which the Ccr4-Not complex has been connected in different organisms. Finally, based upon our current state of knowledge, we will propose a model to explain how one complex can provide such multi-functionality. This model suggests that the Ccr4-Not complex might function as a "chaperone platform".
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Affiliation(s)
- Martine A Collart
- Dpt Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
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Distinct role of Mediator tail module in regulation of SAGA-dependent, TATA-containing genes in yeast. EMBO J 2011; 31:44-57. [PMID: 21971086 DOI: 10.1038/emboj.2011.362] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 09/07/2011] [Indexed: 11/08/2022] Open
Abstract
The evolutionarily conserved Mediator complex is required for transcription of nearly all RNA Pol II-dependent promoters, with the tail module serving to recruit Mediator to active promoters in current models. However, transcriptional dependence on tail module subunits varies in a gene-specific manner, and the generality of the tail module requirement for transcriptional activation has not been explored. Here, we show that tail module subunits function redundantly to recruit Mediator to promoters in yeast, and transcriptome analysis shows stronger effects on genome-wide expression in a double-tail subunit deletion mutant than in single-subunit deletion mutants. Unexpectedly, TATA-containing and SAGA-dependent genes were much more affected by impairment of tail module function than were TFIID-dependent genes. Consistent with this finding, Mediator and preinitiation complex association with SAGA-dependent promoters is substantially reduced in gal11/med15Δ med3Δ yeast, whereas association of TBP, Pol II, and other Mediator modules with TFIID-dependent genes is largely independent of the tail module. Thus, we have identified a connection between the Mediator tail module and the division of promoter dependence between TFIID and SAGA.
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Kruk JA, Dutta A, Fu J, Gilmour DS, Reese JC. The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes Dev 2011; 25:581-93. [PMID: 21406554 DOI: 10.1101/gad.2020911] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Ccr4-Not complex has been implicated in the control of multiple steps of mRNA metabolism; however, its functions in transcription remain ambiguous. The discovery that Ccr4/Pop2 is the major cytoplasmic mRNA deadenylase and the detection of Not proteins within mRNA processing bodies have raised questions about the roles of the Ccr4-Not complex in transcription. Here we firmly establish Ccr4-Not as a positive elongation factor for RNA polymerase II (RNAPII). The Ccr4-Not complex is targeted to the coding region of genes in a transcription-dependent manner similar to RNAPII and promotes elongation in vivo. Furthermore, Ccr4-Not interacts directly with elongating RNAPII complexes and stimulates transcription elongation of arrested polymerase in vitro. Ccr4-Not can reactivate backtracked RNAPII using a mechanism different from that of the well-characterized elongation factor TFIIS. While not essential for its interaction with elongation complexes, Ccr4-Not interacts with the emerging transcript and promotes elongation in a manner dependent on transcript length, although this interaction is not required for it to bind RNAPII. Our comprehensive analysis shows that Ccr4-Not directly regulates transcription, and suggests it does so by promoting the resumption of elongation of arrested RNAPII when it encounters transcriptional blocks in vivo.
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Affiliation(s)
- Jennifer A Kruk
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Li L, Zhu J, Tian J, Liu X, Feng C. A role for Gcn5 in cardiomyocyte differentiation of rat mesenchymal stem cells. Mol Cell Biochem 2010; 345:309-16. [PMID: 20835911 DOI: 10.1007/s11010-010-0586-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 08/28/2010] [Indexed: 01/28/2023]
Abstract
MSCs possess the capacity of self-renewal and potential of differentiation into various kinds of specialized tissue cells including myocardiocytes. From self-renewing to oriented differentiation, chromatin is remodeled into heritable states that allow activation or maintain the repression of regulatory genes, which means specific genes in self-renewing switched off and specific genes in oriented differentiation activated (Bernstein et al. Cell 125:315-326, 2006). These epigenetic states are established and controlled largely by specific patterns of histone posttranslational modifications, in particular, histone acetylation (Li Nat Rev Genet 3:662-673, 2002). In cardiomyocyte differentiation of rat MSCs, we focused on Gcn5, which linked a known transcriptional coactivator with catalytic histone acetyltransferase activity (Brownell et al. Cell 84:843-851, 1996). To clarify participatory in vivo role of Gcn5, using an RNA interference (RNAi) strategy employing shRNA to specifically knockdown Gcn5 expression in MSCs, we found that HAT activity altered dynamically depended on the inhibition of Gcn5 during MSCs differentiation. Chromatin immunoprecipitation (ChIP) assay showed the increased binding of acetyl histone H3 to the early cardiomyocyte-specific genes GATA4 and NKx2.5 promoters in cardiomyocyte differentiation of MSCs by 5-azacytidine inducing, whereas the decreased binding with lower Gcn5 expression. Cell ultrastructure analysis revealed that MSCs induced by 5-azacytidine possess morphological characteristics of cardiomyocyte cells. The shape of MSCs transfected by Gcn5 RNAi was similar to normal MSCs, but the chromatin showed heavy electron-density and a hard-packed structure. This intermediate state of chromatin may be an inactive part of MSCs differentiation. These results demonstrate that Gcn5, possessing acetyltransferase activity, is involved in regulating chromatin configuration around GATA4 and NKx2.5 in cardiomyocyte differentiation of rat MSCs by changing the level of histone acetylation. HAT activity depending on Gcn5 is important in differentiation of MSCs into cardiomyocytes as a consequence of the remodeling of the chromatin configuration caused by modification of histone H3.
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Affiliation(s)
- Li Li
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi-An Men St., West District, 100034, Beijing, People's Republic of China.
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Bhaumik SR. Distinct regulatory mechanisms of eukaryotic transcriptional activation by SAGA and TFIID. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1809:97-108. [PMID: 20800707 DOI: 10.1016/j.bbagrm.2010.08.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 08/18/2010] [Accepted: 08/19/2010] [Indexed: 01/08/2023]
Abstract
A growing number of human diseases are linked to abnormal gene expression which is largely controlled at the level of transcriptional initiation. The gene-specific activator promotes the initiation of transcription through its interaction with one or more components of the transcriptional initiation machinery, hence leading to stimulated transcriptional initiation or activation. However, all activator proteins do not target the same component(s) of the transcriptional initiation machinery. Rather, they can have different target specificities, and thus, can lead to distinct mechanisms of transcriptional activation. Two such distinct mechanisms of transcriptional activation in yeast are mediated by the SAGA (Spt-Ada-Gcn5-Acetyltransferase) and TFIID (Transcription factor IID) complexes, and are termed as "SAGA-dependent" and "TFIID-dependent" transcriptional activation, respectively. SAGA is the target of the activator in case of SAGA-dependent transcriptional activation, while the targeting of TFIID by the activator leads to TFIID-dependent transcriptional activation. Both the SAGA and TFIID complexes are highly conserved from yeast to human, and play crucial roles in gene activation among eukaryotes. The regulatory mechanisms of eukaryotic transcriptional activation by SAGA and TFIID are discussed here. This article is part of a Special Issue entitled The 26S Proteasome: When degradation is just not enough!
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Affiliation(s)
- Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illnois University School of Medicine, Carbondale, IL 62901, USA.
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Mcm1p binding sites in the ARG1 promoter positively regulate ARG1 transcription and S. cerevisiae growth in the absence of arginine and Gcn4p. Amino Acids 2010; 40:623-31. [PMID: 20625780 DOI: 10.1007/s00726-010-0687-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 06/30/2010] [Indexed: 10/19/2022]
Abstract
In this study, we investigated the activating role of Mcm1p at ARG1 during arginine starvation. Our results showed that two Mcm1p binding sites positively contribute to ARG1 transcription and cell growth. Especially, we provide strong evidence that the Mcm1p binding sites play a positive role in ARG1 transcription to overcome arginine starvation in the absence of Gcn4p. In addition, we found that the Mcm1p binding sites are not only regulated by the presence or absence of arginine but also in the presence or absence of other amino acids. These findings suggest that the ARG1 promoter utilizes different DNA elements to control transcription, depending on which amino acids are detected in the medium.
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Rosonina E, Duncan SM, Manley JL. SUMO functions in constitutive transcription and during activation of inducible genes in yeast. Genes Dev 2010; 24:1242-52. [PMID: 20504900 DOI: 10.1101/gad.1917910] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transcription factors represent one of the largest groups of proteins regulated by SUMO (small ubiquitin-like modifier) modification, and their sumoylation is usually associated with transcriptional repression. To investigate whether sumoylation plays a general role in regulating transcription in yeast, we determined the occupancy of sumoylated proteins at a variety of genes by chromatin immunoprecipitation (ChIP) using an antibody that recognizes the yeast SUMO peptide. Surprisingly, we detected sumoylated proteins at all constitutively transcribed genes tested but not at repressed genes. Ubc9, the SUMO conjugation enzyme, was not present on these genes, but its inactivation reduced SUMO at the constitutive promoters and modestly decreased RNA polymerase II levels. In contrast, activation of the inducible GAL1, STL1, and ARG1 genes caused not only a striking accumulation of SUMO at all three promoter regions, but also recruitment of Ubc9, indicating that gene activation involves sumoylation of promoter-bound factors. However, Ubc9 inactivation, while reducing sumoylation at the induced promoters, paradoxically resulted in increased transcription. Providing an explanation for this, the reduced sumoylation impaired the cell's ability to appropriately shut off transcription of the induced ARG1 gene, indicating that SUMO can facilitate transcriptional silencing. Our findings thus establish unexpected roles for sumoylation in both constitutive and activated transcription, and provide a novel mechanism for regulating gene expression.
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Affiliation(s)
- Emanuel Rosonina
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Abstract
The rapid activation of gene expression in response to stimuli occurs largely through the regulation of RNA polymerase II-dependent transcription. In this Review, we discuss events that occur during the transcription cycle in eukaryotes that are important for the rapid and specific activation of gene expression in response to external stimuli. In addition to regulated recruitment of the transcription machinery to the promoter, it has now been shown that control steps can include chromatin remodelling and the release of paused polymerase. Recent work suggests that some components of signal transduction cascades also play an integral part in activating transcription at target genes.
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Staschke KA, Dey S, Zaborske JM, Palam LR, McClintick JN, Pan T, Edenberg HJ, Wek RC. Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast. J Biol Chem 2010; 285:16893-911. [PMID: 20233714 DOI: 10.1074/jbc.m110.121947] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as gamma-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.
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Affiliation(s)
- Kirk A Staschke
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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Jedidi I, Zhang F, Qiu H, Stahl SJ, Palmer I, Kaufman JD, Nadaud PS, Mukherjee S, Wingfield PT, Jaroniec CP, Hinnebusch AG. Activator Gcn4 employs multiple segments of Med15/Gal11, including the KIX domain, to recruit mediator to target genes in vivo. J Biol Chem 2010; 285:2438-55. [PMID: 19940160 PMCID: PMC2807301 DOI: 10.1074/jbc.m109.071589] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/10/2009] [Indexed: 11/06/2022] Open
Abstract
Mediator is a multisubunit coactivator required for initiation by RNA polymerase II. The Mediator tail subdomain, containing Med15/Gal11, is a target of the activator Gcn4 in vivo, critical for recruitment of native Mediator or the Mediator tail subdomain present in sin4Delta cells. Although several Gal11 segments were previously shown to bind Gcn4 in vitro, the importance of these interactions for recruitment of Mediator and transcriptional activation by Gcn4 in cells was unknown. We show that interaction of Gcn4 with the Mediator tail in vitro and recruitment of this subcomplex and intact Mediator to the ARG1 promoter in vivo involve additive contributions from three different segments in the N terminus of Gal11. These include the KIX domain, which is a critical target of other activators, and a region that shares a conserved motif (B-box) with mammalian coactivator SRC-1, and we establish that B-box is a critical determinant of Mediator recruitment by Gcn4. We further demonstrate that Gcn4 binds to the Gal11 KIX domain directly and, by NMR chemical shift analysis combined with mutational studies, we identify the likely binding site for Gcn4 on the KIX surface. Gcn4 is distinctive in relying on comparable contributions from multiple segments of Gal11 for efficient recruitment of Mediator in vivo.
