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Luna-Arias JP, Castro-Muñozledo F. Participation of the TBP-associated factors (TAFs) in cell differentiation. J Cell Physiol 2024; 239:e31167. [PMID: 38126142 DOI: 10.1002/jcp.31167] [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: 09/18/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue-specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA-box binding protein (TBP)-associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.
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Affiliation(s)
- Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Federico Castro-Muñozledo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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2
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Role of the TATA-box binding protein (TBP) and associated family members in transcription regulation. Gene X 2022; 833:146581. [PMID: 35597524 DOI: 10.1016/j.gene.2022.146581] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
The assembly of transcription complexes on eukaryotic promoters involves a series of steps, including chromatin remodeling, recruitment of TATA-binding protein (TBP)-containing complexes, the RNA polymerase II holoenzyme, and additional basal transcription factors. This review describes the transcriptional regulation by TBP and its corresponding homologs that constitute the TBP family and their interactions with promoter DNA. The C-terminal core domain of TBP is highly conserved and contains two structural repeats that fold into a saddle-like structure, essential for the interaction with the TATA-box on DNA. Based on the TBP C-terminal core domain similarity, three TBP-related factors (TRFs) or TBP-like factors (TBPLs) have been discovered in metazoans, TRF1, TBPL1, and TBPL2. TBP is autoregulated, and once bound to DNA, repressors such as Mot1 induce TBP to dissociate, while other factors such as NC2 and the NOT complex convert the active TBP/DNA complex into inactive, negatively regulating TBP. TFIIA antagonizes the TBP repressors but may be effective only in conjunction with the RNA polymerase II holoenzyme recruitment to the promoter by promoter-bound activators. TRF1 has been discovered inDrosophila melanogasterandAnophelesbut found absent in vertebrates and yeast. TBPL1 cannot bind to the TATA-box; instead, TBPL1 prefers binding to TATA-less promoters. However, TBPL1 shows a stronger association with TFIIA than TBP. The TCT core promoter element is present in most ribosomal protein genes inDrosophilaand humans, and TBPL1 is required for the transcription of these genes. TBP directly participates in the DNA repair mechanism, and TBPL1 mediates cell cycle arrest and apoptosis. TBPL2 is closely related to its TBP paralog, showing 95% sequence similarity with the TBP core domain. Like TBP, TBPL2 also binds to the TATA-box and shows interactions with TFIIA, TFIIB, and other basal transcription factors. Despite these advances, much remains to be explored in this family of transcription factors.
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3
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Petrenko N, Struhl K. Comparison of transcriptional initiation by RNA polymerase II across eukaryotic species. eLife 2021; 10:67964. [PMID: 34515029 PMCID: PMC8463073 DOI: 10.7554/elife.67964] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The preinitiation complex (PIC) for transcriptional initiation by RNA polymerase (Pol) II is composed of general transcription factors that are highly conserved. However, analysis of ChIP-seq datasets reveals kinetic and compositional differences in the transcriptional initiation process among eukaryotic species. In yeast, Mediator associates strongly with activator proteins bound to enhancers, but it transiently associates with promoters in a form that lacks the kinase module. In contrast, in human, mouse, and fly cells, Mediator with its kinase module stably associates with promoters, but not with activator-binding sites. This suggests that yeast and metazoans differ in the nature of the dynamic bridge of Mediator between activators and Pol II and the composition of a stable inactive PIC-like entity. As in yeast, occupancies of TATA-binding protein (TBP) and TBP-associated factors (Tafs) at mammalian promoters are not strictly correlated. This suggests that within PICs, TFIID is not a monolithic entity, and multiple forms of TBP affect initiation at different classes of genes. TFIID in flies, but not yeast and mammals, interacts strongly at regions downstream of the initiation site, consistent with the importance of downstream promoter elements in that species. Lastly, Taf7 and the mammalian-specific Med26 subunit of Mediator also interact near the Pol II pause region downstream of the PIC, but only in subsets of genes and often not together. Species-specific differences in PIC structure and function are likely to affect how activators and repressors affect transcriptional activity.
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Affiliation(s)
- Natalia Petrenko
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
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Fittipaldi R, Floris P, Proserpio V, Cotelli F, Beltrame M, Caretti G. The Lysine Methylase SMYD3 Modulates Mesendodermal Commitment during Development. Cells 2021; 10:cells10051233. [PMID: 34069776 PMCID: PMC8157265 DOI: 10.3390/cells10051233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 12/26/2022] Open
Abstract
SMYD3 (SET and MYND domain containing protein 3) is a methylase over-expressed in cancer cells and involved in oncogenesis. While several studies uncovered key functions for SMYD3 in cancer models, the SMYD3 role in physiological conditions has not been fully elucidated yet. Here, we dissect the role of SMYD3 at early stages of development, employing mouse embryonic stem cells (ESCs) and zebrafish as model systems. We report that SMYD3 depletion promotes the induction of the mesodermal pattern during in vitro differentiation of ESCs and is linked to an upregulation of cardiovascular lineage markers at later stages. In vivo, smyd3 knockdown in zebrafish favors the upregulation of mesendodermal markers during zebrafish gastrulation. Overall, our study reveals that SMYD3 modulates levels of mesendodermal markers, both in development and in embryonic stem cell differentiation.
