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Kumari S, Rehman A, Chandra P, Singh KK. Functional role of SAP18 protein: From transcriptional repression to splicing regulation. Cell Biochem Funct 2023; 41:738-751. [PMID: 37486712 DOI: 10.1002/cbf.3830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/18/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Sin3 associated protein 18 (SAP18) is an evolutionary conserved protein, originally discovered in a complex with the transcriptional regulatory protein, Sin3. Subsequent investigations revealed SAP18 as an integral splicing component of the exon junction complex (EJC)-associated apoptosis-and splicing-associated protein (ASAP)/PNN-RNPS1-SAP18 (PSAP) complex. In association with Sin3, SAP18 contributes toward transcriptional repression of genes implicated in embryonic development, stress response, human immunodeficiency virus type 1 replication, and tumorigenesis. As a part of EJC, SAP18 mediates alternative splicing events and suppresses the cryptic splice sites present within flanking regions of exon-exon junctions. In this review, we provide a thorough discussion on SAP18, focussing on its conserved dual role in transcriptional regulation and messenger RNA splicing. Recent research on the involvement of SAP18 in the emergence of cancer and human disorders has also been highlighted. The potential of SAP18 as a therapeutic target is also discussed in these recent studies, particularly related to malignancies of the myeloid lineage.
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Affiliation(s)
- Sweta Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Ayushi Rehman
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Pratap Chandra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Kusum K Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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2
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Park J, Estrada J, Johnson G, Vincent BJ, Ricci-Tam C, Bragdon MDJ, Shulgina Y, Cha A, Wunderlich Z, Gunawardena J, DePace AH. Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity. eLife 2019; 8:e41266. [PMID: 31223115 PMCID: PMC6588347 DOI: 10.7554/elife.41266] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/04/2019] [Indexed: 12/19/2022] Open
Abstract
Developmental enhancers integrate graded concentrations of transcription factors (TFs) to create sharp gene expression boundaries. Here we examine the hunchback P2 (HbP2) enhancer which drives a sharp expression pattern in the Drosophila blastoderm embryo in response to the transcriptional activator Bicoid (Bcd). We systematically interrogate cis and trans factors that influence the shape and position of expression driven by HbP2, and find that the prevailing model, based on pairwise cooperative binding of Bcd to HbP2 is not adequate. We demonstrate that other proteins, such as pioneer factors, Mediator and histone modifiers influence the shape and position of the HbP2 expression pattern. Comparing our results to theory reveals how higher-order cooperativity and energy expenditure impact boundary location and sharpness. Our results emphasize that the bacterial view of transcription regulation, where pairwise interactions between regulatory proteins dominate, must be reexamined in animals, where multiple molecular mechanisms collaborate to shape the gene regulatory function.
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Affiliation(s)
- Jeehae Park
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Javier Estrada
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Gemma Johnson
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Ben J Vincent
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Chiara Ricci-Tam
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Meghan DJ Bragdon
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | | | - Anna Cha
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | - Zeba Wunderlich
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
| | | | - Angela H DePace
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
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3
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Baumgartner S. Seeing is believing: the Bicoid protein reveals its path. Hereditas 2018; 155:28. [PMID: 30220899 PMCID: PMC6134762 DOI: 10.1186/s41065-018-0067-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 11/30/2022] Open
Abstract
In this commentary, I will review the latest findings on the Bicoid (Bcd) morphogen in Drosophila, a paradigm for gradient formation taught to biology students for more than two decades. “Seeing is believing” also summarizes the erroneous steps that were needed to elucidate the mechanisms of gradient formation and the path of movement of Bcd. Initially proclaimed as a dogma in 1988 and later incorporated into the SDD model where the broad diffusion of Bcd throughout the embryo was the predominant step leading to gradient formation, the SDD model was irrefutable for more than two decades until first doubts were raised in 2007 regarding the diffusion properties of Bcd associated with the SDD model. This led to re-thinking of the issue and the definition of a new model, termed the ARTS model which could explain most of the physical constraints that were inherently associated with the SDD model. In the ARTS model, gradient formation is mediated by the mRNA which is redistributed along cortical microtubules to form a mRNA gradient which is translated to form the protein gradient. Contrary to the SDD model, there is no Bcd diffusion from the tip. The ARTS model is also compatible with the observed cortical movement of Bcd. I will critically compare the SDD and the ARTS models as well as other models, analyze the major differences, and highlight the path where Bcd is localized during early nuclear cycles.
