1
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Nguyen MC, Rostamian H, Raman A, Wei P, Becht DC, Erbse AH, Klein BJ, Gilbert TM, Zhang G, Blanco MA, Strahl BD, Taverna SD, Kutateladze TG. Molecular insight into interactions between the Taf14, Yng1 and Sas3 subunits of the NuA3 complex. Nat Commun 2024; 15:5335. [PMID: 38914563 PMCID: PMC11196586 DOI: 10.1038/s41467-024-49730-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
The NuA3 complex is a major regulator of gene transcription and the cell cycle in yeast. Five core subunits are required for complex assembly and function, but it remains unclear how these subunits interact to form the complex. Here, we report that the Taf14 subunit of the NuA3 complex binds to two other subunits of the complex, Yng1 and Sas3, and describe the molecular mechanism by which the extra-terminal domain of Taf14 recognizes the conserved motif present in Yng1 and Sas3. Structural, biochemical, and mutational analyses show that two motifs are sandwiched between the two extra-terminal domains of Taf14. The head-to-toe dimeric complex enhances the DNA binding activity of Taf14, and the formation of the hetero-dimer involving the motifs of Yng1 and Sas3 is driven by sequence complementarity. In vivo assays in yeast demonstrate that the interactions of Taf14 with both Sas3 and Yng1 are required for proper function of the NuA3 complex in gene transcription and DNA repair. Our findings suggest a potential basis for the assembly of three core subunits of the NuA3 complex, Taf14, Yng1 and Sas3.
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Affiliation(s)
- Minh Chau Nguyen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Hosein Rostamian
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pengcheng Wei
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, China
| | - Dustin C Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Tonya M Gilbert
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
| | - M Andres Blanco
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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2
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Nguyen MC, Wang D, Klein BJ, Chen Y, Kutateladze TG. Differences and similarities in recognition of co-factors by Taf14. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194961. [PMID: 37482120 DOI: 10.1016/j.bbagrm.2023.194961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
Taf14 is a subunit of multiple fundamental complexes implicated in transcriptional regulation and DNA damage repair in yeast cells. Here, we investigate the association of Taf14 with the consensus sequence present in other subunits of these complexes and describe the mechanistic features that affect this association. We demonstrate that the precise molecular mechanisms and biological outcomes underlying the Taf14 interactions depend on the accessibility of binding interfaces, the ability to recognize other ligands, and a degree of sensitivity to temperature and chemical and osmotic stresses. Our findings aid in a better understanding of how the distribution of Taf14 among the complexes is mediated.
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Affiliation(s)
- Minh Chau Nguyen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Duo Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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3
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Han H, Lv F, Liu Z, Chen T, Xue T, Liang W, Liu M. BcTaf14 regulates growth and development, virulence, and stress responses in the phytopathogenic fungus Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2023; 24:849-865. [PMID: 37026690 PMCID: PMC10346378 DOI: 10.1111/mpp.13331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
TATA box-binding protein (TBP)-associated factor 14 (Taf14), a transcription-associated factor containing a conserved YEATS domain and an extra-terminal (ET) domain, is a multifunctional protein in Saccharomyces cerevisiae. However, the role of Taf14 in filamentous phytopathogenic fungi is not well understood. In this study, the homologue of ScTaf14 in Botrytis cinerea (named BcTaf14), a destructive phytopathogen causing grey mould, was investigated. The BcTaf14 deletion strain (ΔBcTaf14) showed pleiotropic defects, including slow growth, abnormal colony morphology, reduced conidiation, abnormal conidial morphology, reduced virulence, and altered responses to various stresses. The ΔBcTaf14 strain also exhibited differential expression of numerous genes compared to the wild-type strain. BcTaf14 could interact with the crotonylated H3K9 peptide, and mutation of two key sites (G80 and W81) in the YEATS domain disrupted this interaction. The mutation of G80 and W81 affected the regulatory effect of BcTaf14 on mycelial growth and virulence but did not affect the production and morphology of conidia. The absence of the ET domain at the C-terminus rendered BcTaf14 unable to localize to the nucleus, and the defects of ΔBcTaf14 were not recovered to wild-type levels when BcTaf14 without the ET domain was expressed. Our results provide insight into the regulatory roles of BcTaf14 and its two conserved domains in B. cinerea and will be helpful for understanding the function of the Taf14 protein in plant-pathogenic fungi.
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Affiliation(s)
- Hongjia Han
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Fangjiao Lv
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Zhishan Liu
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Tongge Chen
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Tianzi Xue
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Wenxing Liang
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Mengjie Liu
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
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4
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Peil K, Värv S, Ilves I, Kristjuhan K, Jürgens H, Kristjuhan A. Transcriptional regulator Taf14 binds DNA and is required for the function of transcription factor TFIID in the absence of histone H2A.Z. J Biol Chem 2022; 298:102369. [PMID: 35970389 PMCID: PMC9478928 DOI: 10.1016/j.jbc.2022.102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptional regulator Taf14 is a component of multiple protein complexes involved in transcription initiation and chromatin remodeling in yeast cells. Although Taf14 is not required for cell viability, it becomes essential in conditions where the formation of the transcription preinitiation complex is hampered. The specific role of Taf14 in mediating transcription initiation and preinitiation complex formation is unclear. Here, we explored its role in the general transcription factor IID by mapping Taf14 genetic and proteomic interactions and found that it was needed for the function of the complex if Htz1, the yeast homolog of histone H2A.Z, was absent from chromatin. Dissecting the functional domains of Taf14 revealed that the linker region between the YEATS and ET domains was required for cell viability in the absence of Htz1 protein. We further show that the linker region of Taf14 interacts with DNA. We propose that providing additional DNA binding capacity might be a general role of Taf14 in the recruitment of protein complexes to DNA and chromatin.
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Affiliation(s)
- Kadri Peil
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Signe Värv
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Ivar Ilves
- Institute of Technology, University of Tartu; Nooruse 1, Tartu 50411, Estonia
| | - Kersti Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Henel Jürgens
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia
| | - Arnold Kristjuhan
- Institute of Molecular and Cell Biology, University of Tartu; Riia 23, Tartu 51010, Estonia.
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5
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Klein BJ, Feigerle JT, Zhang J, Ebmeier CC, Fan L, Singh RK, Wang WW, Schmitt LR, Lee T, Hansen KC, Liu WR, Wang YX, Strahl BD, Anthony Weil P, Kutateladze TG. Taf2 mediates DNA binding of Taf14. Nat Commun 2022; 13:3177. [PMID: 35676274 PMCID: PMC9177701 DOI: 10.1038/s41467-022-30937-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/20/2022] [Indexed: 01/13/2023] Open
Abstract
The assembly and function of the yeast general transcription factor TFIID complex requires specific contacts between its Taf14 and Taf2 subunits, however, the mechanism underlying these contacts remains unclear. Here, we determined the molecular and structural basis by which the YEATS and ET domains of Taf14 bind to the C-terminal tail of Taf2 and identified a unique DNA-binding activity of the linker region connecting the two domains. We show that in the absence of ligands the linker region of Taf14 is occluded by the surrounding domains, and therefore the DNA binding function of Taf14 is autoinhibited. Binding of Taf2 promotes a conformational rearrangement in Taf14, resulting in a release of the linker for the engagement with DNA and the nucleosome. Genetic in vivo data indicate that the association of Taf14 with both Taf2 and DNA is essential for transcriptional regulation. Our findings provide a basis for deciphering the role of individual TFIID subunits in mediating gene transcription.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Jordan T Feigerle
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jibo Zhang
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | | | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, MD, 21702, USA
| | - Rohit K Singh
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Wesley W Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lauren R Schmitt
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Thomas Lee
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, MD, 21702, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 27102, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - P Anthony Weil
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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6
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Li X, Liu S, Li X, Li XD. YEATS Domains as Novel Epigenetic Readers: Structures, Functions, and Inhibitor Development. ACS Chem Biol 2022; 18:994-1013. [PMID: 35041380 DOI: 10.1021/acschembio.1c00945] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interpretation of the histone posttranslational modifications (PTMs) by effector proteins, or readers, is an important epigenetic mechanism to regulate gene function. YEATS domains have been recently identified as novel readers of histone lysine acetylation and a variety of nonacetyl acylation marks. Accumulating evidence has revealed the association of dysregulated interactions between YEATS domains and histone PTMs with human diseases, suggesting the therapeutic potential of YEATS domain inhibition. Here, we discuss the molecular mechanisms adopted by YEATS domains in recognizing their preferred histone marks and the biological significance of such recognitions in normal cell physiology and pathogenesis of human diseases. Recent progress in the development of YEATS domain inhibitors is also discussed.
