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Fischer V, Hisler V, Scheer E, Lata E, Morlet B, Plassard D, Helmlinger D, Devys D, Tora L, Vincent S. SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells. Nucleic Acids Res 2022; 50:7972-7990. [PMID: 35871303 PMCID: PMC9371916 DOI: 10.1093/nar/gkac637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Coactivator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved coactivator complex. The core module scaffolds the entire SAGA complex and adopts a histone octamer-like structure, which consists of six histone-fold domain (HFD)-containing proteins forming three histone-fold (HF) pairs, to which the double HFD-containing SUPT3H adds one HF pair. Spt3, the yeast ortholog of SUPT3H, interacts genetically and biochemically with the TATA binding protein (TBP) and contributes to global RNA polymerase II (Pol II) transcription. Here we demonstrate that (i) SAGA purified from human U2OS or mouse embryonic stem cells (mESC) can assemble without SUPT3H, (ii) SUPT3H is not essential for mESC survival, but required for their growth and self-renewal, and (iii) the loss of SUPT3H from mammalian cells affects the transcription of only a specific subset of genes. Accordingly, in the absence of SUPT3H no major change in TBP accumulation at gene promoters was observed. Thus, SUPT3H is not required for the assembly of SAGA, TBP recruitment, or overall Pol II transcription, but plays a role in mESC growth and self-renewal. Our data further suggest that yeast and mammalian SAGA complexes contribute to transcription regulation by distinct mechanisms.
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Affiliation(s)
- Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Vincent Hisler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Elisabeth Lata
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Plateforme GenomEast, infrastructure France Génomique, 67404 Illkirch, France
| | | | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) , UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) , U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
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Early Pregnancy Exposure to Ambient Air Pollution among Late-Onset Preeclamptic Cases Is Associated with Placental DNA Hypomethylation of Specific Genes and Slower Placental Maturation. TOXICS 2021; 9:toxics9120338. [PMID: 34941772 PMCID: PMC8708250 DOI: 10.3390/toxics9120338] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/19/2023]
Abstract
Exposure to ambient air pollution during pregnancy has been associated with an increased risk of preeclampsia (PE). Some suggested mechanisms behind this association are changes in placental DNA methylation and gene expression. The objective of this study was to identify how early pregnancy exposure to ambient nitrogen oxides (NOx) among PE cases and normotensive controls influence DNA methylation (EPIC array) and gene expression (RNA-seq). The study included placentas from 111 women (29 PE cases/82 controls) in Scania, Sweden. First-trimester NOx exposure was assessed at the participants’ residence using a dispersion model and categorized via median split into high or low NOx. Placental gestational epigenetic age was derived from the DNA methylation data. We identified six differentially methylated positions (DMPs, q < 0.05) comparing controls with low NOx vs. cases with high NOx and 14 DMPs comparing cases and controls with high NOx. Placentas with female fetuses showed more DMPs (N = 309) than male-derived placentas (N = 1). Placentas from PE cases with high NOx demonstrated gestational age deceleration compared to controls with low NOx (p = 0.034). No differentially expressed genes (DEGs, q < 0.05) were found. In conclusion, early pregnancy exposure to NOx affected placental DNA methylation in PE, resulting in placental immaturity and showing sexual dimorphism.