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Affiliation(s)
- Stefan Baumgartner
- Department of Experimental Medical Sciences, Lund University, BMC D10, S-22184 Lund, Sweden
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4
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Information Integration and Energy Expenditure in Gene Regulation. Cell 2017; 166:234-44. [PMID: 27368104 DOI: 10.1016/j.cell.2016.06.012] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 03/08/2016] [Accepted: 06/01/2016] [Indexed: 11/22/2022]
Abstract
The quantitative concepts used to reason about gene regulation largely derive from bacterial studies. We show that this bacterial paradigm cannot explain the sharp expression of a canonical developmental gene in response to a regulating transcription factor (TF). In the absence of energy expenditure, with regulatory DNA at thermodynamic equilibrium, information integration across multiple TF binding sites can generate the required sharpness, but with strong constraints on the resultant "higher-order cooperativities." Even with such integration, there is a "Hopfield barrier" to sharpness; for n TF binding sites, this barrier is represented by the Hill function with the Hill coefficient n. If, however, energy is expended to maintain regulatory DNA away from thermodynamic equilibrium, as in kinetic proofreading, this barrier can be breached and greater sharpness achieved. Our approach is grounded in fundamental physics, leads to testable experimental predictions, and suggests how a quantitative paradigm for eukaryotic gene regulation can be formulated.
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5
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Mannervik M. Control of Drosophila embryo patterning by transcriptional co-regulators. Exp Cell Res 2013; 321:47-57. [PMID: 24157250 DOI: 10.1016/j.yexcr.2013.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
A combination of broadly expressed transcriptional activators and spatially restricted repressors are used to pattern embryos into cells of different fate. Transcriptional co-regulators are essential mediators of transcription factor function, and contribute to selective transcriptional responses in embryo development. A two step mechanism of transcriptional regulation is discussed, where remodeling of chromatin is initially required, followed by stimulation of recruitment or release of RNA polymerase from the promoter. Transcriptional co-regulators are essential for both of these steps. In particular, most co-activators are associated with histone acetylation and co-repressors with histone deacetylation. In the early Drosophila embryo, genome-wide studies have shown that the CBP co-activator has a preference for associating with some transcription factors and regulatory regions. The Groucho, CtBP, Ebi, Atrophin and Brakeless co-repressors are selectively used to limit zygotic gene expression. New findings are summarized which show that different co-repressors are often utilized by a single repressor, that the context in which a co-repressor is recruited to DNA can affect its activity, and that co-regulators may switch from co-repressors to co-activators and vice versa. The possibility that co-regulator activity is regulated and plays an instructive role in development is discussed as well. This review highlights how findings in Drosophila embryos have contributed to the understanding of transcriptional regulation in eukaryotes as well as to mechanisms of animal embryo patterning.
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Affiliation(s)
- Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Arrheniuslaboratories E3, SE-106 91 Stockholm, Sweden.
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6
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Kadamb R, Mittal S, Bansal N, Batra H, Saluja D. Sin3: insight into its transcription regulatory functions. Eur J Cell Biol 2013; 92:237-46. [PMID: 24189169 DOI: 10.1016/j.ejcb.2013.09.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022] Open
Abstract
Sin3, a large acidic protein, shares structural similarity with the helix-loop-helix dimerization domain of proteins of the Myc family of transcription factors. Sin3/HDAC corepressor complex functions in transcriptional regulation of several genes and is therefore implicated in the regulation of key biological processes. Knockdown studies have confirmed the role of Sin3 in cellular proliferation, differentiation, apoptosis and cell cycle regulation, emphasizing Sin3 as an essential regulator of critical cellular events in normal and pathological processes. The present review covers the diverse functions of this master transcriptional regulator as well as illustrates the redundant and distinct functions of its two mammalian isoforms.
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Affiliation(s)
- Rama Kadamb
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
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7
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Ilsley GR, Fisher J, Apweiler R, DePace AH, Luscombe NM. Cellular resolution models for even skipped regulation in the entire Drosophila embryo. eLife 2013; 2:e00522. [PMID: 23930223 PMCID: PMC3736529 DOI: 10.7554/elife.00522] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 06/17/2013] [Indexed: 12/14/2022] Open
Abstract
Transcriptional control ensures genes are expressed in the right amounts at the correct times and locations. Understanding quantitatively how regulatory systems convert input signals to appropriate outputs remains a challenge. For the first time, we successfully model even skipped (eve) stripes 2 and 3+7 across the entire fly embryo at cellular resolution. A straightforward statistical relationship explains how transcription factor (TF) concentrations define eve's complex spatial expression, without the need for pairwise interactions or cross-regulatory dynamics. Simulating thousands of TF combinations, we recover known regulators and suggest new candidates. Finally, we accurately predict the intricate effects of perturbations including TF mutations and misexpression. Our approach imposes minimal assumptions about regulatory function; instead we infer underlying mechanisms from models that best fit the data, like the lack of TF-specific thresholds and the positional value of homotypic interactions. Our study provides a general and quantitative method for elucidating the regulation of diverse biological systems. DOI:http://dx.doi.org/10.7554/eLife.00522.001.