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Affiliation(s)
- Xin Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Sha Liu
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
| | - Xiang Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
| | - Xiang David Li
- Departments of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong G01, China
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7
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Li K, Wang Z. Histone crotonylation-centric gene regulation. Epigenetics Chromatin 2021; 14:10. [PMID: 33549150 PMCID: PMC7868018 DOI: 10.1186/s13072-021-00385-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/28/2021] [Indexed: 01/19/2023] Open
Abstract
Histone crotonylation is a recently described post-translational modification that occurs at multiple identified histone lysine crotonylation sites. An increasing number of studies have demonstrated that histone crotonylation at DNA regulatory elements plays an important role in the activation of gene transcription. However, among others, we have shown that elevated cellular crotonylation levels result in the inhibition of endocytosis-related gene expression and pro-growth gene expression, implicating the complexity of histone crotonylation in gene regulation. Therefore, it is important to understand how histone crotonylation is regulated and how it, in turn, regulates the expression of its target genes. In this review, we summarize the regulatory factors that control histone crotonylation and discuss the role of different histone crotonylation sites in regulating gene expression, while providing novel insights into the central role of histone crotonylation in gene regulation.
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Affiliation(s)
- Kun Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250014, China
| | - Ziqiang Wang
- Medical Research Center, The First Affiliated Hospital of Shandong First Medical University, Jinan, 250014, China. .,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
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8
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Chen G, Wang D, Wu B, Yan F, Xue H, Wang Q, Quan S, Chen Y. Taf14 recognizes a common motif in transcriptional machineries and facilitates their clustering by phase separation. Nat Commun 2020; 11:4206. [PMID: 32826896 PMCID: PMC7442819 DOI: 10.1038/s41467-020-18021-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
Saccharomyces cerevisiae TBP associated factor 14 (Taf14) is a well-studied transcriptional regulator that controls diverse physiological processes and that physically interacts with at least seven nuclear complexes in yeast. Despite multiple previous Taf14 structural studies, the nature of its disparate transcriptional regulatory functions remains opaque. Here, we demonstrate that the extra-terminal (ET) domain of Taf14 (Taf14ET) recognizes a common motif in multiple transcriptional coactivator proteins from several nuclear complexes, including RSC, SWI/SNF, INO80, NuA3, TFIID, and TFIIF. Moreover, we show that such partner binding promotes liquid-liquid phase separation (LLPS) of Taf14ET, in a mechanism common to YEATS-associated ET domains (e.g., AF9ET) but not Bromo-associated ET domains from BET-family proteins. Thus, beyond identifying the molecular mechanism by which Taf14ET associates with many transcriptional regulators, our study suggests that Taf14 may function as a versatile nuclear hub that orchestrates transcriptional machineries to spatiotemporally regulate diverse cellular pathways. S. cerevisiae TBP associated factor 14 (Taf14) is a transcriptional regulator that interacts with multiple nuclear complexes. Here, the authors report that the extra-terminal domain of Taf14 (Taf14ET) recognizes a common motif in various transcriptional coactivator proteins and they solve the NMR structure of Taf14ET bound the ET-binding motif of Sth1, the catalytic subunit of the RSC (Remodel the Structure of Chromatin) complex, and furthermore show that Taf14ET undergoes liquid-liquid phase separation, which is enhanced by Taf14 interaction partners.
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Affiliation(s)
- Guochao Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Duo Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Fuxiang Yan
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Quanmeng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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9
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Abstract
ATP-dependent chromatin remodelling enzymes are molecular machines that act to reconfigure the structure of nucleosomes. Until recently, little was known about the structure of these enzymes. Recent progress has revealed that their interaction with chromatin is dominated by ATPase domains that contact DNA at favoured locations on the nucleosome surface. Contacts with histones are limited but play important roles in modulating activity. The ATPase domains do not act in isolation but are flanked by diverse accessory domains and subunits. New structures indicate how these subunits are arranged in multi-subunit complexes providing a framework from which to understand how a common motor is applied to distinct functions.
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Affiliation(s)
- Ramasubramian Sundaramoorthy
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, Dundee, DD1 5EH, UK
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10
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Gopalan S, Gibbon DM, Banks CA, Zhang Y, Florens LA, Washburn MP, Dabas P, Sharma N, Seidel CW, Conaway RC, Conaway JW. Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex. Nucleic Acids Res 2019; 46:10095-10105. [PMID: 30102332 PMCID: PMC6212713 DOI: 10.1093/nar/gky713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
ELL family transcription factors activate the overall rate of RNA polymerase II (Pol II) transcription elongation by binding directly to Pol II and suppressing its tendency to pause. In metazoa, ELL regulates Pol II transcription elongation as part of a large multisubunit complex referred to as the Super Elongation Complex (SEC), which includes P-TEFb and EAF, AF9 or ENL, and an AFF family protein. Although orthologs of ELL and EAF have been identified in lower eukaryotes including Schizosaccharomyces pombe, it has been unclear whether SEC-like complexes function in lower eukaryotes. In this report, we describe isolation from S. pombe of an ELL-containing complex with features of a rudimentary SEC. This complex includes S. pombe Ell1, Eaf1, and a previously uncharacterized protein we designate Ell1 binding protein 1 (Ebp1), which is distantly related to metazoan AFF family members. Like the metazoan SEC, this S. pombe ELL complex appears to function broadly in Pol II transcription. Interestingly, it appears to have a particularly important role in regulating genes involved in cell separation.
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Affiliation(s)
- Sneha Gopalan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,The Open University, Milton Keynes, UK
| | - Dana M Gibbon
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Charles As Banks
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Pathology and Laboratory Med icine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Preeti Dabas
- University School of Biotechnology, G.G.S.Indraprastha University, New Delhi 110078, India
| | - Nimisha Sharma
- University School of Biotechnology, G.G.S.Indraprastha University, New Delhi 110078, India
| | | | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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11
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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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12
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Dutta A, Sardiu M, Gogol M, Gilmore J, Zhang D, Florens L, Abmayr SM, Washburn MP, Workman JL. Composition and Function of Mutant Swi/Snf Complexes. Cell Rep 2017; 18:2124-2134. [PMID: 28249159 PMCID: PMC5837817 DOI: 10.1016/j.celrep.2017.01.058] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 12/09/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022] Open
Abstract
The 12-subunit Swi/Snf chromatin remodeling complex is conserved from yeast to humans. It functions to alter nucleosome positions by either sliding nucleosomes on DNA or evicting histones. Interestingly, 20% of all human cancers carry mutations in subunits of the Swi/Snf complex. Many of these mutations cause protein instability and loss, resulting in partial Swi/Snf complexes. Although several studies have shown that histone acetylation and activator-dependent recruitment of Swi/Snf regulate its function, it is less well understood how subunits regulate stability and function of the complex. Using functional proteomic and genomic approaches, we have assembled the network architecture of yeast Swi/Snf. In addition, we find that subunits of the Swi/Snf complex regulate occupancy of the catalytic subunit Snf2, thereby modulating gene transcription. Our findings have direct bearing on how cancer-causing mutations in orthologous subunits of human Swi/Snf may lead to aberrant regulation of gene expression by this complex.
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Affiliation(s)
- Arnob Dutta
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA.
| | - Mihaela Sardiu
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Joshua Gilmore
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Daoyong Zhang
- Institute of Cancer Biological Therapy, Xuzhou Medical University, Jiangsu 221002, China
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Susan M Abmayr
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.
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13
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Nemet J, Vidan N, Sopta M. A meta-analysis reveals complex regulatory properties at Taf14-repressed genes. BMC Genomics 2017; 18:175. [PMID: 28209126 PMCID: PMC5312515 DOI: 10.1186/s12864-017-3544-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regulation of gene transcription in response to stress is central to a cell's ability to cope with environmental challenges. Taf14 is a YEATS domain protein in S.cerevisiae that physically associates with several transcriptionally relevant multisubunit complexes including the general transcription factors TFIID and TFIIF and the chromatin-modifying complexes SWI/SNF, INO80, RSC and NuA3. TAF14 deletion strains are sensitive to a variety of stresses suggesting that it plays a role in the transcriptional stress response. RESULTS In this report we survey published genome-wide transcriptome and occupancy data to define regulatory properties associated with Taf14-dependent genes. Our transcriptome analysis reveals that stress related, TATA-containing and SAGA-dependent genes were much more affected by TAF14 deletion than were TFIID-dependent genes. Comparison of Taf14 and multiple transcription factor occupancy at promoters genome-wide identified a group of proteins whose occupancy correlates with that of Taf14 and whose proximity to Taf14 suggests functional interactions. We show that Taf14-repressed genes tend to be extensively regulated, positively by SAGA complex and the stress dependent activators, Msn2/4 and negatively by a wide number of repressors that act upon promoter chromatin and TBP. CONCLUSIONS Taken together our analyses suggest a novel role for Taf14 in repression and derepression of stress induced genes, most probably as part of a regulatory network which includes Cyc8-Tup1, Srb10 and histone modifying enzymes.
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Affiliation(s)
- Josipa Nemet
- Department of molecular biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Nikolina Vidan
- Department of molecular biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Mary Sopta
- Department of molecular biology, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.
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14
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Andrews FH, Shanle EK, Strahl BD, Kutateladze TG. The essential role of acetyllysine binding by the YEATS domain in transcriptional regulation. Transcription 2016; 7:14-20. [PMID: 26934307 DOI: 10.1080/21541264.2015.1125987] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The YEATS domains of AF9 and Taf14 have recently been found to recognize the histone H3K9ac modification. In this commentary, we discuss the mechanistic and biological implications of this interaction. We compare structures of the YEATS-H3K9ac complexes the highlighting a novel mechanism for the acetyllysine recognition through the aromatic cage. We also summarize the latest findings underscoring a critical role of the acetyllysine binding function of AF9 and Taf14 in transcriptional regulation and DNA repair.
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Affiliation(s)
- Forest H Andrews
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Erin K Shanle
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Brian D Strahl
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Tatiana G Kutateladze
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
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15
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Feigerle JT, Weil PA. The C Terminus of the RNA Polymerase II Transcription Factor IID (TFIID) Subunit Taf2 Mediates Stable Association of Subunit Taf14 into the Yeast TFIID Complex. J Biol Chem 2016; 291:22721-22740. [PMID: 27587401 DOI: 10.1074/jbc.m116.751107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/31/2016] [Indexed: 12/22/2022] Open
Abstract
The evolutionarily conserved RNA polymerase II transcription factor D (TFIID) complex is composed of TATA box-binding protein (TBP) and 13 TBP-associated factors (Tafs). The mechanisms by which many Taf subunits contribute to the essential function of TFIID are only poorly understood. To address this gap in knowledge, we present the results of a molecular genetic dissection of the TFIID subunit Taf2. Through systematic site-directed mutagenesis, we have discovered 12 taf2 temperature-sensitive (ts) alleles. Two of these alleles display growth defects that can be strongly suppressed by overexpression of the yeast-specific TFIID subunit TAF14 but not by overexpression of any other TFIID subunit. In Saccharomyces cerevisiae, Taf14 is also a constituent of six other transcription-related complexes, making interpretation of its role in each of these complexes difficult. Although Taf14 is not conserved as a TFIID subunit in metazoans, it is conserved through its chromatin-binding YEATS domain. Based on the Taf2-Taf14 genetic interaction, we demonstrate that Taf2 and Taf14 directly interact and mapped the Taf2-Taf14 interaction domains. We used this information to identify a Taf2 separation-of-function variant (Taf2-ΔC). Although Taf2-ΔC no longer interacts with Taf14 in vivo or in vitro, it stably incorporates into the TFIID complex. In addition, purified Taf2-ΔC mutant TFIID is devoid of Taf14, making this variant a powerful reagent for determining the role of Taf14 in TFIID function. Furthermore, we characterized the mechanism through which Taf14 suppresses taf2ts alleles, shedding light on how Taf2-Taf14 interaction contributes to TFIID complex organization and identifying a potential role for Taf14 in mediating TFIID-chromatin interactions.
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Affiliation(s)
- Jordan T Feigerle
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615
| | - P Anthony Weil
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615
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16
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Andrews FH, Shinsky SA, Shanle EK, Bridgers JB, Gest A, Tsun IK, Krajewski K, Shi X, Strahl BD, Kutateladze TG. The Taf14 YEATS domain is a reader of histone crotonylation. Nat Chem Biol 2016; 12:396-8. [PMID: 27089029 PMCID: PMC4871749 DOI: 10.1038/nchembio.2065] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/15/2016] [Indexed: 02/07/2023]
Abstract
The discovery of new histone modifications is unfolding at startling rates; however, the identification of effectors capable of interpreting these modifications has lagged behind. Here we report the YEATS domain as an effective reader of histone lysine crotonylation, an epigenetic signature associated with active transcription. We show that the Taf14 YEATS domain engages crotonyllysine via a unique π-π-π-stacking mechanism and that other YEATS domains have crotonyllysine-binding activity.
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Affiliation(s)
- Forest H. Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Stephen A. Shinsky
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Erin K. Shanle
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Joseph B. Bridgers
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Anneliese Gest
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ian K. Tsun
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Krzysztof Krajewski
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brian D. Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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17
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Shanle EK, Andrews FH, Meriesh H, McDaniel SL, Dronamraju R, DiFiore JV, Jha D, Wozniak GG, Bridgers JB, Kerschner JL, Krajewski K, Martín GM, Morrison AJ, Kutateladze TG, Strahl BD. Association of Taf14 with acetylated histone H3 directs gene transcription and the DNA damage response. Genes Dev 2015; 29:1795-800. [PMID: 26341557 PMCID: PMC4573853 DOI: 10.1101/gad.269977.115] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The YEATS domain, found in a number of chromatin-associated proteins, has recently been shown to have the capacity to bind histone lysine acetylation. Here, we show that the YEATS domain of Taf14, a member of key transcriptional and chromatin-modifying complexes in yeast, is a selective reader of histone H3 Lys9 acetylation (H3K9ac). Structural analysis reveals that acetylated Lys9 is sandwiched in an aromatic cage formed by F62 and W81. Disruption of this binding in cells impairs gene transcription and the DNA damage response. Our findings establish a highly conserved acetyllysine reader function for the YEATS domain protein family and highlight the significance of this interaction for Taf14.
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Affiliation(s)
- Erin K Shanle
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Hashem Meriesh
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Stephen L McDaniel
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA
| | - Raghuvar Dronamraju
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Julia V DiFiore
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA
| | - Deepak Jha
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Glenn G Wozniak
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA
| | - Joseph B Bridgers
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Jenny L Kerschner
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
| | - Glòria Mas Martín
- Department of Biology, Stanford University, Stanford, California 94305 USA
| | - Ashby J Morrison
- Department of Biology, Stanford University, Stanford, California 94305 USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, North Carolina 27599 USA; Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 USA
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18
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Hagen S, Mattay D, Räuber C, Müller KM, Arndt KM. Characterization and inhibition of AF10-mediated interaction. J Pept Sci 2014; 20:385-97. [PMID: 24692230 DOI: 10.1002/psc.2626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 02/13/2014] [Accepted: 02/14/2014] [Indexed: 12/24/2022]
Abstract
The non-random chromosomal translocations t(10;11)(p13;q23) and t(10;11)(p13;q14-21) result in leukemogenic fusion proteins comprising the coiled coil domain of the transcription factor AF10 and the proteins MLL or CALM, respectively, and subsequently cause certain types of acute leukemia. The AF10 coiled-coil domain, which is crucial for the leukemogenic effect, has been shown to interact with GAS41, a protein previously identified as the product of an amplified gene in glioblastoma. Using sequential synthetic peptides, we mapped the potential AF10/GAS41 interaction site, which was subsequently be used as scaffold for a library targeting the AF10 coiled-coil domain. Using phage display, we selected a peptide that binds the AF10 coiled-coil domain with higher affinity than the respective coiled-coil region of wild-type GAS41, as demonstrated by phage ELISA, CD, and PCAs. Furthermore, we were able to successfully deploy the inhibitory peptide in a mammalian cell line to lower the expression of Hoxa genes that have been described to be overexpressed in these leukemias. This work dissects molecular determinants mediating AF10-directed interactions in leukemic fusions comprising the N-terminal parts of the proteins MLL or CALM and the C-terminal coiled-coil domain of AF10. Furthermore, it outlines the first steps in recognizing and blocking the leukemia-associated AF10 interaction in histiocytic lymphoma cells and therefore, may have significant implications in future diagnostics and therapeutics.
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Affiliation(s)
- Sven Hagen
- Molecular Biotechnology, University of Potsdam, Potsdam/Golm, Germany; Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany; Institute for Biology III, University of Freiburg, Freiburg, Germany
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19
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Ding X, Yang Z, Zhou F, Wang F, Li X, Chen C, Li X, Hu X, Xiang S, Zhang J. Transcription factor AP-2α regulates acute myeloid leukemia cell proliferation by influencing Hoxa gene expression. Int J Biochem Cell Biol 2013; 45:1647-56. [DOI: 10.1016/j.biocel.2013.04.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/26/2013] [Accepted: 04/29/2013] [Indexed: 01/28/2023]
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20
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Hybrid electron microscopy-FRET imaging localizes the dynamical C-terminus of Tfg2 in RNA polymerase II-TFIIF with nanometer precision. J Struct Biol 2013; 184:52-62. [PMID: 23732819 DOI: 10.1016/j.jsb.2013.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 05/06/2013] [Accepted: 05/21/2013] [Indexed: 01/23/2023]
Abstract
TFIIF-a general transcription factor comprising two conserved subunits can associate with RNA polymerase II (RNAPII) tightly to regulate the synthesis of messenger RNA in eukaryotes. Herein, a hybrid method that combines electron microscopy (EM) and Förster resonance energy transfer (FRET) is described and used to localize the C-terminus of the second TFIIF subunit (Tfg2) in the architecture of RNAPII-TFIIF. In the first stage, a poly-histidine tag appended to the Tfg2 C-terminus was labeled with nickel-NTA nanogold and a seven-step single particle EM protocol was devised to obtain the region accessible by the nanogold in 3D, suggesting the Tfg2 C-terminus is proximal to the clamp of RNAPII. Next, the C-termini of the Rpb2 and the Rpb4 subunits of RNAPII, adjacent to the clamp, were selected for placing FRET satellites to enable the nano-positioning (NP) analysis, by which the localization precision was improved such that the Tfg2 C-terminus was found to dwell on the clamp ridge but could move to the clamp top during transcription. Because the tag receptive to the EM or FRET probes can be readily introduced to any protein subunit, this hybrid approach is generally applicable to complement cryo-EM study of many protein complexes to nanometer precision.
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21
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Heisel S, Habel NC, Schuetz N, Ruggieri A, Meese E. The YEATS family member GAS41 interacts with the general transcription factor TFIIF. BMC Mol Biol 2010; 11:53. [PMID: 20618999 PMCID: PMC2908078 DOI: 10.1186/1471-2199-11-53] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 07/12/2010] [Indexed: 11/10/2022] Open
Abstract
Background In eukaryotes the transcription initiation by RNA polymerase II requires numerous general and regulatory factors including general transcription factors. The general transcription factor TFIIF controls the activity of the RNA polymerase II both at the initiation and elongation stages. The glioma amplified sequence 41 (GAS41) has been associated with TFIIF via its YEATS domain. Results Using GST pull-down assays, we demonstrated that GAS41 binds to both, the small subunit (RAP30) and the large subunit (RAP74) of TFIIF in vitro. The in vivo interaction of GAS41 and endogenous RAP30 and RAP74 was confirmed by co-immunoprecipitation. GAS41 binds to two non-overlapping regions of the C-terminus of RAP30. There is also an ionic component to the binding between GAS41 and RAP30. There was no evidence for a direct interaction between GAS41 and TBP or between GAS41 and RNA polymerase II. Conclusions Our results demonstrate binding between endogenous GAS41 and the endogenous TFIIF subunits (RAP30 and RAP74). Since we did not find evidence for a binding of GAS41 to TBP or RNA polymerase II, GAS41 seems to preferentially bind to TFIIF. GAS41 that does not contain a DNA-binding domain appears to be a co-factor of TFIIF.
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Affiliation(s)
- Sabrina Heisel
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
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22
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Kerins JA, Hanazawa M, Dorsett M, Schedl T. PRP-17 and the pre-mRNA splicing pathway are preferentially required for the proliferation versus meiotic development decision and germline sex determination in Caenorhabditis elegans. Dev Dyn 2010; 239:1555-72. [PMID: 20419786 PMCID: PMC3097115 DOI: 10.1002/dvdy.22274] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In C. elegans, the decision between germline stem cell proliferation and entry into meiosis is controlled by GLP-1 Notch signaling, which promotes proliferation through repression of the redundant GLD-1 and GLD-2 pathways that direct meiotic entry. We identify prp-17 as another gene functioning downstream of GLP-1 signaling that promotes meiotic entry, largely by acting on the GLD-1 pathway, and that also functions in female germline sex determination. PRP-17 is orthologous to the yeast and human pre-mRNA splicing factor PRP17/CDC40 and can rescue the temperature-sensitive lethality of yeast PRP17. This link to splicing led to an RNAi screen of predicted C. elegans splicing factors in sensitized genetic backgrounds. We found that many genes throughout the splicing cascade function in the proliferation/meiotic entry decision and germline sex determination indicating that splicing per se, rather than a novel function of a subset of splicing factors, is necessary for these processes.
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23
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Lin JJ, Hemenway CS. Hsp90 directly modulates the spatial distribution of AF9/MLLT3 and affects target gene expression. J Biol Chem 2010; 285:11966-73. [PMID: 20159978 PMCID: PMC2852934 DOI: 10.1074/jbc.m110.101642] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/12/2010] [Indexed: 01/28/2023] Open
Abstract
AF9/MLLT3 contributes to the regulation of the gene encoding the epithelial sodium channel alpha, ENaCalpha, in renal tubular cells. Specifically, increases in AF9 protein lead to a reduction in ENaCalpha expression and changes in AF9 activity appear to be an important component of aldosterone signaling in the kidney. Whereas AF9 is found in the nucleus where it interacts with the histone H3 lysine 79 methyltransferase, Dot1, AF9 is also present in the cytoplasm. Data presented in this report indicate that the heat shock protein Hsp90 directly and specifically interacts with AF9 as part of an Hsp90-Hsp70-p60/Hop chaperone complex. Experimental manipulation of Hsp90 function by the inhibitor novobiocin, but not 17-AAG, results in redistribution of AF9 from a primarily nuclear to cytoplasmic location. Knockdown of Hsp90 with siRNA mimics the effect elicited by novobiocin. As expected, a shift in AF9 from the nucleus to the cytoplasm in response to Hsp90 interference leads to increased ENaCalpha expression. This is accompanied by a decrease in AF9 occupancy at the ENaCalpha promoter. Our data suggest that the interaction of Hsp90, Hsp70, and p60/Hop with AF9 is necessary for the proper subnuclear localization and activity of AF9. AF9 is among a growing number of nuclear proteins recognized to rely on the Hsp90 complex for nuclear targeting.
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Affiliation(s)
- Jeffrey J. Lin
- From the Department of Biochemistry, Tulane University School of Medicine, New Orleans, Louisiana 70112 and
| | - Charles S. Hemenway
- the Department of Pediatrics and the Cardinal Bernardin Cancer Center, Loyola University Chicago Stritch School of Medicine, Maywood, Illinois 60153
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24
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Schulze JM, Kane CM, Ruiz-Manzano A. The YEATS domain of Taf14 in Saccharomyces cerevisiae has a negative impact on cell growth. Mol Genet Genomics 2010; 283:365-80. [PMID: 20179968 PMCID: PMC2839515 DOI: 10.1007/s00438-010-0523-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 01/28/2010] [Indexed: 12/15/2022]
Abstract
The role of a highly conserved YEATS protein motif is explored in the context of the Taf14 protein of Saccharomyces cerevisiae. In S. cerevisiae, Taf14 is a protein physically associated with many critical multisubunit complexes including the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes SWI/SNF, Ino80 and RSC, Mediator and the histone modification enzyme NuA3. Taf14 is a member of the YEATS superfamily, conserved from bacteria to eukaryotes and thought to have a transcription stimulatory activity. However, besides its ubiquitous presence and its links with transcription, little is known about Taf14’s role in the nucleus. We use structure–function and mutational analysis to study the function of Taf14 and its well conserved N-terminal YEATS domain. We show here that the YEATS domain is not necessary for Taf14’s association with these transcription and chromatin remodeling complexes, and that its presence in these complexes is dependent only on its C-terminal domain. Our results also indicate that Taf14’s YEATS domain is not necessary for complementing the synthetic lethality between TAF14 and the general transcription factor TFIIS (encoded by DST1). Furthermore, we present evidence that the YEATS domain of Taf14 has a negative impact on cell growth: its absence enables cells to grow better than wild-type cells under stress conditions, like the microtubule destabilizing drug benomyl. Moreover, cells expressing solely the YEATS domain grow worser than cells expressing any other Taf14 construct tested, including the deletion mutant. Thus, this highly conserved domain should be considered part of a negative regulatory loop in cell growth.