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Affiliation(s)
- Iness Jedidi
- From the Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Fan Zhang
- From the Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Hongfang Qiu
- From the Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
| | - Stephen J. Stahl
- the Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Ira Palmer
- the Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Joshua D. Kaufman
- the Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Philippe S. Nadaud
- the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Sujoy Mukherjee
- the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Paul T. Wingfield
- the Protein Expression Laboratory, NIAMS, National Institutes of Health, Bethesda, Maryland 20892 and
| | | | - Alan G. Hinnebusch
- From the Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, and
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Abstract
The budding yeast Gcn5p is a prototypic histone acetyltransferase controlling transcription of diverse genes. Here we show that Gcn5p is itself regulated by Snf1p and Spt3p. Snf1p likely controls Gcn5p via direct interaction. Mutating four residues in the Gcn5p catalytic domain, T203, S204, T211, and Y212 (TSTY), phenocopies snf1 null cells, including Gcn5p hypophosphorylation, hypoacetylation at the HIS3 promoter, and transcriptional defects of the HIS3 gene. However, overexpressing Snf1p suppresses the above phenotypes associated with the phosphodeficient TSTY mutant, suggesting that it is the interaction with Snf1p important for Gcn5p to activate HIS3. A likely mechanism by which Snf1p potentiates Gcn5p function is to antagonize Spt3p, because the HIS3 expression defects caused by snf1 knockout, or by the TSTY gcn5 mutations, can be suppressed by deleting SPT3. In vitro, Spt3p binds Gcn5p, but the interaction is drastically enhanced by the TSTY mutations, indicating that a stabilized Spt3p-Gcn5p interaction may be an underlying cause for the aforementioned HIS3 transcriptional defects. These results suggest that Gcn5p is a target regulated by the competing actions of Snf1p and Spt3p.
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Kremer SB, Gross DS. SAGA and Rpd3 chromatin modification complexes dynamically regulate heat shock gene structure and expression. J Biol Chem 2009; 284:32914-31. [PMID: 19759026 DOI: 10.1074/jbc.m109.058610] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The chromatin structure of heat shock protein (HSP)-encoding genes undergoes dramatic alterations upon transcriptional induction, including, in extreme cases, domain-wide nucleosome disassembly. Here, we use a combination of gene knock-out, in situ mutagenesis, chromatin immunoprecipitation, and expression assays to investigate the role of histone modification complexes in regulating heat shock gene structure and expression in Saccharomyces cerevisiae. Two histone acetyltransferases, Gcn5 and Esa1, were found to stimulate HSP gene transcription. A detailed chromatin immunoprecipitation analysis of the Gcn5-containing SAGA complex (signified by Spt3) revealed its presence within the promoter of every heat shock factor 1-regulated gene examined. The occupancy of SAGA increased substantially upon heat shock, peaking at several HSP promoters within 30-45 s of temperature upshift. SAGA was also efficiently recruited to the coding regions of certain HSP genes (where its presence mirrored that of pol II), although not at others. Robust and rapid recruitment of repressive, Rpd3-containing histone deacetylase complexes was also seen and at all HSP genes examined. A detailed analysis of HSP82 revealed that both Rpd3(L) and Rpd3(S) complexes (signified by Sap30 and Rco1, respectively) were recruited to the gene promoter, yet only Rpd3(S) was recruited to its open reading frame. A consensus URS1 cis-element facilitated the recruitment of each Rpd3 complex to the HSP82 promoter, and this correlated with targeted deacetylation of promoter nucleosomes. Collectively, our observations reveal that SAGA and Rpd3 complexes are rapidly and synchronously recruited to heat shock factor 1-activated genes and suggest that their opposing activities modulate heat shock gene chromatin structure and fine-tune transcriptional output.