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Affiliation(s)
- Garth R Ilsley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jasmin Fisher
- Microsoft Research Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | - Nicholas M Luscombe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- UCL Genetics Institute, Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
- London Research Institute, Cancer Research UK, London, United Kingdom
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8
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Singh N, Morlock H, Hanes SD. The Bin3 RNA methyltransferase is required for repression of caudal translation in the Drosophila embryo. Dev Biol 2011; 352:104-15. [DOI: 10.1016/j.ydbio.2011.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Revised: 01/06/2011] [Accepted: 01/14/2011] [Indexed: 10/18/2022]
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9
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Spain MM, Caruso JA, Swaminathan A, Pile LA. Drosophila SIN3 isoforms interact with distinct proteins and have unique biological functions. J Biol Chem 2010; 285:27457-27467. [PMID: 20566628 DOI: 10.1074/jbc.m110.130245] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The SIN3 corepressor serves as a scaffold for the assembly of histone deacetylase (HDAC) complexes. SIN3 and its associated HDAC have been shown to have critical roles in both development and the regulation of cell cycle progression. Although multiple SIN3 isoforms have been reported in simple to complex eukaryotic organisms, the mechanisms by which such isoforms regulate specific biological processes are still largely uncharacterized. To gain insight into how SIN3 isoform-specific function contributes to the growth and development of a metazoan organism, we have affinity-purified two SIN3 isoform-specific complexes, SIN3 187 and 220, from Drosophila S2 cells and embryos. We have identified a number of proteins common to the complexes, including the HDAC RPD3, as well as orthologs of several proteins known to have roles in regulating cell proliferation in other organisms. We additionally identified factors, including the histone demethylase little imaginal discs and histone-interacting protein p55, that exhibited a preferential interaction with the largest SIN3 isoform. Our experiments indicate that the isoforms are associated with distinct HDAC activity and are recruited to unique and shared sites along polytene chromosome arms. Furthermore, although expression of SIN3 220 can substitute for genetic loss of other isoforms, expression of SIN3 187 does not support Drosophila viability. Together our findings suggest that SIN3 isoforms serve distinct roles in transcriptional regulation by partnering with different histone-modifying enzymes.
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Affiliation(s)
- Marla M Spain
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan 48202
| | | | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202.
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10
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Grzenda A, Lomberk G, Zhang JS, Urrutia R. Sin3: master scaffold and transcriptional corepressor. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:443-50. [PMID: 19505602 DOI: 10.1016/j.bbagrm.2009.05.007] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 05/21/2009] [Accepted: 05/26/2009] [Indexed: 11/17/2022]
Abstract
Sin3 was isolated over two decades ago as a negative regulator of transcription in budding yeast. Subsequent research has established the protein as a master transcriptional scaffold and corepressor capable of transcriptional silencing via associated histone deacetylases (HDACs). The core Sin3-HDAC complex interacts with a wide variety of repressors and corepressors, providing flexibility and expanded specificity in modulating chromatin structure and transcription. As a result, the Sin3/HDAC complex is involved in an array of biological and cellular processes, including cell cycle progression, genomic stability, embryonic development, and homeostasis. Abnormal recruitment of this complex or alteration of its enzymatic activity has been implicated in neoplastic transformation.
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Affiliation(s)
- Adrienne Grzenda
- Department of Biochemistry, Mayo Clinic, Rochester, MN 55905, USA
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11
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Cunliffe VT. Eloquent silence: developmental functions of Class I histone deacetylases. Curr Opin Genet Dev 2008; 18:404-10. [PMID: 18929655 PMCID: PMC2671034 DOI: 10.1016/j.gde.2008.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 09/16/2008] [Accepted: 10/02/2008] [Indexed: 11/10/2022]
Abstract
Histone deacetylases (HDACs) are essential catalytic components of the transcription silencing machinery and they play important roles in the programming of multicellular development. HDACs are present within multisubunit protein complexes, other components of which govern HDAC target gene specificity by controlling interactions with sequence-specific DNA-binding proteins. Here, I review the different developmental roles of the Sin3, NuRD, CoREST and NCoR/SMRT Class I HDAC complexes. With their distinct subunit composition, these versatile molecular devices function in many different settings, to promote axis specification and tissue patterning, to maintain stem cell pluripotency, facilitate self-renewal, guide lineage commitment and drive cell differentiation.