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Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination. PLoS One 2015; 10:e0134709. [PMID: 26263547 PMCID: PMC4532415 DOI: 10.1371/journal.pone.0134709] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 07/13/2015] [Indexed: 01/17/2023] Open
Abstract
The recruitment of RNA polymerase II on a promoter is assisted by the assembly of basal transcriptional machinery in eukaryotes. The Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex plays an important role in transcription regulation in eukaryotes. However, even in the advent of genome sequencing of various plants, SAGA complex has been poorly defined for their components and roles in plant development and physiological functions. Computational analysis of Arabidopsis thaliana and Oryza sativa genomes for SAGA complex resulted in the identification of 17 to 18 potential candidates for SAGA subunits. We have further classified the SAGA complex based on the conserved domains. Phylogenetic analysis revealed that the SAGA complex proteins are evolutionary conserved between plants, yeast and mammals. Functional annotation showed that they participate not only in chromatin remodeling and gene regulation, but also in different biological processes, which could be indirect and possibly mediated via the regulation of gene expression. The in silico expression analysis of the SAGA components in Arabidopsis and O. sativa clearly indicates that its components have a distinct expression profile at different developmental stages. The co-expression analysis of the SAGA components suggests that many of these subunits co-express at different developmental stages, during hormonal interaction and in response to stress conditions. Quantitative real-time PCR analysis of SAGA component genes further confirmed their expression in different plant tissues and stresses. The expression of representative salt, heat and light inducible genes were affected in mutant lines of SAGA subunits in Arabidopsis. Altogether, the present study reveals expedient evidences of involvement of the SAGA complex in plant gene regulation and stress responses.
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Genetic variants in the ADAMTS13 and SUPT3H genes are associated with ADAMTS13 activity. Blood 2015; 125:3949-55. [DOI: 10.1182/blood-2015-02-629865] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/27/2015] [Indexed: 12/21/2022] Open
Abstract
Key Points
We identify rs41314453 as the strongest genetic predictor of ADAMTS13 activity, associated with a decrease of >20%. We present evidence of further independent associations with a common variant in SUPT3H, as well as 5 variants at the ADAMTS13 locus.
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Identification of SUPT3H as a novel 8q24/MYC partner in blastic plasmacytoid dendritic cell neoplasm with t(6;8)(p21;q24) translocation. Blood Cancer J 2015; 5:e301. [PMID: 25860292 PMCID: PMC4450326 DOI: 10.1038/bcj.2015.26] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Barutcu AR, Tai PWL, Wu H, Gordon JAR, Whitfield TW, Dobson JR, Imbalzano AN, Lian JB, van Wijnen AJ, Stein JL, Stein GS. The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter. Nucleic Acids Res 2014; 42:10360-72. [PMID: 25120271 PMCID: PMC4176362 DOI: 10.1093/nar/gku712] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/04/2014] [Accepted: 07/22/2014] [Indexed: 12/25/2022] Open
Abstract
Three-dimensional organization of chromatin is fundamental for transcriptional regulation. Tissue-specific transcriptional programs are orchestrated by transcription factors and epigenetic regulators. The RUNX2 transcription factor is required for differentiation of precursor cells into mature osteoblasts. Although organization and control of the bone-specific Runx2-P1 promoter have been studied extensively, long-range regulation has not been explored. In this study, we investigated higher-order organization of the Runx2-P1 promoter during osteoblast differentiation. Mining the ENCODE database revealed interactions between Runx2-P1 and Supt3h promoters in several non-mesenchymal human cell lines. Supt3h is a ubiquitously expressed gene located within the first intron of Runx2. These two genes show shared synteny across species from humans to sponges. Chromosome conformation capture analysis in the murine pre-osteoblastic MC3T3-E1 cell line revealed increased contact frequency between Runx2-P1 and Supt3h promoters during differentiation. This increase was accompanied by enhanced DNaseI hypersensitivity along with RUNX2 and CTCF binding at the Supt3h promoter. Furthermore, interplasmid-3C and luciferase reporter assays showed that the Supt3h promoter can modulate Runx2-P1 activity via direct association. Taken together, our data demonstrate physical proximity between Runx2-P1 and Supt3h promoters, consistent with their syntenic nature. Importantly, we identify the Supt3h promoter as a potential regulator of the bone-specific Runx2-P1 promoter.
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Affiliation(s)
- A Rasim Barutcu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Phillip W L Tai
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Hai Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jonathan A R Gordon
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Troy W Whitfield
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jason R Dobson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B Lian
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - André J van Wijnen
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Janet L Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S Stein
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
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Nakajima M, Takahashi A, Tsuji T, Karasugi T, Baba H, Uchida K, Kawabata S, Okawa A, Shindo S, Takeuchi K, Taniguchi Y, Maeda S, Kashii M, Seichi A, Nakajima H, Kawaguchi Y, Fujibayashi S, Takahata M, Tanaka T, Watanabe K, Kida K, Kanchiku T, Ito Z, Mori K, Kaito T, Kobayashi S, Yamada K, Takahashi M, Chiba K, Matsumoto M, Furukawa KI, Kubo M, Toyama Y, Ikegawa S. A genome-wide association study identifies susceptibility loci for ossification of the posterior longitudinal ligament of the spine. Nat Genet 2014; 46:1012-6. [PMID: 25064007 DOI: 10.1038/ng.3045] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/30/2014] [Indexed: 12/15/2022]
Abstract
Ossification of the posterior longitudinal ligament of the spine (OPLL) is a common spinal disorder among the elderly that causes myelopathy and radiculopathy. To identify genetic factors for OPLL, we performed a genome-wide association study (GWAS) in ∼8,000 individuals followed by a replication study using an additional ∼7,000 individuals. We identified six susceptibility loci for OPLL: 20p12.3 (rs2423294: P = 1.10 × 10(-13)), 8q23.1 (rs374810: P = 1.88 × 10(-13)), 12p11.22 (rs1979679: P = 4.34 × 10(-12)), 12p12.2 (rs11045000: P = 2.95 × 10(-11)), 8q23.3 (rs13279799: P = 1.28 × 10(-10)) and 6p21.1 (rs927485: P = 9.40 × 10(-9)). Analyses of gene expression in and around the loci suggested that several genes are involved in OPLL etiology through membranous and/or endochondral ossification processes. Our results bring new insight to the etiology of OPLL.
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Affiliation(s)
- Masahiro Nakajima
- 1] Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan. [2]
| | - Atsushi Takahashi
- 1] Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan. [2]
| | - Takashi Tsuji
- 1] Department of Orthopaedic Surgery, School of Medicine, Keio University, Tokyo, Japan. [2]
| | - Tatsuki Karasugi
- 1] Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan. [2] Department of Orthopaedic and Neuro-Musculoskeletal Surgery, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hisatoshi Baba
- Department of Orthopaedics and Rehabilitation Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Kenzo Uchida
- Department of Orthopaedics and Rehabilitation Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Shigenori Kawabata
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Atsushi Okawa
- Department of Orthopaedic Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigeo Shindo
- Department of Orthopedics, Kudanzaka Hospital, Tokyo, Japan
| | - Kazuhiro Takeuchi
- Department of Orthopaedic Surgery, National Okayama Medical Center, Okayama, Japan
| | - Yuki Taniguchi
- Department of Orthopaedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shingo Maeda
- Department of Medical Joint Materials, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Masafumi Kashii
- Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Seichi
- Department of Orthopedics, Jichi Medical University, Shimotsuke, Japan
| | - Hideaki Nakajima
- Department of Orthopaedics and Rehabilitation Medicine, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | | | - Shunsuke Fujibayashi
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Takahata
- Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshihiro Tanaka
- Department of Orthopaedic Surgery, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kei Watanabe
- Department of Orthopaedic Surgery, Niigata University Medical and Dental General Hospital, Niigata, Japan
| | - Kazunobu Kida
- Department of Orthopaedic Surgery, Kochi Medical School, Kochi, Japan
| | - Tsukasa Kanchiku
- Department of Orthopedic Surgery, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Zenya Ito
- Department of Orthopedics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kanji Mori
- Department of Orthopaedic Surgery, Shiga University of Medical Science, Otsu, Japan
| | - Takashi Kaito
- Department of Orthopaedic Surgery, National Hospital Organization Osaka Minami Medical Center, Osaka, Japan
| | - Sho Kobayashi
- Department of Orthopaedic Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kei Yamada
- Department of Orthopaedic Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Masahito Takahashi
- Department of Orthopaedic Surgery, Kyorin University School of Medicine, Tokyo, Japan
| | - Kazuhiro Chiba
- 1] Department of Orthopaedic Surgery, School of Medicine, Keio University, Tokyo, Japan. [2]
| | - