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Kushwaha A, Thakur MK. Suv39h1 Silencing Recovers Memory Decline in Scopolamine-Induced Amnesic Mouse Model. Mol Neurobiol 2024; 61:487-497. [PMID: 37626270 DOI: 10.1007/s12035-023-03570-x] [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: 03/12/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023]
Abstract
Histone post-translational modifications play an important role in the regulation of long-term memory and modulation of expression of neuronal immediate early genes (IEGs). The lysine methyltransferase KMT1A/ Suv39h1 (a mammalian ortholog of the Drosophila melanogaster SU (VAR) 3-9) aids in the methylation of histone H3 at lysine 9. We previously reported that age-related memory decline is associated with an increase in Suv39h1 expression in the hippocampus of male mice. The scopolamine-induced amnesic mouse model is a well-known animal model of memory impairment. In the current study, we have made an attempt to find a link between the changes in the H3K9 trimethylation pattern and memory decline during scopolamine-induced amnesia. It was followed by checking the effect of siRNA-mediated silencing of hippocampal Suv39h1 on memory and expression of neuronal IEGs. Scopolamine treatment significantly increased global levels of H3K9me3 and Suv39h1 in the amnesic hippocampus. Suv39h1 silencing in amnesic mice reduced H3K9me3 levels at the neuronal IEGs (Arc and BDNF) promoter, increased the expression of Arc and BDNF in the hippocampus, and improved recognition memory. Thus, these findings suggest that the silencing of Suv39h1 alone or in combination with other epigenetic drugs might be effective for treating memory decline during amnesia.
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Affiliation(s)
- Akanksha Kushwaha
- Biochemistry and Molecular Biology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, 221 005, India
- K N Govt. P G College, Gyanpur, Sant Ravidas Nagar, 221304, India
| | - Mahendra Kumar Thakur
- Biochemistry and Molecular Biology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, 221 005, India.
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2
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Robert VJ, Caron M, Gely L, Adrait A, Pakulska V, Couté Y, Chevalier M, Riedel CG, Bedet C, Palladino F. SIN-3 acts in distinct complexes to regulate the germline transcriptional program in Caenorhabditis elegans. Development 2023; 150:dev201755. [PMID: 38771303 PMCID: PMC10617626 DOI: 10.1242/dev.201755] [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: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
The transcriptional co-regulator SIN3 influences gene expression through multiple interactions that include histone deacetylases. Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability and autism syndromes, emphasizing its key role in development. However, little is known about the diversity of its interactions and functions in developmental processes. Here, we show that loss of SIN-3, the single SIN3 homolog in Caenorhabditis elegans, results in maternal-effect sterility associated with de-regulation of the germline transcriptome, including de-silencing of X-linked genes. We identify at least two distinct SIN3 complexes containing specific histone deacetylases and show that they differentially contribute to fertility. Single-cell, single-molecule fluorescence in situ hybridization reveals that in sin-3 mutants the X chromosome becomes re-expressed prematurely and in a stochastic manner in individual germ cells, suggesting a role for SIN-3 in its silencing. Furthermore, we identify histone residues whose acetylation increases in the absence of SIN-3. Together, this work provides a powerful framework for the in vivo study of SIN3 and associated proteins.
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Affiliation(s)
- Valerie J. Robert
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Matthieu Caron
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Loic Gely
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Annie Adrait
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Victoria Pakulska
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Yohann Couté
- Grenoble Alpes, CEA, Inserm, UA13 BGE, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Manon Chevalier
- Department of Biosciences and Nutrition, Karolinska Institutet, Blickagången 16, 14157 Huddinge, Sweden
| | - Christian G. Riedel
- Department of Biosciences and Nutrition, Karolinska Institutet, Blickagången 16, 14157 Huddinge, Sweden
| | - Cecile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, 69007 Lyon, France
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3
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Soukar I, Amarasinghe A, Pile LA. Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex. Enzymes 2023; 53:33-68. [PMID: 37748836 DOI: 10.1016/bs.enz.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Post-translational modifications of histone proteins control the expression of genes. Metabolites from central and one-carbon metabolism act as donor moieties to modify histones and regulate gene expression. Thus, histone modification and gene regulation are connected to the metabolite status of the cell. Histone modifiers, such as the SIN3 complex, regulate genes involved in proliferation and metabolism. The SIN3 complex contains a histone deacetylase and a histone demethylase, which regulate the chromatin landscape and gene expression. In this chapter, we review the cross-talk between metabolic pathways that produce donor moieties, and epigenetic complexes regulating proliferation and metabolic genes. This cross-talk between gene regulation and metabolism is tightly controlled, and disruption of this cross-talk leads to metabolic diseases. We discuss promising therapeutics that directly regulate histone modifiers, and can affect the metabolic status of the cell, alleviating some metabolic diseases.
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Affiliation(s)
- Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Anjalie Amarasinghe
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States.
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4
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Rider SD, Damewood FJ, Gadgil RY, Hitch DC, Alhawach V, Shrestha R, Shanahan M, Zavada N, Leffak M. Suppressors of Break-Induced Replication in Human Cells. Genes (Basel) 2023; 14:genes14020398. [PMID: 36833325 PMCID: PMC9956954 DOI: 10.3390/genes14020398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Short tandem DNA repeats are drivers of genome instability. To identify suppressors of break-induced mutagenesis human cells, unbiased genetic screens were conducted using a lentiviral shRNA library. The recipient cells possessed fragile non-B DNA that could induce DNA double-strand breaks (DSBs), integrated at an ectopic chromosomal site adjacent to a thymidine kinase marker gene. Mutagenesis of the thymidine kinase gene rendered cells resistant to the nucleoside analog ganciclovir (GCV). The screen identified genes that have established roles in DNA replication and repair, chromatin modification, responses to ionizing radiation, and genes encoding proteins enriched at replication forks. Novel loci implicated in BIR included olfactory receptors, the G0S2 oncogene/tumor suppressor axis, the EIF3H-METTL3 translational regulator, and the SUDS3 subunit of the Sin3A corepressor. Consistent with a role in suppressing BIR, siRNA knockdown of selected candidates increased the frequency of the GCVr phenotype and increased DNA rearrangements near the ectopic non-B DNA. Inverse PCR and DNA sequence analyses showed that hits identified in the screen increased genome instability. Further analysis quantitated repeat-induced hypermutagenesis at the ectopic site and showed that knockdown of a primary hit, COPS2, induced mutagenic hotspots, remodeled the replication fork, and increased nonallelic chromosome template switches.
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Aparicio-Bautista DI, Chávez-Valenzuela D, Ambriz-Álvarez G, Córdova-Fraga T, Reyes-Grajeda JP, Medina-Contreras Ó, Rodríguez-Cruz F, García-Sierra F, Zúñiga-Sánchez P, Gutiérrez-Gutiérrez AM, Arellanes-Robledo J, Basurto-Islas G. An Extremely Low-Frequency Vortex Magnetic Field Modifies Protein Expression, Rearranges the Cytoskeleton, and Induces Apoptosis of a Human Neuroblastoma Cell Line. Bioelectromagnetics 2022; 43:225-244. [PMID: 35437793 DOI: 10.1002/bem.22400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/10/2021] [Accepted: 03/19/2022] [Indexed: 11/07/2022]
Abstract
Homogeneous extremely low-frequency electromagnetic fields (ELF-EMFs) alter biological phenomena, including the cell phenotype and proliferation rate. Heterogenous vortex magnetic fields (VMFs), a new approach of exposure to magnetic fields, induce systematic movements on charged biomolecules from target cells; however, the effect of VMFs on living systems remains uncertain. Here, we designed, constructed, and characterized an ELF-VMF-modified Rodin's coil to expose SH-SY5Y cells. Samples were analyzed by performing 2D-differential-gel electrophoresis, identified by MALDI-TOF/TOF, validated by western blotting, and characterized by confocal microscopy. A total of 106 protein spots were differentially expressed; 40 spots were downregulated and 66 were upregulated in the exposed cell proteome, compared to the control cell proteome. The identified spots are associated with cytoskeleton and cell viability proteins, and according to the protein-protein interaction network, a significant interaction among them was found. Our data revealed a decrease in cell survival associated with apoptotic cells without effects on the cell cycle, as well as evident changes in the cytoskeleton. We demonstrated that ELF-VMFs, at a specific frequency and exposure time, alter the cell proteome and structurally affect the target cells. This is the first report showing that VMF application might be a versatile system for testing different hypotheses in living systems, using appropriate exposure parameters.© 2022 Bioelectromagnetics Society.