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Affiliation(s)
- Raffaella Fittipaldi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; (R.F.); (P.F.); (V.P.); (F.C.); (M.B.)
| | - Pamela Floris
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; (R.F.); (P.F.); (V.P.); (F.C.); (M.B.)
| | - Valentina Proserpio
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; (R.F.); (P.F.); (V.P.); (F.C.); (M.B.)
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | - Franco Cotelli
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; (R.F.); (P.F.); (V.P.); (F.C.); (M.B.)
| | - Monica Beltrame
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; (R.F.); (P.F.); (V.P.); (F.C.); (M.B.)
| | - Giuseppina Caretti
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy; (R.F.); (P.F.); (V.P.); (F.C.); (M.B.)
- Correspondence: ; Tel.: +39-025-031-5002
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Parra-Marín O, López-Pacheco K, Hernández R, López-Villaseñor I. The highly diverse TATA box-binding proteins among protists: A review. Mol Biochem Parasitol 2020; 239:111312. [PMID: 32771681 DOI: 10.1016/j.molbiopara.2020.111312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/28/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Transcription is the first step of gene expression regulation and is a fundamental mechanism for establishing the viability and development of a cell. The TATA box-binding protein (TBP) interaction with a TATA box in a promoter is one of the best studied mechanisms in transcription initiation. TBP is a transcription factor that is highly conserved from archaea to humans and is essential for the transcription initiated by each of the three RNA polymerases. In addition, the discovery of TBP-related factor 1 (TRF1) and other factors related to TBP shed light on the variability among transcription initiation complexes, thus demonstrating that the compositions of these complexes are, in fact, more complicated than originally believed. Despite these facts, the majority of studies on transcription have been performed on animal, plant and fungal cells, which serve as canonical models, and information regarding protist cells is relatively scarce. The aim of this work is to review the diversity of the TBPs that have been documented in protists and describe some of the specific features that differentiate them from their counterparts in higher eukaryotes.
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Affiliation(s)
- Olivia Parra-Marín
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Karla López-Pacheco
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico.
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TATA box-binding protein-related factor 3 drives the mesendoderm specification of human embryonic stem cells by globally interacting with the TATA box of key mesendodermal genes. Stem Cell Res Ther 2020; 11:196. [PMID: 32448362 PMCID: PMC7245780 DOI: 10.1186/s13287-020-01711-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/23/2020] [Accepted: 05/06/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mesendodermal formation during early gastrulation requires the expression of lineage-specific genes, while the regulatory mechanisms during this process have not yet been fully illustrated. TATA box-binding protein (TBP) and TBP-like factors are general transcription factors responsible for the transcription initiation by recruiting the preinitiation complex to promoter regions. However, the role of TBP family members in the regulation of mesendodermal specification remains largely unknown. METHODS We used an in vitro mesendodermal differentiation system of human embryonic stem cells (hESCs), combining with the microarray and quantitative polymerase chain reaction (qRT-PCR) analysis, loss of function and gain of function to determine the function of the TBP family member TBP-related factor 3 (TRF3) during mesendodermal differentiation of hESCs. The chromatin immunoprecipitation (ChIP) and biochemistry analysis were used to determine the binding of TRF3 to the promoter region of key mesendodermal genes. RESULTS The mesendodermal differentiation of hESCs was confirmed by the microarray gene expression profile, qRT-PCR, and immunocytochemical staining. The expression of TRF3 mRNA was enhanced during mesendodermal differentiation of hESCs. The TRF3 deficiency did not affect the pluripotent marker expression, alkaline phosphatase activity, and cell cycle distribution of undifferentiated hESCs or the expression of early neuroectodermal genes during neuroectodermal differentiation. During the mesendodermal differentiation, the expression of pluripotency markers decreased in both wild-type and TRF3 knockout (TRF3-/-) cells, while the TRF3 deficiency crippled the expression of the mesendodermal markers. The reintroduction of TRF3 into the TRF3-/- hESCs rescued inhibited mesendodermal differentiation. Mechanistically, the TRF3 binding profile was significantly shifted to the mesendodermal specification during mesendodermal differentiation of hESCs based on the ChIP-seq data. Moreover, ChIP and ChIP-qPCR analysis showed that TRF3 was enriched at core promoter regions of mesendodermal developmental genes, EOMESODERMIN, BRACHYURY, mix paired-like homeobox, and GOOSECOID homeobox, during mesendodermal differentiation of hESCs. CONCLUSIONS These results reveal that the TBP family member TRF3 is dispensable in the undifferentiated hESCs and the early neuroectodermal differentiation. However, it directs mesendodermal lineage commitment of hESCs via specifically promoting the transcription of key mesendodermal transcription factors. These findings provide new insights into the function and mechanisms of the TBP family member in hESC early lineage specification.