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Affiliation(s)
- Julia M Schulze
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
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25
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Eichner J, Chen HT, Warfield L, Hahn S. Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex. EMBO J 2009; 29:706-16. [PMID: 20033062 DOI: 10.1038/emboj.2009.386] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 12/01/2009] [Indexed: 11/09/2022] Open
Abstract
The RNA polymerase (pol) II general transcription factor TFIIF functions at several steps in transcription initiation including preinitiation complex (PIC) formation and start site selection. We find that two structured TFIIF domains bind Pol II at separate locations far from the active site with the TFIIF dimerization domain on the Pol II lobe and the winged helix domain of the TFIIF small subunit Tfg2 above the Pol II protrusion where it may interact with upstream promoter DNA. Binding of the winged helix to the protrusion is PIC specific. Anchoring of these two structured TFIIF domains at separate sites locates an essential and unstructured region of Tfg2 near the Pol II active site cleft where it may interact with flexible regions of Pol II and the general factor TFIIB to promote initiation and start site selection. Consistent with this mechanism, mutations far from the enzyme active site, which alter the binding of either structured TFIIF domains to Pol II, have similar defects in transcription start site usage.
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Affiliation(s)
- Jesse Eichner
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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26
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Fission yeast Iec1-ino80-mediated nucleosome eviction regulates nucleotide and phosphate metabolism. Mol Cell Biol 2009; 30:657-74. [PMID: 19933844 DOI: 10.1128/mcb.01117-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Ino80 is an ATP-dependent nucleosome-remodeling enzyme involved in transcription, replication, and the DNA damage response. Here, we characterize the fission yeast Ino80 and find that it is essential for cell viability. We show that the Ino80 complex from fission yeast mediates ATP-dependent nucleosome remodeling in vitro. The purification of the Ino80-associated complex identified a highly conserved complex and the presence of a novel zinc finger protein with similarities to the mammalian transcriptional regulator Yin Yang 1 (YY1) and other members of the GLI-Krüppel family of proteins. Deletion of this Iec1 protein or the Ino80 complex subunit arp8, ies6, or ies2 causes defects in DNA damage repair, the response to replication stress, and nucleotide metabolism. We show that Iec1 is important for the correct expression of genes involved in nucleotide metabolism, including the ribonucleotide reductase subunit cdc22 and phosphate- and adenine-responsive genes. We find that Ino80 is recruited to a large number of promoter regions on phosphate starvation, including those of phosphate- and adenine-responsive genes that depend on Iec1 for correct expression. Iec1 is required for the binding of Ino80 to target genes and subsequent histone loss at the promoter and throughout the body of these genes on phosphate starvation. This suggests that the Iec1-Ino80 complex promotes transcription through nucleosome eviction.
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Yang C, Khaperskyy DA, Hou M, Ponticelli AS. Improved methods for expression and purification of Saccharomyces cerevisiae TFIIF and TFIIH; identification of a functional Escherichia coli promoter and internal translation initiation within the N-terminal coding region of the TFIIF TFG1 subunit. Protein Expr Purif 2009; 70:172-8. [PMID: 19818408 DOI: 10.1016/j.pep.2009.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 09/28/2009] [Accepted: 09/29/2009] [Indexed: 11/26/2022]
Abstract
The basal RNA polymerase II (RNAPII) transcription machinery is composed of RNAPII and the general transcription factors (TF) TATA binding protein (TBP), TFIIB, TFIIE, TFIIF and TFIIH. Due to the powerful genetic and molecular approaches that can be utilized, the budding yeast Saccharomyces cerevisiae has proven to be an invaluable model system for studies of the mechanisms of RNAPII transcription. Complementary biochemical studies of the S. cerevisiae basal transcription machinery, however, have been hampered by difficulties in the purification of TFIIF and TFIIH, most notably due to the severe toxicity of the TFIIF Tfg1 subunit in Escherichia coli and the complexity of the purification scheme for native TFIIH. Here, we report the elimination of TFG1-associated toxicity in E. coli, the identification and removal of a functional E. coli promoter and internal translation initiation within the N-terminal coding region of TFG1, and the efficient production and two-step purification of recombinant TFIIF complexes. We also report conditions for the efficient two-step tandem affinity purification (TAP) of holo-TFIIH, core TFIIH and TFIIK complexes from yeast whole cell extracts.
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Affiliation(s)
- Chen Yang
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY 14214-3000, USA
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28
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Erlich RL, Fry RC, Begley TJ, Daee DL, Lahue RS, Samson LD. Anc1, a protein associated with multiple transcription complexes, is involved in postreplication repair pathway in S. cerevisiae. PLoS One 2008; 3:e3717. [PMID: 19005567 PMCID: PMC2579579 DOI: 10.1371/journal.pone.0003717] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 10/21/2008] [Indexed: 11/18/2022] Open
Abstract
Yeast strains lacking Anc1, a member of the YEATS protein family, are sensitive to several DNA damaging agents. The YEATS family includes two human genes that are common fusion partners with MLL in human acute leukemias. Anc1 is a member of seven multi-protein complexes involved in transcription, and the damage sensitivity observed in anc1Δ cells is mirrored in strains deleted for some other non-essential members of several of these complexes. Here we show that ANC1 is in the same epistasis group as SRS2 and RAD5, members of the postreplication repair (PRR) pathway, but has additive or synergistic interactions with several other members of this pathway. Although PRR is traditionally divided into an “error-prone” and an “error-free” branch, ANC1 is not epistatic with all members of either established branch, and instead defines a new error-free branch of the PRR pathway. Like several genes involved in PRR, an intact ANC1 gene significantly suppresses spontaneous mutation rates, including the expansion of (CAG)25 repeats. Anc1's role in the PRR pathway, as well as its role in suppressing triplet repeats, point to a possible mechanism for a protein of potential medical interest.
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Affiliation(s)
- Rachel L. Erlich
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rebecca C. Fry
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Thomas J. Begley
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Danielle L. Daee
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Robert S. Lahue
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Leona D. Samson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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29
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Vogel T, Gruss P. Expression of Leukaemia associated transcription factor Af9/Mllt3 in the cerebral cortex of the mouse. Gene Expr Patterns 2008; 9:83-93. [PMID: 19000783 DOI: 10.1016/j.gep.2008.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/17/2008] [Accepted: 10/18/2008] [Indexed: 11/18/2022]
Abstract
Mutations of leukaemia associated AF9/MLLT3 are implicated in neurodevelopmental diseases such as epilepsia and ataxia. This study shows for the first time, that murine Af9 is transcribed in various CNS structures including the subventricular zone (SVZ) of the cerebral cortex, hippocampus, cerebellar cortex, septum and various thalamic structures, the choroid plexus, and the midbrain/hindbrain boundary. Expression of Af9 in the SVZ overlaps with Svet1, Cux2, and partially with Tbr2, confining its activity to the neurogenic compartment of the SVZ. In contrast to Svet1 and Cux2 expression, Af9 transcription is not limited to upper layer neurons but is found in the entire cortical plate. As part of an extensive network of interacting proteins involved in epigenetic DNA modification, we could show overlapping expression of Af9 with Af4/Aff1 and Fmr2/Aff2, two genes that are also related to neurodevelopmental diseases, as well as with the highly homologous Enl.
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Affiliation(s)
- Tanja Vogel
- Georg-August-University Goettingen, Centre of Anatomy, Department of Neuroanatomy, Kreuzbergring 36, 37075 Goettingen, Germany.
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30
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Transcriptional regulators of seven yeast species: Comparative genome analysis — Review. Folia Microbiol (Praha) 2008; 53:275-87. [DOI: 10.1007/s12223-008-0044-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 01/24/2008] [Indexed: 01/08/2023]
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31
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Abstract
The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. SWI/SNF interactions with nucleosomes were mapped by DNA footprinting and site-directed DNA and protein cross-linking when SWI/SNF was recruited by a transcription activator. SWI/SNF was found by DNA footprinting to contact tightly around one gyre of DNA spanning approximately 50 bp from the nucleosomal entry site to near the dyad axis. The DNA footprint is consistent with nucleosomes binding to an asymmetric trough of SWI/SNF that was revealed by the improved imaging of free SWI/SNF. The DNA site-directed cross-linking revealed that the catalytic subunit Swi2/Snf2 is associated with nucleosomes two helical turns from the dyad axis and that the Snf6 subunit is proximal to the transcription factor recruiting SWI/SNF. The highly conserved Snf5 subunit associates with the histone octamer and not with nucleosomal DNA. The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI/SNF remains bound.
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32
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Functions of Saccharomyces cerevisiae TFIIF during transcription start site utilization. Mol Cell Biol 2008; 28:3757-66. [PMID: 18362165 DOI: 10.1128/mcb.02272-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have shown that substitutions in the Tfg1 or Tfg2 subunits of Saccharomyces cerevisiae transcription factor IIF (TFIIF) can cause upstream shifts in start site utilization, resulting in initiation patterns that more closely resemble those of higher eukaryotes. In this study, we report the results from multiple biochemical assays analyzing the activities of wild-type yeast TFIIF and the TFIIF Tfg1 mutant containing the E346A substitution (Tfg1-E346A). We demonstrate that TFIIF stimulates formation of the first two phosphodiester bonds and dramatically stabilizes a short RNA-DNA hybrid in the RNA polymerase II (RNAPII) active center and, importantly, that the Tfg1-E346A substitution coordinately enhances early bond formation and the processivity of early elongation in vitro. These results are discussed within a proposed model for the role of yeast TFIIF in modulating conformational changes in the RNAPII active center during initiation and early elongation.
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33
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Sadhale P, Verma J, Naorem A. Basal transcription machinery: role in regulation of stress response in eukaryotes. J Biosci 2007; 32:569-78. [PMID: 17536176 DOI: 10.1007/s12038-007-0056-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The holoenzyme of prokaryotic RNA polymerase consists of the core enzyme, made of two alpha, beta, beta' and omega subunits, which lacks promoter selectivity and a sigma (sigma) subunit which enables the core enzyme to initiate transcription in a promoter dependent fashion. A stress sigma factor sigma(s), in prokaryotes seems to regulate several stress response genes in conjunction with other stress specific regulators. Since the basic principles of transcription are conserved from simple bacteria to multicellular complex organisms, an obvious question is: what is the identity of a counterpart of sigma(s), that is closest to the core polymerase and that dictates transcription of stress regulated genes in general? In this review, we discuss the logic behind the suggestion that like in prokaryotes,eukaryotes also have a common functional unit in the transcription machinery through which the stress specific transcription factors regulate rapid and highly controlled induction of gene expression associated with generalized stress response and point to some candidates that would fit the bill of the eukaryotic sigma(s).
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Affiliation(s)
- Parag Sadhale
- Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560 012, India.
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Lafon A, Chang CS, Scott EM, Jacobson SJ, Pillus L. MYST opportunities for growth control: yeast genes illuminate human cancer gene functions. Oncogene 2007; 26:5373-84. [PMID: 17694079 DOI: 10.1038/sj.onc.1210606] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The MYST family of histone acetyltransferases (HATs) was initially defined by human genes with disease connections and by yeast genes identified for their role in epigenetic transcriptional silencing. Since then, many new MYST genes have been discovered through genetic and genomic approaches. Characterization of the complexes through which MYST proteins act, regions of the genome to which they are targeted and biological consequences when they are disrupted, all deepen the connections of MYST proteins to development, growth control and human cancers. Many of the insights into MYST family function have come from studies in model organisms. Herein, we review functions of two of the founding MYST genes, yeast SAS2 and SAS3, and the essential yeast MYST ESA1. Analysis of these genes in yeast has defined roles for MYST proteins in transcriptional activation and silencing, and chromatin-mediated boundary formation. They have further roles in DNA damage repair and nuclear integrity. The observation that MYST protein complexes share subunits with other HATs, histone deacetylases and other key nuclear proteins, many with connections to human cancers, strengthens the idea that coordinating distinct chromatin modifications is critical for regulation.
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Affiliation(s)
- A Lafon
- Section of Molecular Biology, Division of Biological Sciences, UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
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35
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Yang X, Zaurin R, Beato M, Peterson CL. Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement. Nat Struct Mol Biol 2007; 14:540-7. [PMID: 17496903 DOI: 10.1038/nsmb1238] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 03/23/2007] [Indexed: 01/27/2023]
Abstract
Yeast SWI/SNF is a multisubunit, 1.14-MDa ATP-dependent chromatin-remodeling enzyme required for transcription of a subset of inducible genes. Biochemical studies have demonstrated that SWI/SNF uses the energy from ATP hydrolysis to generate superhelical torsion, mobilize mononucleosomes, enhance the accessibility of nucleosomal DNA and remove H2A-H2B dimers from mononucleosomes. Here we describe the ATP-dependent activities of a SWI/SNF sub complex that is composed of only three subunits, Swi2p, Arp7p and Arp9p. Whereas this sub complex is fully functional in most remodeling assays, Swi2p-Arp7p-Arp9p is defective for ATP-dependent removal of H2A-H2B dimers. We identify the acidic N terminus of the Swi3p subunit as a novel H2A-H2B-binding domain required for ATP-dependent dimer loss. Our data indicate that H2A-H2B dimer loss is not an obligatory consequence of ATP-dependent DNA translocation, and furthermore they suggest that SWI/SNF is composed of at least four interdependent modules.
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Affiliation(s)
- Xiaofang Yang
- Interdisciplinary Graduate Program, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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36
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Lawit SJ, O'Grady K, Gurley WB, Czarnecka-Verner E. Yeast two-hybrid map of Arabidopsis TFIID. PLANT MOLECULAR BIOLOGY 2007; 64:73-87. [PMID: 17340043 DOI: 10.1007/s11103-007-9135-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 01/05/2007] [Indexed: 05/11/2023]
Abstract
General transcription factor IID (TFIID) is a multisubunit protein complex involved in promoter recognition and is fundamental to the nucleation of the RNA polymerase II transcriptional preinitiation complex. TFIID is comprised of the TATA binding protein (TBP) and 12-15 TBP-associated factors (TAFs). While general transcription factors have been extensively studied in metazoans and yeast, little is known about the details of their structure and function in the plant kingdom. This work represents the first attempt to compare the structure of a plant TFIID complex with that determined for other organisms. While no TAF3 homolog has been observed in plants, at least one homolog has been identified for each of the remaining 14 TFIID subunits, including both TAF14 and TAF15 which have previously been shown to be unique to either yeast or humans. The presence of both TAFs 14 and 15 in plants suggests ancient roles for these proteins that were lost in metazoans and fungi, respectively. Yeast two-hybrid interaction assays resulted in a total of 65 binary interactions between putative subunits of Arabidopsis TFIID, including 26 contacts unique to plants. The interaction matrix of Arabidopsis TAFs is largely consistent with the three-lobed topological map for yeast TFIID, which suggests that the structure and composition of TFIID have been highly conserved among eukaryotes.
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Affiliation(s)
- Shai J Lawit
- Pioneer Hi-Bred International, Inc., a DuPont Company, 7300 N.W. 62nd Ave, PO Box 1004, Johnston, IA 50131-1004, USA
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37
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Abstract
ATP-dependent chromatin remodeling complexes contain ATPases of the Swi/Snf superfamily and alter DNA accessibility of chromatin in an ATP-dependent manner. Recently characterized INO80 and SWR1 complexes belong to a subfamily of these chromatin remodelers and are characterized by a split ATPase domain in the core ATPase subunit and the presence of Rvb proteins. INO80 and SWR1 complexes are evolutionarily conserved from yeast to human and have been implicated in transcription regulation, as well as DNA repair. The individual components, assembly patterns, and molecular mechanisms of the INO80 class of chromatin remodeling complexes are discussed in this review.
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Affiliation(s)
- Yunhe Bao
- Department of Carcinogenesis, Science Park Research Division, University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957
| | - Xuetong Shen
- Department of Carcinogenesis, Science Park Research Division, University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957
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38
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Abstract
In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.
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Affiliation(s)
- Mary C Thomas
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4935, USA
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39
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Hawley RS, Gilliland WD. Sometimes the result is not the answer: the truths and the lies that come from using the complementation test. Genetics 2006; 174:5-15. [PMID: 16988106 PMCID: PMC1569807 DOI: 10.1534/genetics.106.064550] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
It is standard genetic practice to determine whether or not two independently obtained mutants define the same or different genes by performing the complementation test. While the complementation test is highly effective and accurate in most cases, there are a number of instances in which the complementation test provides misleading answers, either as a result of the failure of two mutations that are located in different genes to complement each other or by exhibiting complementation between two mutations that lie within the same gene. We are primarily concerned here with those cases in which two mutations lie in different genes, but nonetheless fail to complement each other. This phenomenon is often referred to as second-site noncomplementation (SSNC). The discovery of SSNC led to a large number of screens designed to search for genes that encode interacting proteins. However, screens for dominant enhancer mutations of semidominant alleles of a given gene have proved far more effective at identifying interacting genes whose products interact physically or functionally with the initial gene of interest than have SSNC-based screens.
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Affiliation(s)
- R Scott Hawley
- Stowers Institute for Medical Research, Kansas, City, Missouri 64110, USA.