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Affiliation(s)
- Diana I Aparicio-Bautista
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | | | | | - Teodoro Córdova-Fraga
- División de Ciencias e Ingenierías, Universidad de Guanajuato, León, Guanajuato, México
| | - Juan P Reyes-Grajeda
- Laboratorio de Estructura de Proteínas, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Óscar Medina-Contreras
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Fanny Rodríguez-Cruz
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Zacatenco, Ciudad de México, México
| | - Francisco García-Sierra
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Zacatenco, Ciudad de México, México
| | | | | | - Jaime Arellanes-Robledo
- CONACYT-Laboratorio de Enfermedades Hepáticas, Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Gustavo Basurto-Islas
- División de Ciencias e Ingenierías, Universidad de Guanajuato, León, Guanajuato, México
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6
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Stephan OOH. Interactions, structural aspects, and evolutionary perspectives of the yeast 'START'-regulatory network. FEMS Yeast Res 2021; 22:6461095. [PMID: 34905017 DOI: 10.1093/femsyr/foab064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/11/2021] [Indexed: 11/12/2022] Open
Abstract
Molecular signal transduction networks which conduct transcription at the G1 to S phase transition of the eukaryotic cell division cycle have been identified in diverse taxa from mammals to baker´s yeast with analogous functional organization. However, regarding some network components, such as the transcriptional regulators STB1 and WHI5, only few orthologs exist which are confined to individual Saccharomycotina species. While Whi5 has been characterized as yeast analog of human Rb protein, in the particular case of Stb1 (Sin three binding protein 1) identification of functional analogs emerges as difficult because to date its exact functionality still remains obscured. By aiming to resolve Stb1´s enigmatic role this Perspectives article especially surveys works covering relations between Cyclin/CDKs, the heteromeric transcription factor complexes SBF (Swi4/Swi6) and MBF (Mbp1/Swi6), as well as additional coregulators (Whi5, Sin3, Rpd3, Nrm1) which are collectively associated with the orderly transcription at 'Start' of the Saccharomyces cerevisiae cell cycle. In this context, interaction capacities of the Sin3-scaffold protein are widely surveyed because its four PAH domains (Paired Amphiphatic Helix) represent a 'recruitment-code' for gene-specific targeting of repressive histone deacetylase activity (Rpd3) via different transcription factors. Here Stb1 plays a role in Sin3´s action on transcription at the G1/S-boundary. Through bioinformatic analyses a potential Sin3-interaction domain (SID) was detected in Stb1, and beyond that, connections within the G1/S-regulatory network are discussed in structural and evolutionary context thereby providing conceptual perspectives.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Bavaria, Germany
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7
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Latypova X, Vincent M, Mollé A, Adebambo OA, Fourgeux C, Khan TN, Caro A, Rosello M, Orellana C, Niyazov D, Lederer D, Deprez M, Capri Y, Kannu P, Tabet AC, Levy J, Aten E, den Hollander N, Splitt M, Walia J, Immken LL, Stankiewicz P, McWalter K, Suchy S, Louie RJ, Bell S, Stevenson RE, Rousseau J, Willem C, Retiere C, Yang XJ, Campeau PM, Martinez F, Rosenfeld JA, Le Caignec C, Küry S, Mercier S, Moradkhani K, Conrad S, Besnard T, Cogné B, Katsanis N, Bézieau S, Poschmann J, Davis EE, Isidor B. Haploinsufficiency of the Sin3/HDAC corepressor complex member SIN3B causes a syndromic intellectual disability/autism spectrum disorder. Am J Hum Genet 2021; 108:929-941. [PMID: 33811806 DOI: 10.1016/j.ajhg.2021.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/18/2021] [Indexed: 11/28/2022] Open
Abstract
Proteins involved in transcriptional regulation harbor a demonstrated enrichment of mutations in neurodevelopmental disorders. The Sin3 (Swi-independent 3)/histone deacetylase (HDAC) complex plays a central role in histone deacetylation and transcriptional repression. Among the two vertebrate paralogs encoding the Sin3 complex, SIN3A variants cause syndromic intellectual disability, but the clinical consequences of SIN3B haploinsufficiency in humans are uncharacterized. Here, we describe a syndrome hallmarked by intellectual disability, developmental delay, and dysmorphic facial features with variably penetrant autism spectrum disorder, congenital malformations, corpus callosum defects, and impaired growth caused by disruptive SIN3B variants. Using chromosomal microarray or exome sequencing, and through international data sharing efforts, we identified nine individuals with heterozygous SIN3B deletion or single-nucleotide variants. Five individuals harbor heterozygous deletions encompassing SIN3B that reside within a ∼230 kb minimal region of overlap on 19p13.11, two individuals have a rare nonsynonymous substitution, and two individuals have a single-nucleotide deletion that results in a frameshift and predicted premature termination codon. To test the relevance of SIN3B impairment to measurable aspects of the human phenotype, we disrupted the orthologous zebrafish locus by genome editing and transient suppression. The mutant and morphant larvae display altered craniofacial patterning, commissural axon defects, and reduced body length supportive of an essential role for Sin3 function in growth and patterning of anterior structures. To investigate further the molecular consequences of SIN3B variants, we quantified genome-wide enhancer and promoter activity states by using H3K27ac ChIP-seq. We show that, similar to SIN3A mutations, SIN3B disruption causes hyperacetylation of a subset of enhancers and promoters in peripheral blood mononuclear cells. Together, these data demonstrate that SIN3B haploinsufficiency leads to a hitherto unknown intellectual disability/autism syndrome, uncover a crucial role of SIN3B in the central nervous system, and define the epigenetic landscape associated with Sin3 complex impairment.
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Affiliation(s)
- Xenia Latypova
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Alice Mollé
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | | | - Cynthia Fourgeux
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Tahir N Khan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Department of Biological Sciences, National University of Medical Sciences, 46000 Rawalpindi, Pakistan
| | - Alfonso Caro
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Monica Rosello
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Carmen Orellana
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Dmitriy Niyazov
- Department of Pediatrics, Ochsner Clinic, New Orleans, LA 70128, USA
| | - Damien Lederer
- Centre de Génétique Humaine, IPG, 6041 Gosselies, Belgium
| | - Marie Deprez
- Service de Neuropédiatrie, Clinique Saint Elizabeth, 5000 Namur, Belgium
| | - Yline Capri
- Service de Génétique Médicale, Hôpital Robert Debré, 75019 Paris, France
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Jonathan Levy
- Service de Cytogénétique, Hôpital Robert Debré, 75019 Paris, France
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Nicolette den Hollander
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle Upon Tyne NE1 3BZ, UK
| | - Jagdeep Walia
- Kingston General Hospital Research Institute, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
| | - Ladonna L Immken
- Clinical Genetics, Dell Children's Medical Group, Austin, TX 78731, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sharon Suchy
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Raymond J Louie
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Shannon Bell
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Roger E Stevenson
- Greenwood Genetic Center, 106 Gregor Mendel Cir, Greenwood, SC 29646, USA
| | - Justine Rousseau
- Sainte-Justine Hospital, 3175, Cote-Sainte-Catherine, Montreal, QC, Canada
| | | | - Christelle Retiere
- Etablissement Français du Sang, 44000 Nantes, France; CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, 44000 Nantes, France; LabEx IGO, Nantes 44000, France
| | - Xiang-Jiao Yang
- Rosalind & Morris Goodman Cancer Research Center and Department of Medicine, McGill University, Montreal, QC H3A 1A3, Canada
| | - Philippe M Campeau
- Sainte-Justine Hospital, 3175, Cote-Sainte-Catherine, Montreal, QC, Canada
| | - Francisco Martinez
- Unidad de Genética, Grupo de Investigación Traslacional en Genética, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cédric Le Caignec
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Kamran Moradkhani
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Solène Conrad
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France
| | - Jeremie Poschmann
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France.
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, 44007 Nantes, France.
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Expression of the Neural REST/NRSF-SIN3 Transcriptional Corepressor Complex as a Target for Small-Molecule Inhibitors. Mol Biotechnol 2020; 63:53-62. [PMID: 33130996 DOI: 10.1007/s12033-020-00283-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
The repressor element 1 (RE1) silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) modulates the expression of genes with RE1/neuron-restrictive silencing element (RE1/NRSE) sites by recruiting the switch independent 3 (SIN3) factor and the REST corepressor (COREST) to its N and C-terminal repressor domain, respectively. Both, SIN3 and COREST assemble into protein complexes that are composed of multiple subunits including a druggable histone deacetylase (HDAC) enzyme. The SIN3 core complex comprises the eponymous proteins SIN3A or SIN3B, the catalytically active proteins HDAC1 or HDAC2, the histone chaperone retinoblastoma-associated protein 46/retinoblastoma-binding protein 7 (RBAP46/RBBP7) or RBAP48/RBBP4, the SIN3-associated protein 30 (SAP30), and the suppressor of defective silencing 3 (SDS3). Here, we overcome a bottleneck limiting the molecular characterization of the REST/NRSF-SIN3 transcriptional corepressor complex. To this end, SIN3 genes were amplified from the complementary DNA of neural stem/progenitor cells, and expressed in a baculovirus/insect cell expression system. We show that the isolates bind to DNA harboring RE1/NRSE sites and demonstrate that the histone deacetylase activity is blocked by small-molecule inhibitors. Thus, our isolates open up for future biomedical research on this critical transcriptional repressor complex and are envisioned as tool for drug testing.
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9
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Adams MK, Banks CAS, Thornton JL, Kempf CG, Zhang Y, Miah S, Hao Y, Sardiu ME, Killer M, Hattem GL, Murray A, Katt ML, Florens L, Washburn MP. Differential Complex Formation via Paralogs in the Human Sin3 Protein Interaction Network. Mol Cell Proteomics 2020; 19:1468-1484. [PMID: 32467258 PMCID: PMC8143632 DOI: 10.1074/mcp.ra120.002078] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
Despite the continued analysis of HDAC inhibitors in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The presence of two Sin3 paralogs in humans, SIN3A and SIN3B, may result in a heterogeneous population of Sin3 complexes and contributes to our poor understanding of the functional attributes of these complexes. Here, we profile the interaction networks of SIN3A and SIN3B to gain insight into complex composition and organization. In accordance with existing data, we show that Sin3 paralog identity influences complex composition. Additionally, chemical cross-linking MS identifies domains that mediate interactions between Sin3 proteins and binding partners. The characterization of rare SIN3B proteoforms provides additional evidence for the existence of conserved and divergent elements within human Sin3 proteins. Together, these findings shed light on both the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.
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Affiliation(s)
- Mark K Adams
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Janet L Thornton
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | | | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Sayem Miah
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Mihaela E Sardiu
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maxime Killer
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Gaye L Hattem
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Alexis Murray
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Maria L Katt
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.