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Affiliation(s)
- Selena B Kremer
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130-3932, USA
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Mediator complex association with constitutively transcribed genes in yeast. Proc Natl Acad Sci U S A 2009; 106:16734-9. [PMID: 19805365 DOI: 10.1073/pnas.0905103106] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mediator is a large, multisubunit complex that is essential for transcription of mRNA by RNA Pol II in eukaryotes and is believed to bridge transcriptional activators and the general transcription machinery. However, several recent studies suggest that the requirement for Mediator during transcriptional activation is not universal, but rather activator dependent, and may be indirect for some genes. Here we have investigated Mediator association with several constitutively transcribed genes in yeast by comparing a yeast strain that harbors a temperature-sensitive mutation in an essential Mediator subunit, Srb4, with its wild-type (WT) counterpart. We find modest association of Mediator with constitutively active genes and show that this association is strongly decreased in srb4 ts yeast, whereas association with a nontranscribed region or repressed gene promoters is lower and unaffected in the mutant yeast. The tail module of Mediator remains associated with ribosomal protein (RP) gene promoters in srb4 ts yeast, while subunits from the head and middle modules are lost. Tail module association at Rap1-dependent gene promoters is lost in rap1 ts yeast, indicating that Rap1 is required for Mediator recruitment at these gene promoters and that its recruitment occurs via the tail module. Pol II association is also rapidly and severely affected in srb4 ts yeast, indicating that Mediator is directly required for pol II association at constitutively transcribed genes. Our results are consistent with Mediator functioning as a general transcription factor in yeast.
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Azzouz N, Panasenko OO, Colau G, Collart MA. The CCR4-NOT complex physically and functionally interacts with TRAMP and the nuclear exosome. PLoS One 2009; 4:e6760. [PMID: 19707589 PMCID: PMC2727002 DOI: 10.1371/journal.pone.0006760] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 07/14/2009] [Indexed: 01/14/2023] Open
Abstract
Background Ccr4-Not is a highly conserved multi-protein complex consisting in yeast of 9 subunits, including Not5 and the major yeast deadenylase Ccr4. It has been connected functionally in the nucleus to transcription by RNA polymerase II and in the cytoplasm to mRNA degradation. However, there has been no evidence so far that this complex is important for RNA degradation in the nucleus. Methodology/Principal Findings In this work we point to a new role for the Ccr4-Not complex in nuclear RNA metabolism. We determine the importance of the Ccr4-Not complex for the levels of non-coding nuclear RNAs, such as mis-processed and polyadenylated snoRNAs, whose turnover depends upon the nuclear exosome and TRAMP. Consistently, mutation of both the Ccr4-Not complex and the nuclear exosome results in synthetic slow growth phenotypes. We demonstrate physical interactions between the Ccr4-Not complex and the exosome. First, Not5 co-purifies with the exosome. Second, several exosome subunits co-purify with the Ccr4-Not complex. Third, the Ccr4-Not complex is important for the integrity of large exosome-containing complexes. Finally, we reveal a connection between the Ccr4-Not complex and TRAMP through the association of the Mtr4 helicase with the Ccr4-Not complex and the importance of specific subunits of Ccr4-Not for the association of Mtr4 with the nuclear exosome subunit Rrp6. Conclusions/Significance We propose a model in which the Ccr4-Not complex may provide a platform contributing to dynamic interactions between the nuclear exosome and its co-factor TRAMP. Our findings connect for the first time the different players involved in nuclear and cytoplasmic RNA degradation.
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Affiliation(s)
- Nowel Azzouz
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olesya O. Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Geoffroy Colau
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Martine A. Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
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47
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Peiró-Chova L, Estruch F. The yeast RNA polymerase II-associated factor Iwr1p is involved in the basal and regulated transcription of specific genes. J Biol Chem 2009; 284:28958-67. [PMID: 19679657 DOI: 10.1074/jbc.m109.012153] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA polymerase II (RNA pol II) is a multisubunit enzyme that requires many auxiliary factors for its activity. Over the years, these factors have been identified using both biochemical and genetic approaches. Recently, the systematic characterization of protein complexes by tandem affinity purification and mass spectroscopy has allowed the identification of new components of well established complexes, including the RNA pol II holoenzyme. Using this approach, a novel and highly conserved factor, Iwr1p, that physically interacts with most of the RNA pol II subunits has been described in yeast. Here we show that Iwr1p genetically interacts with components of the basal transcription machinery and plays a role in both basal and regulated transcription. We report that mutation of the IWR1 gene is able to bypass the otherwise essential requirement for the transcriptional regulator negative cofactor 2, which occurs with different components of the basal transcription machinery, including TFIIA and subunits of the mediator complex. Deletion of the IWR1 gene leads to an altered expression of specific genes, including phosphate-responsive genes and SUC2. Our results show that Iwr1p is a nucleocytoplasmic shuttling protein and suggest that Iwr1p acts early in the formation of the pre-initiation complex by mediating the interaction of certain activators with the basal transcription apparatus.