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7
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Sud A, Thomsen H, Law PJ, Försti A, Filho MIDS, Holroyd A, Broderick P, Orlando G, Lenive O, Wright L, Cooke R, Easton D, Pharoah P, Dunning A, Peto J, Canzian F, Eeles R, Kote-Jarai ZS, Muir K, Pashayan N, Hoffmann P, Nöthen MM, Jöckel KH, Strandmann EPV, Lightfoot T, Kane E, Roman E, Lake A, Montgomery D, Jarrett RF, Swerdlow AJ, Engert A, Orr N, Hemminki K, Houlston RS. Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility. Nat Commun 2017; 8:1892. [PMID: 29196614 PMCID: PMC5711884 DOI: 10.1038/s41467-017-00320-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/20/2017] [Indexed: 02/08/2023] Open
Abstract
Several susceptibility loci for classical Hodgkin lymphoma have been reported. However, much of the heritable risk is unknown. Here, we perform a meta-analysis of two existing genome-wide association studies, a new genome-wide association study, and replication totalling 5,314 cases and 16,749 controls. We identify risk loci for all classical Hodgkin lymphoma at 6q22.33 (rs9482849, P = 1.52 × 10-8) and for nodular sclerosis Hodgkin lymphoma at 3q28 (rs4459895, P = 9.43 × 10-17), 6q23.3 (rs6928977, P = 4.62 × 10-11), 10p14 (rs3781093, P = 9.49 × 10-13), 13q34 (rs112998813, P = 4.58 × 10-8) and 16p13.13 (rs34972832, P = 2.12 × 10-8). Additionally, independent loci within the HLA region are observed for nodular sclerosis Hodgkin lymphoma (rs9269081, HLA-DPB1*03:01, Val86 in HLA-DRB1) and mixed cellularity Hodgkin lymphoma (rs1633096, rs13196329, Val86 in HLA-DRB1). The new and established risk loci localise to areas of active chromatin and show an over-representation of transcription factor binding for determinants of B-cell development and immune response.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Oleg Lenive
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Lauren Wright
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London, SM2 5NG, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M1 3BB, UK
- Division of Health Sciences, Warwick Medical School, Warwick University, Warwick, CV4 7AL, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Per Hoffmann
- Department of Biomedicine, Division of Medical Genetics, University of Basel, Basel, 4031, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | | | | | - Tracy Lightfoot
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Eve Roman
- Department of Health Sciences, University of York, York, YO10 5DD, UK
| | - Annette Lake
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Dorothy Montgomery
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Ruth F Jarrett
- MRC University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Andreas Engert
- Department of Internal Medicine, University Hospital of Cologne, Cologne, 50937, Germany
| | - Nick Orr
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, 69120, Germany
- Centre for Primary Health Care Research, Lund University, Malmö, 221 00, Sweden
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK.
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Abstract
This review by Vo ngoc et al. expands the view of the RNA polymerase II core promoter, which is comprised of classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.
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Affiliation(s)
- Long Vo Ngoc
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Yuan-Liang Wang
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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9
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Hueso M, De Ramon L, Navarro E, Ripoll E, Cruzado JM, Grinyo JM, Torras J. Silencing of CD40 in vivo reduces progression of experimental atherogenesis through an NF-κB/miR-125b axis and reveals new potential mediators in the pathogenesis of atherosclerosis. Atherosclerosis 2016; 255:80-89. [DOI: 10.1016/j.atherosclerosis.2016.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 10/06/2016] [Accepted: 11/01/2016] [Indexed: 02/08/2023]
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10
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Stijf-Bultsma Y, Sommer L, Tauber M, Baalbaki M, Giardoglou P, Jones DR, Gelato KA, van Pelt J, Shah Z, Rahnamoun H, Toma C, Anderson KE, Hawkins P, Lauberth SM, Haramis APG, Hart D, Fischle W, Divecha N. The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output. Mol Cell 2015; 58:453-67. [PMID: 25866244 PMCID: PMC4429956 DOI: 10.1016/j.molcel.2015.03.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 01/20/2015] [Accepted: 03/06/2015] [Indexed: 12/17/2022]
Abstract
Phosphoinositides (PI) are important signaling molecules in the nucleus that influence gene expression. However, if and how nuclear PI directly affects the transcriptional machinery is not known. We report that the lipid kinase PIP4K2B regulates nuclear PI5P and the expression of myogenic genes during myoblast differentiation. A targeted screen for PI interactors identified the PHD finger of TAF3, a TATA box binding protein-associated factor with important roles in transcription regulation, pluripotency, and differentiation. We show that the PI interaction site is distinct from the known H3K4me3 binding region of TAF3 and that PI binding modulates association of TAF3 with H3K4me3 in vitro and with chromatin in vivo. Analysis of TAF3 mutants indicates that TAF3 transduces PIP4K2B-mediated alterations in PI into changes in specific gene transcription. Our study reveals TAF3 as a direct target of nuclear PI and further illustrates the importance of basal transcription components as signal transducers.