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10
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Beurton F, Stempor P, Caron M, Appert A, Dong Y, Chen RAJ, Cluet D, Couté Y, Herbette M, Huang N, Polveche H, Spichty M, Bedet C, Ahringer J, Palladino F. Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans. Nucleic Acids Res 2019; 47:11164-11180. [PMID: 31602465 PMCID: PMC6868398 DOI: 10.1093/nar/gkz880] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/13/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022] Open
Abstract
The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Lys4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss vary, suggesting additional chromatin factors contribute to context dependent effects. Using a proteomics approach, we identified CFP1 associated proteins and an unexpected direct link between Caenorhabditis elegans CFP-1 and an Rpd3/Sin3 small (SIN3S) histone deacetylase complex. Supporting a functional connection, we find that mutants of COMPASS and SIN3 complex components genetically interact and have similar phenotypic defects including misregulation of common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3S HDAC complex at promoters.
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Affiliation(s)
- Flore Beurton
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Matthieu Caron
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ron A-j Chen
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - David Cluet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Yohann Couté
- Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Marion Herbette
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Ni Huang
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Hélène Polveche
- INSERM UMR 861, I-STEM, 28, Rue Henri Desbruères, 91100 Corbeil-Essonnes, France
| | - Martin Spichty
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Cécile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
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11
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Zhang Y, Wang L, Liang S, Zhang P, Kang R, Zhang M, Wang M, Chen L, Yuan H, Ding S, Li H. FpDep1, a component of Rpd3L histone deacetylase complex, is important for vegetative development, ROS accumulation, and pathogenesis in Fusarium pseudograminearum. Fungal Genet Biol 2019; 135:103299. [PMID: 31706014 DOI: 10.1016/j.fgb.2019.103299] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
Histone deacetylases (HDACs) play essential roles in modulating chromatin structure to provide accessibility to gene regulators. Increasing evidence has linked HADCs to pathogenesis control in the filamentous plant fungi. However, its function remains unclear in Fusarium pseudograminearum, which has led to the emergence of the disease Fusarium crown rot in China. Here we identified the FpDEP1 gene, an orthologue of Saccharomyces cerevisiae DEP1 encoding a component of the Rpd3 histone deacetylase complex in F. pseudograminearum. The gene deletion mutant, ΔFpdep1, showed significantly retarded growth on PDA plates with reduced aerial hyphae formation. Pathogenicity tests displayed no typical leaf lesions and limited expansion capability of coleoptiles. Histopathological analysis indicated the ΔFpdep1 deletion mutant differentiated infectious hyphae and triggered massive reactive oxygen species (ROS) accumulation during the early infection stage, resulting in limited expansion to neighbor cells which was concurring with sensitivity to H2O2 and SDS tests in vitro. FM4-64 staining revealed that the ΔFpdep1 deletion mutant was delayed in endocytosis. The FpDEP1-GFP transgene complemented the mutant phenotypes and the fusion protein co-localized with DAPI staining, indicating that the FpDEP1 gene product is localized to the nucleus in spores and mycelia. Immunoprecipitation coupled with LC-MS/MS and yeast two-hybrid screening identified the Rpd3L-like HDAC complex containing at least FpDep1, FpSds3, FpSin3, FpRpd3, FpRxt3, FpCti6, FpRho23, and FpUme6. These results suggest that FpDep1 is involved in a HDAC complex functioning on fungal development and pathogenesis in F. pseudograminearum.
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Affiliation(s)
- Yinshan Zhang
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Limin Wang
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Shen Liang
- Horticulture Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450009 China
| | - Panpan Zhang
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Ruijiao Kang
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Mengjuan Zhang
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Min Wang
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Linlin Chen
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Hongxia Yuan
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Shengli Ding
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China.
| | - Honglian Li
- Henan Agricultural University/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China.
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12
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Blondel A, Benberghout A, Pedeux R, Ricordel C. Exploiting ING2 Epigenetic Modulation as a Therapeutic Opportunity for Non-Small Cell Lung Cancer. Cancers (Basel) 2019; 11:cancers11101601. [PMID: 31640185 PMCID: PMC6827349 DOI: 10.3390/cancers11101601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) has been the leading cause of cancer-related death worldwide, over the last few decades. Survival remains extremely poor in the metastatic setting and, consequently, innovative therapeutic strategies are urgently needed. Inhibitor of Growth Gene 2 (ING2) is a core component of the mSin3A/Histone deacetylases complex (HDAC), which controls the chromatin acetylation status and modulates gene transcription. This gene has been characterized as a tumor suppressor gene and its status in cancer has been scarcely explored. In this review, we focused on ING2 and other mSin3A/HDAC member statuses in NSCLC. Taking advantage of existing public databases and known pharmacological properties of HDAC inhibitors, finally, we proposed a therapeutic model based on an ING2 biomarker-guided strategy.
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Affiliation(s)
- Alice Blondel
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, 35033 Rennes, France.
| | - Amine Benberghout
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, 35033 Rennes, France.
| | - Rémy Pedeux
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, 35033 Rennes, France.
| | - Charles Ricordel
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, 35033 Rennes, France.
- CHU Rennes, Service de Pneumologie, Université de Rennes 1, 35033 Rennes, France.
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13
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Lee CG, Kwon HK, Kang H, Kim Y, Nam JH, Won YH, Park S, Kim T, Kang K, Rudra D, Jun CD, Park ZY, Im SH. Ets1 suppresses atopic dermatitis by suppressing pathogenic T cell responses. JCI Insight 2019; 4:124202. [PMID: 30843878 DOI: 10.1172/jci.insight.124202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/29/2019] [Indexed: 01/03/2023] Open
Abstract
Atopic dermatitis (AD) is a complex inflammatory skin disease mediated by immune cells of both adaptive and innate types. Among them, CD4+ Th cells are one of major players of AD pathogenesis. Although the pathogenic role of Th2 cells has been well characterized, Th17/Th22 cells are also implicated in the pathogenesis of AD. However, the molecular mechanisms underlying pathogenic immune responses in AD remain unclear. We sought to investigate how the defect in the AD susceptibility gene, Ets1, is involved in AD pathogenesis in human and mice and its clinical relevance in disease severity by identifying Ets1 target genes and binding partners. Consistent with the decrease in ETS1 levels in severe AD patients and the experimental AD-like skin inflammation model, T cell-specific Ets1-deficient mice (Ets1ΔdLck) developed severe AD-like symptoms with increased pathogenic Th cell responses. A T cell-intrinsic increase of gp130 expression upon Ets1 deficiency promotes the gp130-mediated IL-6 signaling pathway, thereby leading to the development of severe AD-like symptoms. Functional blocking of gp130 by selective inhibitor SC144 ameliorated the disease pathogenesis by reducing pathogenic Th cell responses. Our results reveal a protective role of Ets1 in restricting pathogenic Th cell responses and suggest a potential therapeutic target for AD treatment.
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Affiliation(s)
- Choong-Gu Lee
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute of Natural Products, Gangneung, South Korea.,Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea
| | - Ho-Keun Kwon
- Department of Microbiology, College of Medicine, Yonsei University, Seoul, South Korea
| | - Hyeji Kang
- Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea
| | - Young Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, South Korea
| | | | - Young Ho Won
- Department of Dermatology, Chonnam National University Medical School, Gwangju, South Korea
| | - Sunhee Park
- Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea
| | - Taemook Kim
- Department of Microbiology, Dankook University, Cheonan, South Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, South Korea
| | - Dipayan Rudra
- Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea.,Division of Integrative Biosciences and Biotechnology (IBB), Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Chang-Duk Jun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
| | - Zee Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
| | - Sin-Hyeog Im
- Academy of Immunology and Microbiology (AIM), Institute for Basic Science (IBS), Pohang, South Korea.,Division of Integrative Biosciences and Biotechnology (IBB), Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
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14
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Lee HG, Hong C, Seo PJ. The Arabidopsis Sin3-HDAC Complex Facilitates Temporal Histone Deacetylation at the CCA1 and PRR9 Loci for Robust Circadian Oscillation. FRONTIERS IN PLANT SCIENCE 2019; 10:171. [PMID: 30833956 PMCID: PMC6387943 DOI: 10.3389/fpls.2019.00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
The circadian clock synchronizes endogenous rhythmic processes with environmental cycles and maximizes plant fitness. Multiple regulatory layers shape circadian oscillation, and chromatin modification is emerging as an important scheme for precise circadian waveforms. Here, we report the role of an evolutionarily conserved Sin3-histone deacetylase complex (HDAC) in circadian oscillation in Arabidopsis. SAP30 FUNCTION-RELATED 1 (AFR1) and AFR2, which are key components of Sin3-HDAC complex, are circadianly-regulated and possibly facilitate the temporal formation of the Arabidopsis Sin3-HDAC complex at dusk. The evening-expressed AFR proteins bind directly to the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and PSEUDO-RESPONSE REGULATOR 9 (PRR9) promoters and catalyze histone 3 (H3) deacetylation at the cognate regions to repress expression, allowing the declining phase of their expression at dusk. In support, the CCA1 and PRR9 genes were de-repressed around dusk in the afr1-1afr2-1 double mutant. These findings indicate that periodic histone deacetylation at the morning genes by the Sin3-HDAC complex contributes to robust circadian maintenance in higher plants.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Cheljong Hong
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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15
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Co-repressor, co-activator and general transcription factor: the many faces of the Sin3 histone deacetylase (HDAC) complex. Biochem J 2018; 475:3921-3932. [PMID: 30552170 PMCID: PMC6295471 DOI: 10.1042/bcj20170314] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 12/21/2022]
Abstract
At face value, the Sin3 histone deacetylase (HDAC) complex appears to be a prototypical co-repressor complex, that is, a multi-protein complex recruited to chromatin by DNA bound repressor proteins to facilitate local histone deacetylation and transcriptional repression. While this is almost certainly part of its role, Sin3 stubbornly refuses to be pigeon-holed in quite this way. Genome-wide mapping studies have found that Sin3 localises predominantly to the promoters of actively transcribed genes. While Sin3 knockout studies in various species result in a combination of both up- and down-regulated genes. Furthermore, genes such as the stem cell factor, Nanog, are dependent on the direct association of Sin3 for active transcription to occur. Sin3 appears to have properties of a co-repressor, co-activator and general transcription factor, and has thus been termed a co-regulator complex. Through a series of unique domains, Sin3 is able to assemble HDAC1/2, chromatin adaptors and transcription factors in a series of functionally and compositionally distinct complexes to modify chromatin at both gene-specific and global levels. Unsurprisingly, therefore, Sin3/HDAC1 have been implicated in the regulation of numerous cellular processes, including mammalian development, maintenance of pluripotency, cell cycle regulation and diseases such as cancer.