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40
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Fish RN, Ammerman ML, Davie JK, Lu BF, Pham C, Howe L, Ponticelli AS, Kane CM. Genetic interactions between TFIIF and TFIIS. Genetics 2006; 173:1871-84. [PMID: 16648643 PMCID: PMC1569716 DOI: 10.1534/genetics.106.058834] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2006] [Accepted: 04/28/2006] [Indexed: 11/18/2022] Open
Abstract
The eukaryotic transcript elongation factor TFIIS is encoded by a nonessential gene, PPR2, in Saccharomyces cerevisiae. Disruptions of PPR2 are lethal in conjunction with a disruption in the nonessential gene TAF14/TFG3. While investigating which of the Taf14p-containing complexes may be responsible for the synthetic lethality between ppr2Delta and taf14Delta, we discovered genetic interactions between PPR2 and both TFG1 and TFG2 encoding the two larger subunits of the TFIIF complex that also contains Taf14p. Mutant alleles of tfg1 or tfg2 that render cells cold sensitive have improved growth at low temperature in the absence of TFIIS. Remarkably, the amino-terminal 130 amino acids of TFIIS, which are dispensable for the known in vitro and in vivo activities of TFIIS, are required to complement the lethality in taf14Delta ppr2Delta cells. Analyses of deletion and chimeric gene constructs of PPR2 implicate contributions by different regions of this N-terminal domain. No strong common phenotypes were identified for the ppr2Delta and taf14Delta strains, implying that the proteins are not functionally redundant. Instead, the absence of Taf14p in the cell appears to create a dependence on an undefined function of TFIIS mediated by its N-terminal region. This region of TFIIS is also at least in part responsible for the deleterious effect of TFIIS on tfg1 or tfg2 cold-sensitive cells. Together, these results suggest a physiologically relevant functional connection between TFIIS and TFIIF.
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Affiliation(s)
- Rachel N Fish
- Department of Molecular and Cell Biology, University of California, Berkeley 94720-3202, USA
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41
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Ding X, Fan C, Zhou J, Zhong Y, Liu R, Ren K, Hu X, Luo C, Xiao S, Wang Y, Feng D, Zhang J. GAS41 interacts with transcription factor AP-2beta and stimulates AP-2beta-mediated transactivation. Nucleic Acids Res 2006; 34:2570-8. [PMID: 16698963 PMCID: PMC3303177 DOI: 10.1093/nar/gkl319] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Transcription factor AP-2 regulates transcription of a number of genes involving mammalian development, differentiation and carcinogenesis. Recent studies have shown that interaction partners can modulate the transcriptional activity of AP-2 over the downstream targets. In this study, we reported the identification of GAS41 as an interaction partner of AP-2β. We documented the interaction both in vivo by co-immunoprecipitation as well as in vitro through glutathione S-transferase (GST) pull-down assays. We also showed that the two proteins are co-localized in the nuclei of mammalian cells. We further mapped the interaction domains between the two proteins to the C-termini of both AP-2β and GAS41, respectively. Furthermore, we have identified three critical residues of GAS41 that are important for the interaction between the two proteins. In addition, by transient co-expression experiments using reporter containing three AP-2 consensus binding sites in the promoter region, we found that GAS41 stimulates the transcriptional activity of AP-2β over the reporter. Finally, electrophoretic mobility shift assay (EMSA) suggested that GAS41 enhances the DNA-binding activity of AP-2β. Our data provide evidence for a novel cellular function of GAS41 as a transcriptional co-activator for AP-2β.
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Affiliation(s)
- Xiaofeng Ding
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Changzheng Fan
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Jianlin Zhou
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Yingli Zhong
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Rushi Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Kaiqun Ren
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Xiang Hu
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Chang Luo
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Shunyong Xiao
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Yeqi Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Du Feng
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
| | - Jian Zhang
- Key Laboratory of Protein Chemistry and Developmental Biology of State Education Ministry of China, College of Life Science, Hunan Normal University Changsha, Hunan 410081, China
- Model Organism Division, E-Institutes of Shanghai Universities, Shanghai Second Medical University Shanghai 200025, China
- To whom correspondence should be addressed. Tel/Fax: +86 731 8872792;
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42
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Bittner CB, Zeisig DT, Zeisig BB, Slany RK. Direct physical and functional interaction of the NuA4 complex components Yaf9p and Swc4p. EUKARYOTIC CELL 2005; 3:976-83. [PMID: 15302830 PMCID: PMC500879 DOI: 10.1128/ec.3.4.976-983.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Saccharomyces cerevisiae Yaf9p and the mammalian leukemia-associated protein ENL share a high degree of similarity. To investigate the biological function of Yaf9p, this protein was used to search for interacting proteins in a two-hybrid system. Here, we demonstrate that Yaf9p binds directly to Swc4p, the yeast homolog of the mammalian DNA-methyltransferase-associated protein 1. Yaf9p and Swc4p associate through C-terminal domains, and both proteins coprecipitate in vitro in pull-down experiments and in vivo by immunoprecipitation. In living cells, Swc4p is present in a megadalton protein complex that shows a fractionation behavior in gel filtration similar to that of Esa1p, the histone acetyltransferase of the NuA4 complex. Recruitment of Yaf9p to DNA leads to promoter-specific transcriptional activation that can be inhibited by dominant negative Swc4p lacking the Yaf9p binding domain. Interference with Swc4p function also increases sensitivity to the microtubule toxin benomyl, a trait that corresponds to the known phenotype of a yaf9(-) knockout strain. In summary, the results suggest that Yaf9p and Swc4p form a protein pair that has a role in chromatin modification with possible implications also for the function of their mammalian counterparts.
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Affiliation(s)
- Claudia B Bittner
- Department of Genetics, University Erlangen, Staudtstrasse 5, 91058 Erlangen, Germany
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43
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Kabani M, Michot K, Boschiero C, Werner M. Anc1 interacts with the catalytic subunits of the general transcription factors TFIID and TFIIF, the chromatin remodeling complexes RSC and INO80, and the histone acetyltransferase complex NuA3. Biochem Biophys Res Commun 2005; 332:398-403. [PMID: 15896708 DOI: 10.1016/j.bbrc.2005.04.158] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 04/29/2005] [Indexed: 12/01/2022]
Abstract
The Anc1 protein co-purifies with general transcription factors, chromatin remodeling complexes, and histone modification enzymes and is required for efficient transcription in yeast. We show here that Anc1 interacts with Tsm1, Tfg1, Sth1, Ino80, and Sas3 that are, respectively, the catalytic subunits of the general transcription factors TFIID and TFIIF, of the chromatin remodeling complexes RSC and INO80, and of the histone H3-acetyltransferase complex NuA3. We show that Anc1 is required for growth on galactose as the sole carbon source, and that it is recruited to the UAS of the GAL1 gene after induction.
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Affiliation(s)
- Mehdi Kabani
- Laboratoire de Physiogénomique, Service de Biochimie et Génétique Moléculaire, Departement de Biologie Joliot Curie, Bâtiment 144, CEA/Saclay, F-91191 Gif-sur-Yvette, France.
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44
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Abstract
Chromosome translocations disrupting the MLL gene are associated with various hematologic malignancies but are particularly common in infant and secondary therapy-related acute leukemias. The normal MLL-encoded protein is an essential component of a supercomplex with chromatin-modulating activity conferred by histone acetylase and methyltransferase activities, and the protein plays a key role in the developmental regulation of gene expression, including Hox gene expression. In leukemia, this function is subverted by breakage, recombination, and the formation of chimeric fusion with one of many alternative partners. Such MLL translocations result in the replacement of the C-terminal functional domains of MLL with those of a fusion partner, yielding a newly formed MLL chimeric protein with an altered function that endows hematopoietic progenitors with self-renewing and leukemogenic activity. This potent impact of the MLL chimera can be attributed to one of 2 kinds of activity of the fusion partner: direct transcriptional transactivation or dimerization/oligomerization. Key unresolved issues currently being addressed include the set of target genes for MLL fusions, the stem cell of origin for the leukemias, the role of additional secondary mutations, and the origins or etiology of the MLL gene fusions themselves. Further elaboration of the biology of MLL gene-associated leukemia should lead to novel and specific therapeutic strategies.
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Affiliation(s)
- Mariko Eguchi
- Section of Haemato-Oncology, Institute of Cancer Research, London, UK.
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45
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Zeisig DT, Bittner CB, Zeisig BB, García-Cuéllar MP, Hess JL, Slany RK. The eleven-nineteen-leukemia protein ENL connects nuclear MLL fusion partners with chromatin. Oncogene 2005; 24:5525-32. [PMID: 15856011 DOI: 10.1038/sj.onc.1208699] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mixed lineage leukemia (MLL) fusion proteins are derived from translocations at 11q23 that occur in aggressive subtypes of leukemia. As a consequence, MLL is joined to different unrelated proteins to form oncogenic transcription factors. Here we demonstrate a direct interaction between several nuclear MLL fusion partners and present evidence for a role of these proteins in histone binding. In two-hybrid studies, ENL interacted with AF4 and AF5q31 as well as with a fragment of AF10. A structure-function analysis revealed that the AF4/AF5q31/AF10 binding domain in ENL coincided with the C-terminus that is essential for transformation by MLL-ENL. The ENL/AF4 association was corroborated by GST-pulldown experiments and by mutual coprecipitation. Both proteins colocalized in vivo in a nuclear speckled pattern. Moreover, AF4 and ENL coeluted on sizing columns together with the known ENL binding partner Polycomb3, suggesting the presence of a multiprotein complex. The overexpression of ENL alone activated a reporter construct and a mutational screen indicated the conserved YEATS domain as essential for this function. Overlay and pulldown-assays finally showed a specific and YEATS domain-dependent association of ENL with histones H3 and H1. In summary, our studies support a common role for nuclear MLL fusion partners in chromatin biology.