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Affiliation(s)
- Lorena Peiró-Chova
- Department of Biochemistry and Molecular Biology, Universitat de València, 46100 Burjassot, Spain
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48
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Abstract
Eukaryotic DNA is packaged into a nucleoprotein structure known as chromatin, which is comprised of DNA, histones, and nonhistone proteins. Chromatin structure is highly dynamic, and can shift from a transcriptionally inactive state to an active form in response to intra- and extracellular signals. A major factor in chromatin architecture is the covalent modification of histones through the addition of chemical moieties, such as acetyl, methyl, ubiquitin, and phosphate groups. The acetylation of the amino-terminal tails of histones is a process that is highly conserved in eukaryotes, and was one of the earliest histone modifications characterized. Since its identification in 1964, a large body of evidence has accumulated demonstrating that histone acetylation plays an important role in transcription. Despite our ever-growing understanding of the nuclear processes involved in nucleosome acetylation, however, the exact biochemical mechanisms underlying the downstream effects of histone acetylation have yet to be fully elucidated. To date, histone acetylation has been proposed to function in 2 nonmutually exclusive manners: by directly altering chromatin structure, and by acting as a molecular tag for the recruitment of chromatin-modifying complexes. Here, we discuss recent research focusing on these 2 potential roles of histone acetylation and clarify what we actually know about the function of this modification.
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Affiliation(s)
- Jennifer K Choi
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BCV6T1Z3, Canada
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49
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Abstract
Activated transcription in eukaryotes requires the aid of numerous co-factors to overcome the physical barriers chromatin poses to activation, bridge the gap between activators and polymerase, and ensure appropriate regulation. S. cerevisiae has long been a model organism for studying the role of co-activators in the steps leading up to gene activation. Detailed studies on the recruitment of these co-activators have been carried out for more than a dozen promoters. Taking a step back to survey these results, however, suggests that there are few generalizations that could be used to guide future studies of uncharacterized promoters.
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Affiliation(s)
- Rhiannon Biddick
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
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50
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Qiu H, Hu C, Hinnebusch AG. Phosphorylation of the Pol II CTD by KIN28 enhances BUR1/BUR2 recruitment and Ser2 CTD phosphorylation near promoters. Mol Cell 2009; 33:752-62. [PMID: 19328068 DOI: 10.1016/j.molcel.2009.02.018] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/15/2009] [Accepted: 02/20/2009] [Indexed: 11/19/2022]
Abstract
Cyclin-dependent kinase BUR1/BUR2 appears to be the yeast ortholog of P-TEFb, which phosphorylates Ser2 of the RNA Pol II CTD, but the importance of BUR1/BUR2 in CTD phosphorylation is unclear. We show that BUR1/BUR2 is cotranscriptionally recruited to the 5' end of ARG1 in a manner stimulated by interaction of the BUR1 C terminus with CTD repeats phosphorylated on Ser5 by KIN28. Impairing BUR1/BUR2 function, or removing the CTD-interaction domain in BUR1, reduces Ser2 phosphorylation in bulk Pol II and eliminates the residual Ser2P in cells lacking the major Ser2 CTD kinase, CTK1. Impairing BUR1/BUR2 or CTK1 evokes a similar reduction of Ser2P in Pol II phosphorylated on Ser5 and in elongating Pol II near the ARG1 promoter. By contrast, CTK1 is responsible for the bulk of Ser2P in total Pol II and at promoter-distal sites. In addition to phosphorylating Ser2 near promoters, BUR1/BUR2 also stimulates Ser2P formation by CTK1 during transcription elongation.
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Affiliation(s)
- Hongfang Qiu
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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