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16
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Banks CAS, Thornton JL, Eubanks CG, Adams MK, Miah S, Boanca G, Liu X, Katt ML, Parmely TJ, Florens L, Washburn MP. A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry. Mol Cell Proteomics 2018; 17:1432-1447. [PMID: 29599190 PMCID: PMC6030732 DOI: 10.1074/mcp.tir118.000661] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 01/03/2023] Open
Abstract
Although a variety of affinity purification mass spectrometry (AP-MS) strategies have been used to investigate complex interactions, many of these are susceptible to artifacts because of substantial overexpression of the exogenously expressed bait protein. Here we present a logical and systematic workflow that uses the multifunctional Halo tag to assess the correct localization and behavior of tagged subunits of the Sin3 histone deacetylase complex prior to further AP-MS analysis. Using this workflow, we modified our tagging/expression strategy with 21.7% of the tagged bait proteins that we constructed, allowing us to quickly develop validated reagents. Specifically, we apply the workflow to map interactions between stably expressed versions of the Sin3 subunits SUDS3, SAP30, or SAP30L and other cellular proteins. Here we show that the SAP30 and SAP30L paralogues strongly associate with the core Sin3 complex, but SAP30L has unique associations with the proteasome and the myelin sheath. Next, we demonstrate an advancement of the complex NSAF (cNSAF) approach, in which normalization to the scaffold protein SIN3A accounts for variations in the proportion of each bait capturing Sin3 complexes and allows a comparison among different baits capturing the same protein complex. This analysis reveals that although the Sin3 subunit SUDS3 appears to be used in both SIN3A and SIN3B based complexes, the SAP30 subunit is not used in SIN3B based complexes. Intriguingly, we do not detect the Sin3 subunits SAP18 and SAP25 among the 128 high-confidence interactions identified, suggesting that these subunits may not be common to all versions of the Sin3 complex in human cells. This workflow provides the framework for building validated reagents to assemble quantitative interaction networks for chromatin remodeling complexes and provides novel insights into focused protein interaction networks.
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Affiliation(s)
- Charles A S Banks
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Janet L Thornton
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Mark K Adams
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Sayem Miah
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Gina Boanca
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Xingyu Liu
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Maria L Katt
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Tari J Parmely
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Laurence Florens
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Michael P Washburn
- From the ‡Stowers Institute for Medical Research, Kansas City, MO 64110;
- §Departments of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
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17
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Srivas S, Thakur MK. Transcriptional co-repressor SIN3A silencing rescues decline in memory consolidation during scopolamine-induced amnesia. J Neurochem 2018; 145:204-216. [PMID: 29494759 DOI: 10.1111/jnc.14320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/27/2018] [Accepted: 01/30/2018] [Indexed: 12/13/2022]
Abstract
Epigenetic modifications through methylation of DNA and acetylation of histones modulate neuronal gene expression and regulate long-term memory. Earlier we demonstrated that scopolamine-induced decrease in memory consolidation is correlated with enhanced expression of hippocampal DNA methyltransferase 1 (DNMT1) and histone deacetylase 2 (HDAC2) in mice. DNMT1 and HDAC2 act together by recruiting a co-repressor complex and deacetylating the chromatin. The catalytic activity of HDACs is mainly dependent on its incorporation into multiprotein co-repressor complexes, among which SIN3A-HDAC2 co-repressor is widely studied to regulate synaptic plasticity. However, the involvement of co-repressor complex in regulating memory loss or amnesia is unexplored. This study examines the role of co-repressor SIN3A in scopolamine-induced amnesia through epigenetic changes in the hippocampus. Scopolamine treatment remarkably enhanced hippocampal SIN3A expression in mice. To prevent such increase in SIN3A expression, we used hippocampal infusion of SIN3A-siRNA and assessed the effect of SIN3A silencing on scopolamine-induced amnesia. Silencing of SIN3A in amnesic mice reduced the binding of HDAC2 at neuronal immediate early genes (IEGs) promoter, but did not change the expression of HDAC2. Furthermore, it increased acetylation of H3K9 and H3K14 at neuronal IEGs (Arc, Egr1, Homer1 and Narp) promoter, prevented scopolamine-induced down-regulation of IEGs and improved consolidation of memory during novel object recognition task. These findings together suggest that SIN3A has a critical role in regulation of synaptic plasticity and might act as a potential therapeutic target to rescue memory decline during amnesia and other neuropsychiatric pathologies.
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Affiliation(s)
- Sweta Srivas
- Department of Zoology, Biochemistry and Molecular Biology Laboratory, Brain Research Centre, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mahendra K Thakur
- Department of Zoology, Biochemistry and Molecular Biology Laboratory, Brain Research Centre, Institute of Science, Banaras Hindu University, Varanasi, India
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18
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Drosophila Kruppel homolog 1 represses lipolysis through interaction with dFOXO. Sci Rep 2017; 7:16369. [PMID: 29180716 PMCID: PMC5703730 DOI: 10.1038/s41598-017-16638-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/15/2017] [Indexed: 12/29/2022] Open
Abstract
Transcriptional coordination is a vital process contributing to metabolic homeostasis. As one of the key nodes in the metabolic network, the forkhead transcription factor FOXO has been shown to interact with diverse transcription co-factors and integrate signals from multiple pathways to control metabolism, oxidative stress response, and cell cycle. Recently, insulin/FOXO signaling has been implicated in the regulation of insect development via the interaction with insect hormones, such as ecdysone and juvenile hormone. In this study, we identified an interaction between Drosophila FOXO (dFOXO) and the zinc finger transcription factor Kruppel homolog 1 (Kr-h1), one of the key players in juvenile hormone signaling. We found that Kr-h1 mutants show delayed larval development and altered lipid metabolism, in particular induced lipolysis upon starvation. Notably, Kr-h1 physically and genetically interacts with dFOXO in vitro and in vivo to regulate the transcriptional activation of insulin receptor (InR) and adipose lipase brummer (bmm). The transcriptional co-regulation by Kr-h1 and dFOXO may represent a broad mechanism by which Kruppel-like factors integrate with insulin signaling to maintain metabolic homeostasis and coordinate organism growth.
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19
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a‐Hdac complex in embryonic stem cells required for self‐renewal. EMBO J 2017. [DOI: https://doi.org/10.15252/embj.201696307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology British Columbia Cancer Research Center Vancouver BC Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics Royal College of Surgeons in Ireland Dublin 2 Ireland
| | - Diego Pasini
- Department of Experimental Oncology European Institute of Oncology Milan Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science University College Dublin Dublin 4 Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics Trinity College Dublin Dublin 2 Ireland
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20
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Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP. Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal. EMBO J 2017; 36:2216-2232. [PMID: 28554894 DOI: 10.15252/embj.201696307] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/18/2017] [Accepted: 04/22/2017] [Indexed: 12/15/2022] Open
Abstract
Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ES cells, which also contains Ogt and Tet1. Fam60a binds on H3K4me3-positive promoters in ES cells, together with Ogt, Tet1 and Sin3a, and is essential to maintain the complex on chromatin. Finally, we show that depletion of Fam60a phenocopies the loss of Sin3a, leading to reduced proliferation, an extended G1-phase and the deregulation of lineage genes. Taken together, Fam60a is an essential core subunit of a variant Sin3a complex in ES cells that is required to promote rapid proliferation and prevent unscheduled differentiation.
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Affiliation(s)
- Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Bruce Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Sudipto Das
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Research Center, Vancouver, BC, Canada
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - SriGanesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Darran P O'Connor
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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21
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Moores RC, Brilha S, Schutgens F, Elkington PT, Friedland JS. Epigenetic Regulation of Matrix Metalloproteinase-1 and -3 Expression in Mycobacterium tuberculosis Infection. Front Immunol 2017; 8:602. [PMID: 28596772 PMCID: PMC5442172 DOI: 10.3389/fimmu.2017.00602] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/08/2017] [Indexed: 12/20/2022] Open
Abstract
In pulmonary tuberculosis (TB), the inflammatory immune response against Mycobacterium tuberculosis (Mtb) is associated with tissue destruction and cavitation, which drives disease transmission, chronic lung disease, and mortality. Matrix metalloproteinase (MMP)-1 is a host enzyme critical for the development of cavitation. MMP expression has been shown to be epigenetically regulated in other inflammatory diseases, but the importance of such mechanisms in Mtb-associated induction of MMP-1 is unknown. We investigated the role of changes in histone acetylation in Mtb-induced MMP expression using inhibitors of histone deacetylases (HDACs) and histone acetyltransferases (HAT), HDAC siRNA, promoter-reporter constructs, and chromatin immunoprecipitation assays. Mtb infection decreased Class I HDAC gene expression by over 50% in primary human monocyte-derived macrophages but not in normal human bronchial epithelial cells (NHBEs). Non-selective inhibition of HDAC activity decreased MMP-1/-3 expression by Mtb-stimulated macrophages and NHBEs, while class I HDAC inhibition increased MMP-1 secretion by Mtb-stimulated NHBEs. MMP-3 expression, but not MMP-1, was downregulated by siRNA silencing of HDAC1. Inhibition of HAT activity also significantly decreased MMP-1/-3 secretion by Mtb-infected macrophages. The MMP-1 promoter region between −2,001 and −2,942 base pairs from the transcriptional start site was key in control of Mtb-driven MMP-1 gene expression. Histone H3 and H4 acetylation and RNA Pol II binding in the MMP-1 promoter region were increased in stimulated NHBEs. In summary, epigenetic modification of histone acetylation via HDAC and HAT activity has a key regulatory role in Mtb-dependent gene expression and secretion of MMP-1 and -3, enzymes which drive human immunopathology. Manipulation of epigenetic regulatory mechanisms may have potential as a host-directed therapy to improve outcomes in the era of rising TB drug resistance.
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Affiliation(s)
- Rachel C Moores
- Section of Infectious Diseases and Immunity, Imperial College London, London, UK
| | - Sara Brilha
- Section of Infectious Diseases and Immunity, Imperial College London, London, UK.,Centre for Inflammation and Tissue Repair, Respiratory Medicine, University College London, London, UK
| | - Frans Schutgens
- Section of Infectious Diseases and Immunity, Imperial College London, London, UK
| | - Paul T Elkington
- Section of Infectious Diseases and Immunity, Imperial College London, London, UK.,National Institute of Health Research (NIHR) Respiratory Biomedical Research Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jon S Friedland
- Section of Infectious Diseases and Immunity, Imperial College London, London, UK
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22
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Redchuk TA, Omelina ES, Chernov KG, Verkhusha VV. Near-infrared optogenetic pair for protein regulation and spectral multiplexing. Nat Chem Biol 2017; 13:633-639. [PMID: 28346403 DOI: 10.1038/nchembio.2343] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022]
Abstract
Multifunctional optogenetic systems are in high demand for use in basic and biomedical research. Near-infrared-light-inducible binding of bacterial phytochrome BphP1 to its natural PpsR2 partner is beneficial for simultaneous use with blue-light-activatable tools. However, applications of the BphP1-PpsR2 pair are limited by the large size, multidomain structure and oligomeric behavior of PpsR2. Here, we engineered a single-domain BphP1 binding partner, Q-PAS1, which is three-fold smaller and lacks oligomerization. We exploited a helix-PAS fold of Q-PAS1 to develop several near-infrared-light-controllable transcription regulation systems, enabling either 40-fold activation or inhibition. The light-induced BphP1-Q-PAS1 interaction allowed modification of the chromatin epigenetic state. Multiplexing the BphP1-Q-PAS1 pair with a blue-light-activatable LOV-domain-based system demonstrated their negligible spectral crosstalk. By integrating the Q-PAS1 and LOV domains in a single optogenetic tool, we achieved tridirectional protein targeting, independently controlled by near-infrared and blue light, thus demonstrating the superiority of Q-PAS1 for spectral multiplexing and engineering of multicomponent systems.
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Affiliation(s)
- Taras A Redchuk
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Evgeniya S Omelina
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Konstantin G Chernov
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vladislav V Verkhusha
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
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23
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Liaw GJ. Pits, a protein interacting with Ttk69 and Sin3A, has links to histone deacetylation. Sci Rep 2016; 6:33388. [PMID: 27622813 PMCID: PMC5020733 DOI: 10.1038/srep33388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/25/2016] [Indexed: 01/09/2023] Open
Abstract
Histone deacetylation plays an important role in transcriptional repression. Previous results showed that the genetic interaction between ttk and rpd3, which encodes a class I histone deacetylase, is required for tll repression. This study investigated the molecular mechanism by which Ttk69 recruits Rpd3. Using yeast two-hybrid screening and datamining, one novel protein was found that weakly interacts with Ttk69 and Sin3A, designated as Protein interacting with Ttk69 and Sin3A (Pits). Pits protein expressed in the early stages of embryos and bound to the region of the tor response element in vivo. Expanded tll expression patterns were observed in embryos lacking maternal pits activity and the expansion was not widened by reducing either maternal ttk or sin3A activity. However, in embryos with simultaneously reduced maternal pits and sin3A activities or maternal pits, sin3A and ttk activities, the proportions of the embryos with expanded tll expression were significantly increased. These results indicate that all three gene activities are involved in tll repression. Level of histone H3 acetylation in the tll proximal region was found to be elevated in embryo with reduced these three gene activities. In conclusion, Ttk69 causes the histone deacetylation-mediated repression of tll via the interaction of Pits and Sin3A.
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Affiliation(s)
- Gwo-Jen Liaw
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112-22, Taiwan, Republic of China
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24
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Miles S, Breeden L. A common strategy for initiating the transition from proliferation to quiescence. Curr Genet 2016; 63:179-186. [PMID: 27544284 DOI: 10.1007/s00294-016-0640-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/04/2016] [Accepted: 08/06/2016] [Indexed: 10/21/2022]
Abstract
Development, tissue renewal and long term survival of multi-cellular organisms is dependent upon the persistence of stem cells that are quiescent, but retain the capacity to re-enter the cell cycle to self-renew, or to produce progeny that can differentiate and re-populate the tissue. Deregulated release of these cells from the quiescent state, or preventing them from entering quiescence, results in uncontrolled proliferation and cancer. Conversely, loss of quiescent cells, or their failure to re-enter cell division, disrupts organ development and prevents tissue regeneration and repair. Understanding the quiescent state and how cells control the transitions in and out of this state is of fundamental importance. Investigations into the mechanics of G1 arrest during the transition to quiescence continue to identify striking parallels between the strategies used by yeast and mammals to regulate this transition. When cells commit to a stable but reversible arrest, the G1/S genes responsible for promoting S phase must be inhibited. This process, from yeast to humans, involves the formation of quiescence-specific complexes on their promoters. In higher cells, these so-called DREAM complexes of E2F4/DP/RBL/MuvB recruit the highly conserved histone deacetylase HDAC1, which leads to local histone deacetylation and repression of S phase-promoting transcripts. Quiescent yeast cells also show pervasive histone deacetylation by the HDAC1 counterpart Rpd3. In addition, these cells contain quiescence-specific regulators of G1/S genes: Msa1 and Msa2, which can be considered components of the yeast equivalent of the DREAM complex. Despite a lack of physical similarities, the goals and the strategies used to achieve a reversible transition to quiescence are highly conserved. This motivates a detailed study of this process in the simple model organism: budding yeast.
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Affiliation(s)
- Shawna Miles
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Linda Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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25
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Clark MD, Zhang Y, Radhakrishnan I. Solution NMR Studies of an Alternative Mode of Sin3 Engagement by the Sds3 Subunit in the Histone Deacetylase-Associated Sin3L/Rpd3L Corepressor Complex. J Mol Biol 2015; 427:3817-23. [PMID: 26522936 DOI: 10.1016/j.jmb.2015.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
The Sds3 transcriptional corepressor facilitates the assembly of the 1- to 2-MDa histone deacetylase-associated Sin3L/Rpd3L complex by providing a crucial homodimerization activity. Sds3 engages the scaffolding protein Sin3A, via a bipartite motif within the Sin3 interaction domain (SID) comprising a helix and an extended segment. Here, we show that the SID samples two discrete, substantially populated conformations with lifetimes in the tens of milliseconds range. The two conformations differ via a translation of the main chain and the corresponding side chains in the 5- to 7-Å range. Given the close proximity of the SID to other functional motifs in Sds3 at the sequence level, the conformational exchange has the potential to regulate these activities.
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Affiliation(s)
- Michael David Clark
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Yongbo Zhang
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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26
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Rockowitz S, Zheng D. Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development. Nucleic Acids Res 2015; 43:5730-43. [PMID: 25990720 PMCID: PMC4499139 DOI: 10.1093/nar/gkv514] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Abstract
Recent studies have employed cross-species comparisons of transcription factor binding, reporting significant regulatory network 'rewiring' between species. Here, we address how a transcriptional repressor targets and regulates neural genes differentially between human and mouse embryonic stem cells (ESCs). We find that the transcription factor, Repressor Element 1 Silencing Transcription factor (REST; also called neuron restrictive silencer factor) binds to a core group of ∼1200 syntenic genomic regions in both species, with these conserved sites highly enriched with co-factors, selective histone modifications and DNA hypomethylation. Genes with conserved REST binding are enriched with neural functions and more likely to be upregulated upon REST depletion. Interestingly, we identified twice as many REST peaks in human ESCs compared to mouse ESCs. Human REST cistrome expansion involves additional peaks in genes targeted by REST in both species and human-specific gene targets. Genes with expanded REST occupancy in humans are enriched for learning or memory functions. Analysis of neurological disorder associated genes reveals that Amyotrophic Lateral Sclerosis and oxidative stress genes are particularly enriched with human-specific REST binding. Overall, our results demonstrate that there is substantial rewiring of human and mouse REST cistromes, and that REST may have human-specific roles in brain development and functions.
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Affiliation(s)
- Shira Rockowitz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex. Proc Natl Acad Sci U S A 2015; 112:E3669-78. [PMID: 26124119 DOI: 10.1073/pnas.1504021112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ∼ 150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. The Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.