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Affiliation(s)
- Yvette Stijf-Bultsma
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK; The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Lilly Sommer
- The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Maria Tauber
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mai Baalbaki
- University of California, San Francisco, Mail Code 3120, Smith Cardiovascular Research Building, 555 Mission Bay Boulevard, South San Francisco, CA 94158-9001, USA
| | - Panagiota Giardoglou
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - David R Jones
- The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Kathy A Gelato
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jason van Pelt
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Zahid Shah
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK
| | - Homa Rahnamoun
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clara Toma
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karen E Anderson
- Signaling Laboratory, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK
| | - Philip Hawkins
- Signaling Laboratory, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK
| | - Shannon M Lauberth
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna-Pavlina G Haramis
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Daniel Hart
- University of California, San Francisco, Mail Code 3120, Smith Cardiovascular Research Building, 555 Mission Bay Boulevard, South San Francisco, CA 94158-9001, USA
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Nullin Divecha
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK; The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK.
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11
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Salazar KA, Joffe NR, Dinguirard N, Houde P, Castillo MG. Transcriptome analysis of the white body of the squid Euprymna tasmanica with emphasis on immune and hematopoietic gene discovery. PLoS One 2015; 10:e0119949. [PMID: 25775132 PMCID: PMC4361686 DOI: 10.1371/journal.pone.0119949] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/27/2015] [Indexed: 02/07/2023] Open
Abstract
In the mutualistic relationship between the squid Euprymna tasmanica and the bioluminescent bacterium Vibrio fischeri, several host factors, including immune-related proteins, are known to interact and respond specifically and exclusively to the presence of the symbiont. In squid and octopus, the white body is considered to be an immune organ mainly due to the fact that blood cells, or hemocytes, are known to be present in high numbers and in different developmental stages. Hence, the white body has been described as the site of hematopoiesis in cephalopods. However, to our knowledge, there are no studies showing any molecular evidence of such functions. In this study, we performed a transcriptomic analysis of white body tissue of the Southern dumpling squid, E. tasmanica. Our primary goal was to gain insights into the functions of this tissue and to test for the presence of gene transcripts associated with hematopoietic and immune processes. Several hematopoiesis genes including CPSF1, GATA 2, TFIID, and FGFR2 were found to be expressed in the white body. In addition, transcripts associated with immune-related signal transduction pathways, such as the toll-like receptor/NF-κβ, and MAPK pathways were also found, as well as other immune genes previously identified in E. tasmanica's sister species, E. scolopes. This study is the first to analyze an immune organ within cephalopods, and to provide gene expression data supporting the white body as a hematopoietic tissue.
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Affiliation(s)
- Karla A. Salazar
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Nina R. Joffe
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Nathalie Dinguirard
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Maria G. Castillo
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
- * E-mail:
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12
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Abstract
Transcriptional regulation is pivotal for development and differentiation of organisms. Transcription of eukaryotic protein-coding genes by RNA polymerase II (Pol II) initiates at the core promoter. Core promoters, which encompass the transcription start site, may contain functional core promoter elements, such as the TATA box, initiator, TCT and downstream core promoter element. TRF2 (TATA-box-binding protein-related factor 2) does not bind TATA box-containing promoters. Rather, it is recruited to core promoters via sequences other than the TATA box. We review the recent findings implicating TRF2 as a basal transcription factor in the regulation of diverse biological processes and specialized transcriptional programs.
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Key Words
- BREd, downstream TFIIB recognition element
- BREu, upstream TFIIB recognition element
- ChIP, Chromatin immunoprecipitation
- DPE
- DPE, downstream core promoter element
- Inr, initiator
- MTE, motif ten element
- PIC, preinitiation complex
- Pol II, RNA polymerase II
- RNA Pol II transcription
- TAF, TBP-associated factor
- TBP, TATA-box binding protein
- TBP-related factors
- TCT
- TFIIA (transcription factor, RNA polymerase II A)
- TFIIB (transcription factor, RNA polymerase II B)
- TFIID (transcription factor, RNA polymerase II D)
- TRF, TATA-box-binding protein-related factor
- TRF2
- TSS, transcription start site
- core promoter elements/motifs
- embryonic development
- histone gene cluster
- ribosomal protein genes
- spermiogenesis
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Affiliation(s)
- Yonathan Zehavi
- a The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University , Ramat Gan , 5290002 , Israel
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13
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Diversity in TAF proteomics: consequences for cellular differentiation and migration. Int J Mol Sci 2014; 15:16680-97. [PMID: 25244017 PMCID: PMC4200853 DOI: 10.3390/ijms150916680] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 12/31/2022] Open
Abstract
Development is a highly controlled process of cell proliferation and differentiation driven by mechanisms of dynamic gene regulation. Specific DNA binding factors for establishing cell- and tissue-specific transcriptional programs have been characterised in different cell and animal models. However, much less is known about the role of “core transcription machinery” during cell differentiation, given that general transcription factors and their spatiotemporally patterned activity govern different aspects of cell function. In this review, we focus on the role of TATA-box associated factor 4 (TAF4) and its functional isoforms generated by alternative splicing in controlling lineage-specific differentiation of normal mesenchymal stem cells and cancer stem cells. In the light of our recent findings, induction, control and maintenance of cell differentiation status implies diversification of the transcription initiation apparatus orchestrated by alternative splicing.
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14
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Xie G, Yu Z, Jia D, Jiao R, Deng WM. E(y)1/TAF9 mediates the transcriptional output of Notch signaling in Drosophila. J Cell Sci 2014; 127:3830-9. [PMID: 25015288 DOI: 10.1242/jcs.154583] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcriptional activation of Notch signaling targets requires the formation of a ternary complex that involves the intracellular domain of the Notch receptor (NICD), DNA-binding protein Suppressor of Hairless [Su(H), RPBJ in mammals] and coactivator Mastermind (Mam). Here, we report that E(y)1/TAF9, a component of the transcription factor TFIID complex, interacts specifically with the NICD-Su(H)-Mam complex to facilitate the transcriptional output of Notch signaling. We identified E(y)1/TAF9 in a large-scale in vivo RNA interference (RNAi) screen for genes that are involved in a Notch-dependent mitotic-to-endocycle transition in Drosophila follicle cells. Knockdown of e(y)1/TAF9 displayed Notch-mutant-like phenotypes and defects in target gene and activity reporter expression in both the follicle cells and wing imaginal discs. Epistatic analyses in these two tissues indicated that E(y)1/TAF9 functions downstream of Notch cleavage. Biochemical studies in S2 cells demonstrated that E(y)1/TAF9 physically interacts with the transcriptional effectors of Notch signaling Su(H) and NICD. Taken together, our data suggest that the association of the NICD-Su(H)-Mastermind complex with E(y)1/TAF9 in response to Notch activation recruits the transcription initiation complex to induce Notch target genes, coupling Notch signaling with the transcription machinery.
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Affiliation(s)
- Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
| | - Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Datun Road 15, Beijing 100101, China
| | - Dongyu Jia
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
| | - Renjie Jiao
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
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15
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Moore JC, Sheppard-Tindell S, Shestopalov IA, Yamazoe S, Chen JK, Lawson ND. Post-transcriptional mechanisms contribute to Etv2 repression during vascular development. Dev Biol 2013; 384:128-40. [PMID: 24036310 DOI: 10.1016/j.ydbio.2013.08.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 08/05/2013] [Accepted: 08/30/2013] [Indexed: 01/08/2023]
Abstract
etv2 is an endothelial-specific ETS transcription factor that is essential for vascular differentiation and morphogenesis in vertebrates. While recent data suggest that Etv2 is dynamically regulated during vascular development, little is known about the mechanisms involved in this process. Here, we find that etv2 transcript and protein expression are highly dynamic during zebrafish vascular development, with both apparent during early somitogenesis and subsequently down-regulated as development proceeds. Inducible knockdown of Etv2 in zebrafish embryos prior to mid-somitogenesis stages, but not later, caused severe vascular defects, suggesting a specific role in early commitment of lateral mesoderm to the endothelial linage. Accordingly, Etv2-overexpressing cells showed an enhanced ability to commit to endothelial lineages in mosaic embryos. We further find that the etv2 3' untranslated region (UTR) is capable of repressing an endothelial autonomous transgene and contains binding sites for members of the let-7 family of microRNAs. Ectopic expression of let-7a could repress the etv2 3'UTR in sensor assays and was also able to block endogenous Etv2 protein expression, leading to concomitant reduction of endothelial genes. Finally, we observed that Etv2 protein levels persisted in maternal-zygotic dicer1 mutant embryos, suggesting that microRNAs contribute to its repression during vascular development. Taken together, our results suggest that etv2 acts during early development to specify endothelial lineages and is then down-regulated, in part through post-transcriptional repression by microRNAs, to allow normal vascular development.
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Affiliation(s)
- John C Moore
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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16
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Pistis G, Okonkwo SU, Traglia M, Sala C, Shin SY, Masciullo C, Buetti I, Massacane R, Mangino M, Thein SL, Spector TD, Ganesh S, Pirastu N, Gasparini P, Soranzo N, Camaschella C, Hart D, Green MR, Toniolo D. Genome wide association analysis of a founder population identified TAF3 as a gene for MCHC in humans. PLoS One 2013; 8:e69206. [PMID: 23935956 PMCID: PMC3729833 DOI: 10.1371/journal.pone.0069206] [Citation(s) in RCA: 9] [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: 02/21/2013] [Accepted: 06/06/2013] [Indexed: 11/18/2022] Open
Abstract
The red blood cell related traits are highly heritable but their genetics are poorly defined. Only 5-10% of the total observed variance is explained by the genetic loci found to date, suggesting that additional loci should be searched using approaches alternative to large meta analysis. GWAS (Genome Wide Association Study) for red blood cell traits in a founder population cohort from Northern Italy identified a new locus for mean corpuscular hemoglobin concentration (MCHC) in the TAF3 gene. The association was replicated in two cohorts (rs1887582, P = 4.25E-09). TAF3 encodes a transcription cofactor that participates in core promoter recognition complex, and is involved in zebrafish and mouse erythropoiesis. We show here that TAF3 is required for transcription of the SPTA1 gene, encoding alpha spectrin, one of the proteins that link the plasma membrane to the actin cytoskeleton. Mutations in SPTA1 are responsible for hereditary spherocytosis, a monogenic disorder of MCHC, as well as for the normal MCHC level. Based on our results, we propose that TAF3 is required for normal erythropoiesis in human and that it might have a role in controlling the ratio between hemoglobin (Hb) and cell volume and in the dynamics of RBC maturation in healthy individuals. Finally, TAF3 represents a potential candidate or a modifier gene for disorders of red cell membrane.
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Affiliation(s)
- Giorgio Pistis
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
| | - Shawntel U. Okonkwo
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Michela Traglia
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Corrado Masciullo
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
| | - Iwan Buetti
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
| | | | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Swee-Lay Thein
- Department of Molecular Hematology, King’s College London, London, United Kingdom
| | - Timothy D. Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Santhi Ganesh
- Division of Cardiovascular Medicine, University of Michigan Health System, Ann Arbor, Michigan, United States of America
| | - Nicola Pirastu
- Medical Genetics, Department of Reproductive Sciences and Development, University of Trieste, Trieste, Italy
| | - Paolo Gasparini
- Medical Genetics, Department of Reproductive Sciences and Development, University of Trieste, Trieste, Italy
- Medical Genetics, Department of Laboratory Medicine, Institute for Maternal and Child Health IRCCS-Burlo Garofolo, Trieste, Italy
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Clara Camaschella
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
| | - Daniel Hart
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Program in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michael R. Green
- Howard Hughes Medical Institute, Program in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milano, Italy
- Institute of Molecular Genetics-CNR, Pavia, Italy
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17
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Lauberth SM, Nakayama T, Wu X, Ferris AL, Tang Z, Hughes SH, Roeder RG. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 2013; 152:1021-36. [PMID: 23452851 DOI: 10.1016/j.cell.2013.01.052] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 07/31/2012] [Accepted: 01/28/2013] [Indexed: 10/27/2022]
Abstract
Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (1) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (2) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (3) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes.
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Affiliation(s)
- Shannon M Lauberth
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
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18
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Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R. Dual functions of TAF7L in adipocyte differentiation. eLife 2013; 2:e00170. [PMID: 23326641 PMCID: PMC3539393 DOI: 10.7554/elife.00170] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 11/09/2012] [Indexed: 12/22/2022] Open
Abstract
The diverse transcriptional mechanisms governing cellular differentiation and development of mammalian tissue remains poorly understood. Here we report that TAF7L, a paralogue of TFIID subunit TAF7, is enriched in adipocytes and white fat tissue (WAT) in mouse. Depletion of TAF7L reduced adipocyte-specific gene expression, compromised adipocyte differentiation, and WAT development as well. Ectopic expression of TAF7L in myoblasts reprograms these muscle precursors into adipocytes upon induction. Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters. In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ. These findings suggest that TAF7L plays an integral role in adipocyte gene expression by targeting enhancers as a cofactor for PPARγ and promoters as a component of the core transcriptional machinery.DOI:http://dx.doi.org/10.7554/eLife.00170.001.
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Affiliation(s)
- Haiying Zhou
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center For Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Tommy Kaplan
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yan Li
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Ivan Grubisic
- Li Ka Shing Center For Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- UC Berkeley-UCSF Graduate Program in Bioengineering, Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Zhengjian Zhang
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - P Jeremy Wang
- Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, United States
| | - Michael B Eisen
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center For Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
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19
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Das S, Levasseur D. Transcriptional regulatory mechanisms that govern embryonic stem cell fate. Methods Mol Biol 2013; 1029:191-203. [PMID: 23756950 DOI: 10.1007/978-1-62703-478-4_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Embryonic stem cells (ESCs) are defined by their simultaneous capacity for limitless self-renewal and the ability to specify cells borne of all germ layers. The regulation of ESC pluripotency is governed by a set of core transcription factors that regulate transcription by interfacing with nuclear proteins that include the RNA polymerase II core transcriptional machinery, histone modification enzymes, and chromatin remodeling protein complexes. The growing adoption of systems biological approaches used in stem cell biology over last few years has contributed significantly to our understanding of pluripotency. Multilayered approaches coupling transcriptome profiling and proteomics (Nanog-, Oct4-, and Sox2-centered protein interaction networks or "interactomes") with transcription factor chromatin occupancy and epigenetic footprint measurements have enabled a more comprehensive understanding of ESC pluripotency and self-renewal. Together with the genetic and biochemical characterization of promising pluripotency modifying proteins, these systems biological approaches will continue to clarify the molecular underpinnings of the ESC state. This will most certainly contribute to the improvement of current methodologies for the derivation of pluripotent cells from adult tissues.
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Affiliation(s)
- Satyabrata Das
- Division of Immunology, University of Iowa, Iowa City, IA, USA
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20
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Liu Z, Scannell DR, Eisen MB, Tjian R. Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell 2011; 146:720-31. [PMID: 21884934 PMCID: PMC3191068 DOI: 10.1016/j.cell.2011.08.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 06/06/2011] [Accepted: 08/03/2011] [Indexed: 11/26/2022]
Abstract
Deciphering the molecular basis of pluripotency is fundamental to our understanding of development and embryonic stem cell function. Here, we report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells. In this context, TAF3 is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. In addition to its role in the core promoter recognition complex TFIID, genome-wide binding studies reveal that TAF3 localizes to a subset of chromosomal regions bound by CTCF/cohesin that are selectively associated with genes upregulated by TAF3. Notably, CTCF directly recruits TAF3 to promoter distal sites and TAF3-dependent DNA looping is observed between the promoter distal sites and core promoters occupied by TAF3/CTCF/cohesin. Together, our findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions that safeguard the finely-balanced transcriptional programs underlying pluripotency.
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Affiliation(s)
- Zhe Liu
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Devin R. Scannell
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael B. Eisen
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, CA 94720, USA
- LKS Bio-medical and Health Sciences Center, CIRM Center of Excellence, University of California, Berkeley, Berkeley, California 94720, USA
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21
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Akhtar W, Veenstra GJC. TBP-related factors: a paradigm of diversity in transcription initiation. Cell Biosci 2011; 1:23. [PMID: 21711503 PMCID: PMC3142196 DOI: 10.1186/2045-3701-1-23] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/27/2011] [Indexed: 01/24/2023] Open
Abstract
TATA binding protein (TBP) is a key component of the eukaryotic transcription initiation machinery. It functions in several complexes involved in core promoter recognition and assembly of the pre-initiation complex. Through gene duplication eukaryotes have expanded their repertoire of TATA binding proteins, leading to a variable composition of the transcription machinery. In vertebrates this repertoire consists of TBP, TBP-like factor (TLF, also known as TBPL1, TRF2) and TBP2 (also known as TBPL2, TRF3). All three factors are essential, with TLF and TBP2 playing important roles in development and differentiation, in particular gametogenesis and early embryonic development, whereas TBP dominates somatic cell transcription. TBP-related factors may compete for promoters when co-expressed, but also show preferential interactions with subsets of promoters. Initiation factor switching occurs on account of differential expression of these proteins in gametes, embryos and somatic cells. Paralogs of TFIIA and TAF subunits account for additional variation in the transcription initiation complex. This variation in core promoter recognition accommodates the expanded regulatory capacity and specificity required for germ cells and embryonic development in higher eukaryotes.
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Affiliation(s)
- Waseem Akhtar
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.
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22
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Core promoter recognition complex changes accompany liver development. Proc Natl Acad Sci U S A 2011; 108:3906-11. [PMID: 21368148 DOI: 10.1073/pnas.1100640108] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Recent studies of several key developmental transitions have brought into question the long held view of the basal transcriptional apparatus as ubiquitous and invariant. In an effort to better understand the role of core promoter recognition and coactivator complex switching in cellular differentiation, we have examined changes in transcription factor IID (TFIID) and cofactor required for Sp1 activation/Mediator during mouse liver development. Here we show that the differentiation of fetal liver progenitors to adult hepatocytes involves a wholesale depletion of canonical cofactor required for Sp1 activation/Mediator and TFIID complexes at both the RNA and protein level, and that this alteration likely involves silencing of transcription factor promoters as well as protein degradation. It will be intriguing for future studies to determine if a novel and as yet unknown core promoter recognition complex takes the place of TFIID in adult hepatocytes and to uncover the mechanisms that down-regulate TFIID during this critical developmental transition.
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23
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Clinical findings associated with a de novo partial trisomy 10p11.22p15.3 and monosomy 7p22.3 detected by chromosomal microarray analysis. Case Rep Genet 2011; 2011:131768. [PMID: 23074670 PMCID: PMC3447257 DOI: 10.1155/2011/131768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 09/15/2011] [Indexed: 11/18/2022] Open
Abstract
We present the case of an 18-month-old boy with dysmorphic facial features, developmental delay, growth retardation, bilateral clubfeet, thrombocytopenia, and strabismus, whose array CGH analysis revealed concurrent de novo trisomy 10p11.22p15.3 and monosomy 7p22.3. We describe the patient's clinical presentation, along with his cytogenetic analysis, and we compare the findings to those of similar case reports in the literature. We also perform a bioinformatic analysis in the chromosomal regions of segmental aneuploidy to find genes that could potentially explain the patient's phenotype.
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24
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Goodrich JA, Tjian R. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat Rev Genet 2010; 11:549-58. [PMID: 20628347 DOI: 10.1038/nrg2847] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The eukaryotic core promoter recognition complex was generally thought to play an essential but passive role in the regulation of gene expression. However, recent evidence now indicates that core promoter recognition complexes together with 'non-prototypical' subunits may have a vital regulatory function in driving cell-specific programmes of transcription during development. Furthermore, new roles for components of these complexes have been identified beyond development; for example, in mediating interactions with chromatin and in maintaining active gene expression across cell divisions.
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Affiliation(s)
- James A Goodrich
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Colorado 80309, USA
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25
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Müller F, Zaucker A, Tora L. Developmental regulation of transcription initiation: more than just changing the actors. Curr Opin Genet Dev 2010; 20:533-40. [PMID: 20598874 DOI: 10.1016/j.gde.2010.06.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 05/26/2010] [Accepted: 06/02/2010] [Indexed: 11/29/2022]
Abstract
The traditional model of transcription initiation nucleated by the TFIID complex has suffered significant erosion in the last decade. The discovery of cell-specific paralogs of TFIID subunits and a variety of complexes that replace TFIID in transcription initiation of protein coding genes have been paralleled by the description of diverse core promoter sequences. These observations suggest an additional level of regulation of developmental and tissue-specific gene expression at the core promoter level. Recent work suggests that this regulation may function through specific roles of distinct TBP-type factors and TBP-associated factors (TAFs), however the picture emerging is still far from complete. Here we summarize the proposed models of transcription initiation by alternative initiation complexes in distinct stages of developmental specialization during vertebrate ontogeny.
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Affiliation(s)
- Ferenc Müller
- Department of Medical and Molecular Genetics, Division of Reproductive and Child Health, Institute of Biomedical Research, University of Birmingham, B15 2TT Edgbaston, Birmingham, UK
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D'Alessio JA, Wright KJ, Tjian R. Shifting players and paradigms in cell-specific transcription. Mol Cell 2009; 36:924-31. [PMID: 20064459 PMCID: PMC2807468 DOI: 10.1016/j.molcel.2009.12.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 12/08/2009] [Indexed: 01/28/2023]
Abstract
Historically, developmental-stage- and tissue-specific patterns of gene expression were assumed to be determined primarily by DNA regulatory sequences and their associated activators, while the general transcription machinery including core promoter recognition complexes, coactivators, and chromatin modifiers was held to be invariant. New evidence suggests that significant changes in these general transcription factors including TFIID, BAF, and Mediator may facilitate global changes in cell-type-specific transcription.
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Affiliation(s)
- Joseph A D'Alessio
- Howard Hughes Medical Institute, University of California, Berkeley, 94720, USA
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