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Affiliation(s)
- Vincent T Cunliffe
- MRC Centre for Developmental and Biomedical Genetics and Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom.
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12
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Hill K, Wang H, Perry SE. A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2008; 53:172-85. [PMID: 17999645 DOI: 10.1111/j.1365-313x.2007.03336.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
AGAMOUS-like 15 (AGL15) encodes a MADS-domain transcription factor that is preferentially expressed in the plant embryo. A number of direct downstream targets of AGL15 have been identified, and although some of these target genes are induced in response to AGL15, others are repressed. Additionally, direct target genes have been analyzed that exhibit strong association with AGL15 in vivo, yet in vitro AGL15 binds only weakly. These data suggest that AGL15 may form complexes with other proteins, thus modulating the specificity and function of AGL15 in planta. Here we report that AGL15 interacts with members of the SWI-independent 3/histone deacetylase (SIN3/HDAC) complex, and that AGL15 target genes are also responsive to an AGL15 interacting protein that is also a member of this complex, SIN3-associated polypeptide of 18 kDa (SAP18). AGL15 can repress transcription in vivo, and a region essential to this repressive function contains a motif that is conserved among putative orthologs of AGL15. This motif mediates the association of AGL15 with SAP18, thus providing a possible mechanism for the role of AGL15 in regulating gene expression via recruitment of an HDAC complex.
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Affiliation(s)
- Kristine Hill
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA
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13
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Costa E, Canudas S, Garcia-Bassets I, Pérez S, Fernández I, Giralt E, Azorín F, Espinás ML. Drosophila dSAP18 is a nuclear protein that associates with chromosomes and the nuclear matrix, and interacts with pinin, a protein factor involved in RNA splicing. Chromosome Res 2006; 14:515-26. [PMID: 16823614 DOI: 10.1007/s10577-006-1046-5] [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] [Received: 01/20/2006] [Revised: 02/17/2006] [Accepted: 02/17/2006] [Indexed: 11/30/2022]
Abstract
SAP18 is a highly conserved protein that was proposed to be involved in multiple cellular processes from autophagy to gene regulation and mRNA processing. In this paper we show that, in Drosophila, dSAP18 is a predominantly nuclear protein that associates to both chromosomes and the nuclear matrix. dSAP18 becomes nuclear early during development, at the onset of cellularization, and remains so all through embryo development. dSAP18 is also nuclear in salivary glands, ovaries and cultured S2 cells. Here we also show that dSAP18 forms a complex with the Drosophila homolog of pinin (dPnn), a protein factor involved in mRNA splicing. dSAP18-dPnn interaction was confirmed in vivo, through co-immunoprecipitation experiments, as well as in vitro, through GST pull-down assays. These results are discussed in the context of the possible functions played by SAP18.
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Affiliation(s)
- Elisabet Costa
- Departament de Biologia Molecular i Cellular, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Josep Samitier 1-5, 08028, Barcelona, Spain
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14
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Stepanyan R, Day K, Urban J, Hardin DL, Shetty RS, Derby CD, Ache BW, McClintock TS. Gene expression and specificity in the mature zone of the lobster olfactory organ. Physiol Genomics 2006; 25:224-33. [PMID: 16614458 DOI: 10.1152/physiolgenomics.00276.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The lobster olfactory organ is an important model for investigating many aspects of the olfactory system. To facilitate study of the molecular basis of olfaction in lobsters, we made a subtracted cDNA library from the mature zone of the olfactory organ of Homarus americanus, the American lobster. Sequencing of the 5′-end of 5,184 cDNA clones produced 2,389 distinct high-quality sequences consisting of 1,944 singlets and 445 contigs. Matches to known sequences corresponded with the types of cells present in the olfactory organ, including specific markers of olfactory sensory neurons, auxiliary cells, secretory cells of the aesthetasc tegumental gland, and epithelial cells. The wealth of neuronal mRNAs represented among the sequences reflected the preponderance of neurons in the tissue. The sequences identified candidate genes responsible for known functions and suggested new functions not previously recognized in the olfactory organ. A cDNA microarray was designed and tested by assessing mRNA abundance differences between two of the lobster's major chemosensory structures: the mature zone of the olfactory organ and the dactyl of the walking legs, a taste organ. The 115 differences detected again emphasized the abundance of neurons in the olfactory organ, especially a cluster of mRNAs encoding cytoskeletal-associated proteins and cell adhesion molecules such as 14-3-3ζ, actins, tubulins, trophinin, Fax, Yel077cp, suppressor of profilin 2, and gelsolin.