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28
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Lanouette S, Davey JA, Elisma F, Ning Z, Figeys D, Chica RA, Couture JF. Discovery of substrates for a SET domain lysine methyltransferase predicted by multistate computational protein design. Structure 2014; 23:206-215. [PMID: 25533488 DOI: 10.1016/j.str.2014.11.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 01/01/2023]
Abstract
Characterization of lysine methylation has proven challenging despite its importance in biological processes such as gene transcription, protein turnover, and cytoskeletal organization. In contrast to other key posttranslational modifications, current proteomics techniques have thus far shown limited success at characterizing methyl-lysine residues across the cellular landscape. To complement current biochemical characterization methods, we developed a multistate computational protein design procedure to probe the substrate specificity of the protein lysine methyltransferase SMYD2. Modeling of substrate-bound SMYD2 identified residues important for substrate recognition and predicted amino acids necessary for methylation. Peptide- and protein- based substrate libraries confirmed that SMYD2 activity is dictated by the motif [LFM]-1-K(∗)-[AFYMSHRK]+1-[LYK]+2 around the target lysine K(∗). Comprehensive motif-based searches and mutational analysis further established four additional substrates of SMYD2. Our methodology paves the way to systematically predict and validate posttranslational modification sites while simultaneously pairing them with their associated enzymes.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - James A Davey
- Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Fred Elisma
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Roberto A Chica
- Department of Chemistry, University of Ottawa, Ottawa, ON, K1N 6N5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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29
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Wambua MK, Nalawansha DA, Negmeldin AT, Pflum MKH. Mutagenesis studies of the 14 Å internal cavity of histone deacetylase 1: insights toward the acetate-escape hypothesis and selective inhibitor design. J Med Chem 2014; 57:642-50. [PMID: 24405391 PMCID: PMC3983352 DOI: 10.1021/jm401837e] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Histone
deacetylase (HDAC) proteins are promising targets for cancer
treatment, as shown by the approval of two HDAC inhibitors for the
treatment of cutaneous T-cell lymphoma. HDAC1 in particular has been
linked to cell growth and cell cycle regulation and is therefore an
attractive target for anticancer drugs. The HDAC1 active site contains
a hydrophobic 11 Å active-site channel, with a 14 Å internal
cavity at the bottom of the active site. Several computational and
biochemical studies have proposed an acetate-escape hypothesis where
the acetate byproduct of the deacetylation reaction escapes via the
14 Å internal cavity. Selective HDAC inhibitors that bind to
the 14 Å cavity have also been created. To understand the influence
of amino acids lining the HDAC1 14 Å cavity in acetate escape
and inhibitor binding, we used mutagenesis coupled with acetate competition
assays. The results indicate that amino acids lining the 14 Å
cavity are critical for catalytic activity and acetate competition,
confirming the role of the cavity in acetate escape. In addition,
these mutagenesis studies will aid in HDAC1-inhibitor design that
exploits the 14 Å cavity.
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Affiliation(s)
- Magdalene K Wambua
- Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States
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30
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The physiological roles of histone deacetylase (HDAC) 1 and 2: complex co-stars with multiple leading parts. Biochem Soc Trans 2013; 41:741-9. [PMID: 23697933 DOI: 10.1042/bst20130010] [Citation(s) in RCA: 232] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
HDACs (histone deacetylases) 1 and 2 are ubiquitous long-lived proteins, which are often found together in three major multiprotein co-repressor complexes: Sin3, NuRD (nucleosome remodelling and deacetylation) and CoREST (co-repressor for element-1-silencing transcription factor). Although there is a burgeoning number of non-histone proteins within the acetylome, these complexes contain multiple DNA/chromatin-recognition motifs, which, in combination with transcription factors, target HDAC1/2 to chromatin. Their physiological roles should therefore be viewed within the framework of chromatin manipulation. Classically, HDACs were thought to be recruited predominantly by transcriptional repressors to facilitate local histone deacetylation and transcriptional repression. More recently, genome-wide assays have mapped HDAC1/2 and their associated proteins to transcriptionally active loci and have provided alternative context-specific functions, whereby their repressive functions are subtly exerted to balance transcriptional activation and repression. With a few significant exceptions (early embryogenesis, brain development), HDAC1 and HDAC2 are functionally redundant. In most mouse knockout studies, deletion of both enzymes is required in order to produce a substantial phenotype. HDAC1/2 activity has been implicated in the development of numerous tissue and cell types, including heart, skin, brain, B-cells and T-cells. A common feature in all HDAC1/2-knockout, -knockdown and small-molecule inhibitor studies is a reduction in cell proliferation. A generic role in cell cycle progression could be exploited in cancer cells, by blocking HDAC1/2 activity with small-molecule inhibitors, making them potentially useful drug targets.
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31
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Moser MA, Hagelkruys A, Seiser C. Transcription and beyond: the role of mammalian class I lysine deacetylases. Chromosoma 2013; 123:67-78. [PMID: 24170248 PMCID: PMC3967066 DOI: 10.1007/s00412-013-0441-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/07/2013] [Accepted: 10/14/2013] [Indexed: 11/25/2022]
Abstract
The Rpd3-like members of the class I lysine deacetylase family are important regulators of chromatin structure and gene expression and have pivotal functions in the control of proliferation, differentiation and development. The highly related class I deacetylases HDAC1 and HDAC2 have partially overlapping but also isoform-specific roles in diverse biological processes, whereas HDAC3 and HDAC8 have unique functions. This review describes the role of class I KDACs in the regulation of transcription as well as their non-transcriptional functions, in particular their contributions to splicing, mitosis/meiosis, replication and DNA repair. During the past years, a number of mouse loss-of-function studies provided new insights into the individual roles of class I deacetylases in cell cycle control, differentiation and tumorigenesis. Simultaneous ablation of HDAC1 and HDAC2 or single deletion of Hdac3 severely impairs cell cycle progression in all proliferating cell types indicating that these class I deacetylases are promising targets for small molecule inhibitors as anti-tumor drugs.
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Affiliation(s)
- Mirjam Andrea Moser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Astrid Hagelkruys
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
| | - Christian Seiser
- Department of Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohr-Gasse 9/2, 1030 Vienna, Austria
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Song S, Yuan Y, Lu J, Li Q, Zhu Z, Fan Q, Xue Y, Lai ZC, Zhang W. The Drosophila ortholog of breast cancer metastasis suppressor gene, dBrms1, is critical for developmental timing through regulating ecdysone signaling. Dev Biol 2013; 380:344-50. [DOI: 10.1016/j.ydbio.2013.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/10/2013] [Accepted: 05/12/2013] [Indexed: 01/24/2023]
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Metastasis suppression by BRMS1 associated with SIN3 chromatin remodeling complexes. Cancer Metastasis Rev 2013; 31:641-51. [PMID: 22678236 DOI: 10.1007/s10555-012-9363-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Epigenetic regulation of gene transcription by histone modification and chromatin remodeling has been linked to many biological and pathological events including cancer metastasis. Breast cancer metastasis suppressor 1 (BRMS1) interacts with SIN3 chromatin remodeling complexes, and, upon forced expression in metastatic cells, a nearly complete suppression of metastasis is noted without preventing primary tumor growth. The data for BRMS1-mediated metastasis suppression and SIN3 interaction are clear; however, connecting the inhibition directly to the association of BRMS1 with SIN3 complexes is currently not well defined. Considering the recent advancements in developing epigenetic drugs for cancer therapy, an improved understanding of how the interactions between BRMS1 and SIN3 regulate the process of metastasis should lead to novel therapies specifically targeting the most deadly aspect of tumor progression. In this article, the data for BRMS1-mediated metastasis suppression are reviewed with a focus on how the SIN3 chromatin remodeling complexes may be functionally involved.
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35
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Lee DM, Lee SH, Jeong KT, Hwang SJ, Park JH. SDS3 interacts with ARNT in an AhR ligand-specific manner regulating expression of cKrox and S100A4 in CD4+CD8+ DPK thymocytes differentiation. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2012; 34:858-868. [PMID: 22981438 DOI: 10.1016/j.etap.2012.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 07/02/2012] [Accepted: 08/24/2012] [Indexed: 06/01/2023]
Abstract
To study mechanisms underlying differential effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and benzo(a)pyrene (B(a)P) on thymocyte differentiation, we examined effects of AhR ligands on the differentiation of DPK cells, a CD4(+)CD8(+) thymic lymphoma cell line which can differentiate into CD4(+)CD8(-) thymocytes. In contrast to TCDD, which inhibited the differentiation, B(a)P showed little effect. Antigen-mediated up-regulation of S100A4, S100A6, galectin-1, and TRAF5-like protein was remarkably suppressed by TCDD, but slightly by B(a)P. Immunoprecipitation using anti-ARNT Ab revealed that SDS3, a component of the Sin3/HDAC repressor complex, was associated with ARNT only when DPK cells were incubated with TCDD. Expression of cKrox S100A4 was derepressed when SDS3 protein was reduced. These results indicate that although it is generally known that many AhR ligands such as TCDD and B(a)P function mainly by the AhR/ARNT complex, ligand-specific interaction between SDS3 and ARNT exerts differential effects on the expression of genes associated with thymocyte differentiation.
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Affiliation(s)
- Dong-Min Lee
- Department of Biology, Changwon National University, Changwon, Kyungnam 641-773, South Korea
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Zhang K, Dai X, Wallingford MC, Mager J. Depletion of Suds3 reveals an essential role in early lineage specification. Dev Biol 2012; 373:359-72. [PMID: 23123966 DOI: 10.1016/j.ydbio.2012.10.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/20/2012] [Accepted: 10/24/2012] [Indexed: 10/27/2022]
Abstract
Preimplantation development culminates with the emergence of three distinct populations: the inner cell mass, primitive endoderm and trophectoderm. Here, we define the mechanisms underlying the requirement of Suds3 in pre/peri-implantation development. Suds3 knockdown blastocysts exhibit a failure of both trophectoderm proliferation as well as a conspicuous lack of primitive endoderm. Expression of essential lineage factors Nanog, Sox2, Cdx2, Eomes, Elf5 and Sox17 are severely reduced in the absence of Suds3. Importantly, we document deficient FGF4/ERK signaling and show that exogenous FGF4 rescues primitive endoderm formation and trophectoderm proliferation in Suds3 knockdown blastocysts. We also show that Hdac1 knockdown reduces Sox2/FGF4/ERK signaling in blastocysts. Collectively, these data define a role for Suds3 in activation of FGF4/ERK signaling and determine an essential molecular role of Suds3/Sin3/HDAC complexes in lineage specification in vivo.