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Affiliation(s)
- Deniz T Zeisig
- Department of Genetics, University Erlangen, Staudtstrasse 5, 91058 Erlangen, Germany
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Shia WJ, Osada S, Florens L, Swanson SK, Washburn MP, Workman JL. Characterization of the yeast trimeric-SAS acetyltransferase complex. J Biol Chem 2005; 280:11987-94. [PMID: 15659401 DOI: 10.1074/jbc.m500276200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast SAS2 (Something About Silencing 2) gene encodes a member of the MYST protein family of histone acetyltransferases (HATs) and is involved in transcriptional silencing at all silent loci (HML, HMR, telomeres, and rDNA) in Saccharomyces cerevisiae. Sas2 is the catalytic subunit of a yeast histone acetyltransferase complex termed SAS complex. The enzymatic activity of SAS complex on free histones has been reported, but nucleosomal HAT activity has not yet been documented. Here we show that the native yeast SAS complex is a small trimeric protein complex composed solely of Sas2, Sas4, and Sas5 with a molecular mass of about 125 kDa. It is capable of acetylating both free histones and nucleosomes, although the nucleosomal HAT activity of SAS complex is very weak when compared with that of NuA4, the other member of MYST HAT complex. We also demonstrate that the putative acetyl CoA binding motif in Sas2 is essential for both the in vivo silencing function and the enzymatic activity of SAS complex. Unlike NuA4, which acetylates all four available lysines at the N-terminal tail of histone H4, SAS complex exclusively acetylates lysine 16 of histone H4 in vitro and is required for the bulk of H4 lysine 16 acetylation in vivo. This specific lysine preference corresponds to the role of SAS complex in antagonizing the spreading of Sir proteins at silent loci in S. cerevisiae.
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Affiliation(s)
- Wei-Jong Shia
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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Kimura M, Ishihama A. Tfg3, a subunit of the general transcription factor TFIIF in Schizosaccharomyces pombe, functions under stress conditions. Nucleic Acids Res 2004; 32:6706-15. [PMID: 15616156 PMCID: PMC545442 DOI: 10.1093/nar/gkh1000] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TFIIF is a general transcription factor (GTF) that binds to RNA polymerase II (pol II) for subsequent recruitment of pol II to a promoter. TFIIF of Saccharomyces cerevisiae contains a small subunit, designated Tfg3, in addition to two conserved subunits, TFIIFalpha (Tfg1) and TFIIFbeta (Tfg2). In this study, we characterized Tfg3 of Schizosaccharomyces pombe. Using Tfg3 fused to green fluorescent protein (GFP), we found that Tfg3 is located in nuclei, and it is assembled into the C-terminal domain phosphatase (Fcp1)/TFIIF/pol II complex via interactions with TFIIFalpha and TFIIFbeta. As in the case of S.cerevisiae, Tfg3 in S.pombe forms part of another GTF, namely TFIID. The TFIID complex isolated from S.pombe that had been cultured at elevated temperatures included increased levels of Tfg3. The interaction of recombinant Tfg3 with TATA-binding protein (TBP), the central subunit of TFIID, was temperature-dependent. Moreover, a mutant of S.pombe that lacked the gene for Tfg3 was sensitive to a battery of stresses including temperature up-shift. Starting from a mutant with tfg3- mutation, we isolated five species of multicopy suppressors. Expression levels of the suppressor genes were lower in the mutant cell than in wild-type cell at an elevated temperature. Taken together, we propose that Tfg3 is involved in transcriptional regulation under stress conditions, in particular, at high temperatures.
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Affiliation(s)
- Makoto Kimura
- Gene Engineering Division, BioResource Center, RIKEN (Institute of Physical and Chemical Research), Tsukuba, Ibaraki 305-0074, Japan and Nippon Institute for Biological Science, Ome, Tokyo 198-0024, Japan.
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Zhang H, Richardson DO, Roberts DN, Utley R, Erdjument-Bromage H, Tempst P, Côté J, Cairns BR. The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres. Mol Cell Biol 2004; 24:9424-36. [PMID: 15485911 PMCID: PMC522225 DOI: 10.1128/mcb.24.21.9424-9436.2004] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yaf9, Taf14, and Sas5 comprise the YEATS domain family in Saccharomyces cerevisiae, which in humans includes proteins involved in acute leukemias. The YEATS domain family is essential, as a yaf9Delta taf14Delta sas5Delta triple mutant is nonviable. We verify that Yaf9 is a stable component of NuA4, an essential histone H4 acetyltransferase complex. Yaf9 is also associated with the SWR1 complex, which deposits the histone H2A variant Htz1. However, the functional contribution of Yaf9 to these complexes has not been determined. Strains lacking YAF9 are sensitive to DNA-damaging agents, cold, and caffeine, and the YEATS domain is required for full Yaf9 function. NuA4 lacking Yaf9 retains histone acetyltransferase activity in vitro, and Yaf9 does not markedly reduce bulk H4 acetylation levels, suggesting a role for Yaf9 in the targeting or regulation of NuA4. Interestingly, yaf9Delta strains display reduced transcription of genes near certain telomeres, and their repression is correlated with reduced H4 acetylation, reduced occupancy by Htz1, and increased occupancy by the silencing protein Sir3. Additionally, the spectra of phenotypes, genes, and telomeres affected in yaf9Delta and htz1Delta strains are significantly similar, further supporting a role for Yaf9 in Htz1 deposition. Taken together, these data indicate that Yaf9 may function in NuA4 and SWR1 complexes to help antagonize silencing near telomeres.
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Affiliation(s)
- Haiying Zhang
- Department of Oncological Sciences, School of Medicine, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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Lago C, Clerici E, Mizzi L, Colombo L, Kater MM. TBP-associated factors in Arabidopsis. Gene 2004; 342:231-41. [PMID: 15527982 DOI: 10.1016/j.gene.2004.08.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Revised: 07/08/2004] [Accepted: 08/19/2004] [Indexed: 11/19/2022]
Abstract
Initiation of transcription mediated by RNA polymerase II requires a number of transcription factors among which TFIID is the major core promoter recognition factor. TFIID is composed of highly conserved factors which include the TATA-binding protein (TBP) and about 14 TBP-associated factors (TAFs). Since TAFs play important roles in transcription they have been extensively studied in organisms like yeast, Drosophila and human. Surprisingly, TAFs have been poorly characterized in plants. With the completion of the Arabidopsis genome sequence, it is possible to search for TAFs, since many of them have conserved amino acid sequences. Mining the genome of Arabidopsis for TAFs resulted in the identification of 18 putative Arabidopsis TAFs (AtTAFs). We have analyzed their protein structure and their genomic localisation. Expression profiling by RT-PCR showed that these TAFs are expressed in all parts of the plant which is in agreement with their general role in transcription. These analyses in combination with their evolutionary conservation with TAFs of other organisms are discussed.
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Affiliation(s)
- Clara Lago
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli studi di Milano, via Celoria 26, 20133, Milan, Italy
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50
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Dror V, Winston F. The Swi/Snf chromatin remodeling complex is required for ribosomal DNA and telomeric silencing in Saccharomyces cerevisiae. Mol Cell Biol 2004; 24:8227-35. [PMID: 15340082 PMCID: PMC515061 DOI: 10.1128/mcb.24.18.8227-8235.2004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Swi/Snf chromatin remodeling complex has been previously demonstrated to be required for transcriptional activation and repression of a subset of genes in Saccharomyces cerevisiae. In this work we demonstrate that Swi/Snf is also required for repression of RNA polymerase II-dependent transcription in the ribosomal DNA (rDNA) locus (rDNA silencing). This repression appears to be independent of both Sir2 and Set1, two factors known to be required for rDNA silencing. In contrast to many other rDNA silencing mutants that have elevated levels of rDNA recombination, snf2Delta mutants have a significantly decreased level of rDNA recombination. Additional studies have demonstrated that Swi/Snf is also required for silencing of genes near telomeres while having no detectable effect on silencing of HML or HMR.
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Affiliation(s)
- Vardit Dror
- Department of Genetics, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA 02115, USA
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