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Affiliation(s)
- Ruben Stepanyan
- Department of Physiology, Cellular and Molecular Neuroscience of Sensory Systems Training Program, University of Kentucky, Lexington, Kentucky 40536-0298, USA
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15
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Struffi P, Arnosti DN. Functional interaction between the Drosophila knirps short range transcriptional repressor and RPD3 histone deacetylase. J Biol Chem 2005; 280:40757-65. [PMID: 16186109 PMCID: PMC1802102 DOI: 10.1074/jbc.m506819200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Knirps and other short range transcriptional repressors play critical roles in patterning the early Drosophila embryo. These repressors are known to bind the C-terminal binding protein corepressor, but their mechanism of action is poorly understood. We purified functional recombinant Knirps protein from transgenic embryos to identify possible cofactors that contribute to the activity of this protein. The protein migrates in a complex of approximately 450 kDa and was found to copurify with the Rpd3 histone deacetylase protein during a double affinity purification procedure. Association of Rpd3 with Knirps was dependent on the presence of the C-terminal binding protein-dependent repression domain of Knirps. Previous studies of an rpd3 mutant had not shown defects in the pattern of expression of even-skipped, a target of the Knirps repressor. However, in embryos doubly heterozygous for knirps and rpd3, a marked increase in the frequency of defects in the Knirps-regulated posterior domain of even-skipped expression was found, indicating that Rpd3 contributes to Knirps repression activity in vivo. This finding implicates deacetylation in the mechanism of short range repression in Drosophila.
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Affiliation(s)
- Paolo Struffi
- Department of Biochemistry and Molecular Biology and Program in Genetics, Michigan State University, East Lansing, Michigan 48824, USA
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16
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Lebrecht D, Foehr M, Smith E, Lopes FJP, Vanario-Alonso CE, Reinitz J, Burz DS, Hanes SD. Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. Proc Natl Acad Sci U S A 2005; 102:13176-81. [PMID: 16150708 PMCID: PMC1201621 DOI: 10.1073/pnas.0506462102] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Indexed: 11/18/2022] Open
Abstract
Cooperative interactions by DNA-binding proteins have been implicated in cell-fate decisions in a variety of organisms. To date, however, there are few examples in which the importance of such interactions has been explicitly tested in vivo. Here, we tested the importance of cooperative DNA binding by the Bicoid protein in establishing a pattern along the anterior-posterior axis of the early Drosophila embryo. We found that bicoid mutants specifically defective in cooperative DNA binding fail to direct proper development of the head and thorax, leading to embryonic lethality. The mutants did not faithfully stimulate transcription of downstream target genes such as hunchback (hb), giant, and Krüppel. Quantitative analysis of gene expression in vivo indicated that bcd cooperativity mutants were unable to accurately direct the extent to which hb is expressed along the anterior-posterior axis and displayed a reduced ability to generate sharp on/off transitions for hb gene expression. These failures in precise transcriptional control demonstrate the importance of cooperative DNA binding for embryonic patterning in vivo.
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Affiliation(s)
- Danielle Lebrecht
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, USA
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17
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Shetty RS, Bose SC, Nickell MD, McIntyre JC, Hardin DH, Harris AM, McClintock TS. Transcriptional changes during neuronal death and replacement in the olfactory epithelium. Mol Cell Neurosci 2005; 30:90-107. [PMID: 16027002 DOI: 10.1016/j.mcn.2005.06.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 06/10/2005] [Accepted: 06/13/2005] [Indexed: 11/30/2022] Open
Abstract
The olfactory epithelium has the unusual ability to replace its neurons. We forced replacement of mouse olfactory sensory neurons by bulbectomy. Microarray, bioinformatics, and in situ hybridization techniques detected a rapid shift in favor of pro-apoptotic proteins, a progressive immune response by macrophages and dendritic cells, and identified or predicted 439 mRNAs enriched in olfactory sensory neurons, including gene silencing factors and sperm flagellar proteins. Transcripts encoding cell cycle regulators, axonogenesis proteins, and transcription factors and signaling proteins that promote proliferation and differentiation were increased at 5--7 days after bulbectomy and were expressed by basal progenitor cells or immature neurons. The transcription factors included Nhlh 1, Hes 6, Lmyc 1, c-Myc, Mxd 4, Id 1, Nmyc 1, Cited 2, c-Myb, Mybl 1, Tead 2, Dp 1, Gata 2, Lmo 1, and Sox1 1. The data reveal significant similarities with embryonic neurogenesis and make several mechanistic predictions, including the roles of the transcription factors in the olfactory sensory neuron lineage.
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Affiliation(s)
- Ranjit S Shetty
- Department of Physiology, Cellular and Molecular Neuroscience of Sensory Systems Training Program, University of Kentucky, 800 Rose Street, Lexington, KY 40536-0298, USA
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Canudas S, Pérez S, Fanti L, Pimpinelli S, Singh N, Hanes SD, Azorín F, Espinás ML. dSAP18 and dHDAC1 contribute to the functional regulation of the Drosophila Fab-7 element. Nucleic Acids Res 2005; 33:4857-64. [PMID: 16135462 PMCID: PMC1196206 DOI: 10.1093/nar/gki776] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
It was described earlier that the Drosophila GAGA factor [Trithorax-like (Trl)] interacts with dSAP18, which, in mammals, was reported to be a component of the Sin3–HDAC co-repressor complex. GAGA–dSAP18 interaction was proposed to contribute to the functional regulation of the bithorax complex (BX-C). Here, we show that mutant alleles of Trl, dsap18 and drpd3/hdac1 enhance A6-to-A5 transformation indicating a contribution to the regulation of Abd-B expression at A6. In A6, expression of Abd-B is driven by the iab-6 enhancer, which is insulated from iab-7 by the Fab-7 element. Here, we report that GAGA, dSAP18 and dRPD3/HDAC1 co-localize to ectopic Fab-7 sites in polytene chromosomes and that mutant Trl, dsap18 and drpd3/hdac1 alleles affect Fab-7-dependent silencing. Consistent with these findings, chromatin immunoprecipitation analysis shows that, in Drosophila embryos, the endogenous Fab-7 element is hypoacetylated at histones H3 and H4. These results indicate a contribution of GAGA, dSAP18 and dRPD3/HDAC1 to the regulation of Fab-7 function.
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Affiliation(s)
| | | | - Laura Fanti
- Dipartimento di Genetica e Biologia Molecolare, Università ‘La Sapienza’00185 Rome, Italy
| | - Sergio Pimpinelli
- Dipartimento di Genetica e Biologia Molecolare, Università ‘La Sapienza’00185 Rome, Italy
| | - Navjot Singh
- New York State Department of Health, Wadsworth Center, State University of New YorkAlbany, NY 12208, USA
| | - Steven D. Hanes
- New York State Department of Health, Wadsworth Center, State University of New YorkAlbany, NY 12208, USA
| | - Fernando Azorín
- To whom correspondence should be addressed. Tel: +34 93 4034958; Fax: +34 93 4034979;
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Fu D, Ma J. Interplay between positive and negative activities that influence the role of Bicoid in transcription. Nucleic Acids Res 2005; 33:3985-93. [PMID: 16030350 PMCID: PMC1178001 DOI: 10.1093/nar/gki691] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/20/2005] [Accepted: 06/16/2005] [Indexed: 11/13/2022] Open
Abstract
The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57-61), which has a strengthened self-inhibitory function and is unable to activate the hb-CAT reporter in Drosophila cells, to analyze the role of co-factors in regulating Bcd function. We show that increased concentrations of the co-activator dCBP in cells can switch this protein from its inactive state to an active state on the hb-CAT reporter. The C-terminal portion of Bcd(A57-61) is required to mediate such activity-rescuing function of dCBP. Although capable of binding to DNA in vitro, Bcd(A57-61) is unable to access the hb enhancer element in cells, suggesting that its DNA binding defect is only manifested in a cellular context. Increased concentrations of dCBP restore not only the ability of Bcd(A57-61) to access the hb enhancer element in cells but also the occupancy of the general transcription factors TBP and TFIIB at the reporter promoter. These and other results suggest that an activator can undergo switches between its active and inactive states through sensing the opposing actions of positive and negative co-factors.
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Affiliation(s)
- Dechen Fu
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Jun Ma
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine3333 Burnet Avenue Cincinnati, OH 45229, USA
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