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Affiliation(s)
- Kun Zhang
- Department of Veterinary and Animal Sciences, University of Massachusetts at Amherst, 455, 661 N. Pleasant Street, Amherst, MA 01003, USA
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37
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Smith KT, Sardiu ME, Martin-Brown SA, Seidel C, Mushegian A, Egidy R, Florens L, Washburn MP, Workman JL. Human family with sequence similarity 60 member A (FAM60A) protein: a new subunit of the Sin3 deacetylase complex. Mol Cell Proteomics 2012; 11:1815-28. [PMID: 22984288 DOI: 10.1074/mcp.m112.020255] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Here we describe the function of a previously uncharacterized protein, named family with sequence similarity 60 member A (FAM60A) that maps to chromosome 12p11 in humans. We use quantitative proteomics to determine that the main biochemical partners of FAM60A are subunits of the Sin3 deacetylase complex and show that FAM60A resides in active HDAC complexes. In addition, we conduct gene expression pathway analysis and find that FAM60A regulates expression of genes that encode components of the TGF-beta signaling pathway. Moreover, our studies reveal that loss of FAM60A or another component of the Sin3 complex, SDS3, leads to a change in cell morphology and an increase in cell migration. These studies reveal the function of a previously uncharacterized protein and implicate the Sin3 complex in suppressing cell migration.
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Affiliation(s)
- Karen T Smith
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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38
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Winter SF, Lukes L, Walker RC, Welch DR, Hunter KW. Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis. PLoS Genet 2012; 8:e1002735. [PMID: 22693453 PMCID: PMC3364935 DOI: 10.1371/journal.pgen.1002735] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/12/2012] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence suggests that breast cancer metastatic progression is modified by germline polymorphism, although specific modifier genes have remained largely undefined. In the current study, we employ the MMTV-PyMT transgenic mouse model and the AKXD panel of recombinant inbred mice to identify AT-rich interactive domain 4B (Arid4b; NM_194262) as a breast cancer progression modifier gene. Ectopic expression of Arid4b promoted primary tumor growth in vivo as well as increased migration and invasion in vitro, and the phenotype was associated with polymorphisms identified between the AKR/J and DBA/2J alleles as predicted by our genetic analyses. Stable shRNA-mediated knockdown of Arid4b caused a significant reduction in pulmonary metastases, validating a role for Arid4b as a metastasis modifier gene. ARID4B physically interacts with the breast cancer metastasis suppressor BRMS1, and we detected differential binding of the Arid4b alleles to histone deacetylase complex members mSIN3A and mSDS3, suggesting that the mechanism of Arid4b action likely involves interactions with chromatin modifying complexes. Downregulation of the conserved Tpx2 gene network, which is comprised of many factors regulating cell cycle and mitotic spindle biology, was observed concomitant with loss of metastatic efficiency in Arid4b knockdown cells. Consistent with our genetic analysis and in vivo experiments in our mouse model system, ARID4B expression was also an independent predictor of distant metastasis-free survival in breast cancer patients with ER+ tumors. These studies support a causative role of ARID4B in metastatic progression of breast cancer.
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Affiliation(s)
- Scott F Winter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Ramakrishna S, Suresh B, Bae SM, Ahn WS, Lim KH, Baek KH. Hyaluronan binding motifs of USP17 and SDS3 exhibit anti-tumor activity. PLoS One 2012; 7:e37772. [PMID: 22662218 PMCID: PMC3360616 DOI: 10.1371/journal.pone.0037772] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 04/23/2012] [Indexed: 01/08/2023] Open
Abstract
Background We previously reported that the USP17 deubiquitinating enzyme having hyaluronan binding motifs (HABMs) interacts with human SDS3 (suppressor of defective silencing 3) and specifically deubiquitinates Lys-63 branched polyubiquitination of SDS3 resulting in negative regulation of histone deacetylase (HDAC) activity in cancer cells. Furthermore, USP17 and SDS3 mutually interact with each other to block cell proliferation in HeLa cells but the mechanism for this inhibition in cell proliferation is not known. We wished to investigate whether the HABMs of USP17 were responsible for tumor suppression activity. Methodology/Principal Findings Similarly to USP17, we have identified that SDS3 also has three consecutive HABMs and shows direct binding with hyaluronan (HA) using cetylpyridinium chloride (CPC) assay. Additionally, HA oligosaccharides (6-18 sugar units) competitively block binding of endogenous HA polymer to HA binding proteins. Thus, administration of HA oligosaccharides antagonizes the interaction between HA and USP17 or SDS3. Interestingly, HABMs deleted USP17 showed lesser interaction with SDS3 but retain its deubiquitinating activity towards SDS3. The deletion of HABMs of USP17 could not alter its functional regulation on SDS3-associated HDAC activity. Furthermore, to explore whether HABMs in USP17 and SDS3 are responsible for the inhibition of cell proliferation, we investigated the effect of USP17 and SDS3-lacking HABMs on cell proliferation by soft agar, apoptosis, cell migration and cell proliferation assays. Conclusions Our results have demonstrated that these HABMs in USP17 and its substrate SDS3 are mainly involved in the inhibition of anchorage-independent tumor growth.
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Affiliation(s)
- Suresh Ramakrishna
- Department of Biomedical Science, CHA University, CHA General Hospital, Gyeonggi-Do, Republic of Korea
| | - Bharathi Suresh
- Department of Biomedical Science, CHA University, CHA General Hospital, Gyeonggi-Do, Republic of Korea
| | - Su-Mi Bae
- Catholic Research Institute of Medical Science, The Catholic University of Korea College of Medicine, Seoul, Republic of Korea
| | - Woong-Shick Ahn
- Catholic Research Institute of Medical Science, The Catholic University of Korea College of Medicine, Seoul, Republic of Korea
| | - Key-Hwan Lim
- Department of Biomedical Science, CHA University, CHA General Hospital, Gyeonggi-Do, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, CHA General Hospital, Gyeonggi-Do, Republic of Korea
- * E-mail:
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Contreras-Vallejos E, Utreras E, Gonzalez-Billault C. Going out of the brain: non-nervous system physiological and pathological functions of Cdk5. Cell Signal 2011; 24:44-52. [PMID: 21924349 DOI: 10.1016/j.cellsig.2011.08.022] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 08/29/2011] [Indexed: 12/23/2022]
Abstract
Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase that is mostly active in the nervous system, where it regulates several processes such as neuronal migration, actin and microtubule dynamics, axonal guidance, and synaptic plasticity, among other processes. In addition to these known functions, in the past few years, novel roles for Cdk5 outside of the nervous system have been proposed. These include roles in gene transcription, vesicular transport, apoptosis, cell adhesion, and migration in many cell types and tissues such as pancreatic cells, muscle cells, neutrophils, and others. In this review, we will summarize the recently studied non-neuronal functions of Cdk5, with a thorough analysis of the biological consequences of these novel roles.
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Affiliation(s)
- Erick Contreras-Vallejos
- Department of Biology and Institute for Cell Dynamics and Biotechnology, Faculty of Sciences, Universidad de Chile, Santiago, Chile.
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41
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Magnusson K, Mendes AM, Windbichler N, Papathanos PA, Nolan T, Dottorini T, Rizzi E, Christophides GK, Crisanti A. Transcription regulation of sex-biased genes during ontogeny in the malaria vector Anopheles gambiae. PLoS One 2011; 6:e21572. [PMID: 21738713 PMCID: PMC3128074 DOI: 10.1371/journal.pone.0021572] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 06/03/2011] [Indexed: 11/18/2022] Open
Abstract
In Anopheles gambiae, sex-regulated genes are responsible for controlling gender dimorphism and are therefore crucial in determining the ability of female mosquitoes to transmit human malaria. The identification and functional characterization of these genes will shed light on the sexual development and maturation of mosquitoes and provide useful targets for genetic control measures aimed at reducing mosquito fertility and/or distorting the sex ratio. We conducted a genome wide transcriptional analysis of sex-regulated genes from early developmental stages through adulthood combined with functional screening of novel gonadal genes. Our results demonstrate that the male-biased genes undergo a major transcription turnover starting from larval stages to adulthood. The male biased genes at the adult stage include a significant high number of unique sequences compared to the rest of the genome. This is in contrast to female-biased genes that are much more conserved and are mainly activated during late developmental stages. The high frequency of unique sequences would indicate that male-biased genes evolve more rapidly than the rest of the genome. This finding is particularly intriguing because A. gambiae is a strictly female monogamous species suggesting that driving forces in addition to sperm competition must account for the rapid evolution of male-biased genes. We have also identified and functionally characterized a number of previously unknown A. gambiae testis- and ovary-specific genes. Two of these genes, zero population growth and a suppressor of defective silencing 3 domain of the histone deacetylase co-repressor complex, were shown to play a key role in gonad development.
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Affiliation(s)
- Kalle Magnusson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Antonio M. Mendes
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Tony Nolan
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tania Dottorini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | | | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- * E-mail:
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42
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Ramakrishna S, Suresh B, Lee EJ, Lee HJ, Ahn WS, Baek KH. Lys-63-specific deubiquitination of SDS3 by USP17 regulates HDAC activity. J Biol Chem 2011; 286:10505-14. [PMID: 21239494 DOI: 10.1074/jbc.m110.162321] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SDS3 is a key component of the histone deacetylase (HDAC)-dependent Sin3A co-repressor complex, serving to maintain its HDAC activity. Here, we report both exogenous and endogenous functional interaction between deubiquitinating enzyme USP17 and human SDS3 by MALDI-TOF-MS, co-immunoprecipitation assay, and GST pull-down assay. In this study, we demonstrated that SDS3 readily undergoes endogenous polyubiquitination, which is associated specifically with Lys-63-branched polyubiquitin chains and not with Lys-48-branched polyubiquitin chains. Further, we also demonstrated that USP17 specifically deubiquitinates Lys-63-linked ubiquitin chains from SDS3 and regulates its biological functions. The deubiquitinating activity of USP17 on SDS3 negatively regulates SDS3-associated HDAC activity. The constitutive expression of USP17 and its substrate SDS3 was involved in the inhibition of anchorage-independent tumor growth and blocks cell proliferation, leading to apoptosis in cervical carcinoma cells. Furthermore, we showed that USP17 and SDS3 mutually interact with each other to regulate cancer cell viability. These data support the possibility that SDS3, being a substrate of USP17, may play an important role in developing a novel therapeutic means to inhibit specific HDAC activities in cancer.
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Affiliation(s)
- Suresh Ramakrishna
- Department of Biomedical Science, CHA University, CHA General Hospital, Seoul 135-081, Korea
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43
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Segré CV, Chiocca S. Regulating the regulators: the post-translational code of class I HDAC1 and HDAC2. J Biomed Biotechnol 2010; 2011:690848. [PMID: 21197454 PMCID: PMC3004424 DOI: 10.1155/2011/690848] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 10/15/2010] [Indexed: 11/18/2022] Open
Abstract
Class I histone deacetylases (HDACs) are cellular enzymes expressed in many tissues and play crucial roles in differentiation, proliferation, and cancer. HDAC1 and HDAC2 in particular are highly homologous proteins that show redundant or specific roles in different cell types or in response to different stimuli and signaling pathways. The molecular details of this dual regulation are largely unknown. HDAC1 and HDAC2 are not only protein modifiers, but are in turn regulated by post-translational modifications (PTMs): phosphorylation, acetylation, ubiquitination, SUMOylation, nitrosylation, and carbonylation. Some of these PTMs occur and crosstalk specifically on HDAC1 or HDAC2, creating a rational "code" for a differential, context-related regulation. The global comprehension of this PTM code is central for dissecting the role of single HDAC1 and HDAC2 in physiology and pathology.
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Affiliation(s)
- Chiara V. Segré
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
| | - Susanna Chiocca
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy
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44
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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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45
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Deacetylase inhibitors dissociate the histone-targeting ING2 subunit from the Sin3 complex. ACTA ACUST UNITED AC 2010; 17:65-74. [PMID: 20142042 DOI: 10.1016/j.chembiol.2009.12.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 12/08/2009] [Accepted: 12/15/2009] [Indexed: 02/08/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are in clinical development for several diseases, including cancers and neurodegenerative disorders. HDACs 1 and 2 are among the targets of these inhibitors and are part of multisubunit protein complexes. HDAC inhibitors (HDACis) block the activity of HDACs by chelating a zinc molecule in their catalytic sites. It is not known if the inhibitors have any additional functional effects on the multisubunit HDAC complexes. Here, we find that suberoylanilide hydroxamic acid (SAHA), the first FDA-approved HDACi for cancer, causes the dissociation of the PHD-finger-containing ING2 subunit from the Sin3 deacetylase complex. Loss of ING2 disrupts the in vivo binding of the Sin3 complex to the p21 promoter, an important target gene for cell growth inhibition by SAHA. Our findings reveal a molecular mechanism by which HDAC inhibitors disrupt deacetylase function.
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46
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Stewart MD, Wong J. Nuclear receptor repression: regulatory mechanisms and physiological implications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:235-59. [PMID: 20374706 DOI: 10.1016/s1877-1173(09)87007-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ability to associate with corepressors and to inhibit transcription is an intrinsic property of most members of the nuclear receptor (NR) superfamily. NRs induce transcriptional repression by recruiting multiprotein corepressor complexes. Nuclear receptor corepressor (NCoR) and silencing mediator of retinoic and thyroid receptors (SMRT) are the most well characterized corepressor complexes and mediate repression for virtually all NRs. In turn, corepressor complexes repress transcription because they either contain or associate with chromatin modifying enzymes. These include histone deacetylases, histone H3K4 demethylases, histone H3K9 or H3K27 methyltransferases, and ATP-dependent chromatin remodeling factors. Two types of NR-interacting corepressors exist. Ligand-independent corepressors, like NCoR/SMRT, bind to unliganded or antagonist-bound NRs, whereas ligand-dependent corepressors (LCoRs) associate with NRs in the presence of agonist. Therefore, LCoRs may serve to attenuate NR-mediated transcriptional activation. Somewhat unexpectedly, classical coactivators may also function as "corepressors" to mediate repression by agonist-bound NRs. In this chapter, we will discuss the various modes and mechanisms of repression by NRs as well as discuss the known physiological functions of NR-mediated repression.
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Affiliation(s)
- M David Stewart
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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47
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Sardiu ME, Gilmore JM, Carrozza MJ, Li B, Workman JL, Florens L, Washburn MP. Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics. PLoS One 2009; 4:e7310. [PMID: 19806189 PMCID: PMC2751824 DOI: 10.1371/journal.pone.0007310] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 09/07/2009] [Indexed: 11/19/2022] Open
Abstract
Protein complexes are key molecular machines executing a variety of essential cellular processes. Despite the availability of genome-wide protein-protein interaction studies, determining the connectivity between proteins within a complex remains a major challenge. Here we demonstrate a method that is able to predict the relationship of proteins within a stable protein complex. We employed a combination of computational approaches and a systematic collection of quantitative proteomics data from wild-type and deletion strain purifications to build a quantitative deletion-interaction network map and subsequently convert the resulting data into an interdependency-interaction model of a complex. We applied this approach to a data set generated from components of the Saccharomyces cerevisiae Rpd3 histone deacetylase complexes, which consists of two distinct small and large complexes that are held together by a module consisting of Rpd3, Sin3 and Ume1. The resulting representation reveals new protein-protein interactions and new submodule relationships, providing novel information for mapping the functional organization of a complex.
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Affiliation(s)
- Mihaela E. Sardiu
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Joshua M. Gilmore
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Michael J. Carrozza
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Bing Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Michael P. Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- * E-mail:
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48
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He Y, Imhoff R, Sahu A, Radhakrishnan I. Solution structure of a novel zinc finger motif in the SAP30 polypeptide of the Sin3 corepressor complex and its potential role in nucleic acid recognition. Nucleic Acids Res 2009; 37:2142-52. [PMID: 19223330 PMCID: PMC2673417 DOI: 10.1093/nar/gkp051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment of the corepressor complex by transcription factors to specific regions of the genome is mediated by Sin3 as well as 10 distinct polypeptides that comprise the corepressor complex. Here we report the solution structure of a novel CCCH zinc finger (ZnF) motif in the SAP30 polypeptide, a key component of the corepressor complex. The structure represents a novel fold comprising two beta-strands and two alpha-helices with the zinc organizing center showing remote resemblance to the treble clef motif. In silico analysis of the structure revealed a highly conserved surface that is dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 ZnF motif indicated a strong preference for nucleic acid substrates. We propose that the SAP30 ZnF functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 corepressor complex. Our results also call into question the common assumption about the exclusion of DNA-binding core subunits within chromatin-modifying/remodeling complexes.
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Affiliation(s)
| | | | | | - Ishwar Radhakrishnan
- *To whom correspondence should be addressed. Tel: +1 847 467 1173; Fax: +1 847 467 6489;
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49
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van Oevelen C, Wang J, Asp P, Yan Q, Kaelin WG, Kluger Y, Dynlacht BD. A role for mammalian Sin3 in permanent gene silencing. Mol Cell 2008; 32:359-70. [PMID: 18995834 DOI: 10.1016/j.molcel.2008.10.015] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 08/19/2008] [Accepted: 10/17/2008] [Indexed: 12/29/2022]
Abstract
The multisubunit Sin3 corepressor complex regulates gene transcription through deacetylation of nucleosomes. However, the full range of Sin3 activities and targets is not well understood. Here, we have investigated genome-wide binding of mouse Sin3 and RBP2 as well as histone modifications and nucleosome positioning as a function of myogenic differentiation. Remarkably, we find that Sin3 complexes spread immediately downstream of the transcription start site on repressed and transcribed genes during differentiation. We show that RBP2 is part of a Sin3 complex and that on a subset of E2F4 target genes, the coordinated activity of Sin3 and RBP2 leads to deacetylation, demethylation, and repositioning of nucleosomes. Our work provides evidence for coordinated binding of Sin3, chromatin modifications, and chromatin remodeling within discrete regulatory regions, suggesting a model in which spreading of Sin3 binding is ultimately linked to permanent gene silencing on a subset of E2F4 target genes.
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Affiliation(s)
- Chris van Oevelen
- New York University School of Medicine, NYU Cancer Institute, 522 1st Avenue, New York, NY 10016, USA
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50
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Silveira AC, Hurst DR, Vaidya KS, Ayer DE, Welch DR. Over-expression of the BRMS1 family member SUDS3 does not suppress metastasis of human cancer cells. Cancer Lett 2008; 276:32-7. [PMID: 19070953 DOI: 10.1016/j.canlet.2008.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 10/20/2008] [Accepted: 10/22/2008] [Indexed: 10/21/2022]
Abstract
BRMS1 and SUDS3 are related members of SIN3-HDAC chromatin remodeling complexes. We hypothesized that they might have overlapping functions and that SUDS3 over-expression could compensate for BRMS1 deficiency. SUDS3 expression was ubiquitous in seven breast cell lines, regardless of metastatic potential. SUDS3 over-expression in BRMS1-non-expressing metastatic cells did not suppress metastasis, motility, osteopontin secretion, or EGF receptor expression, phenotypes associated with BRMS1-mediated metastasis suppression. This study demonstrates functional differences for BRMS1 family members and highlights how the composition of SIN3-HDAC (BRMS1/SUDS3) complexes uniquely affects protein expression and biological behaviors.
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Affiliation(s)
- Alexandra C Silveira
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35209, USA
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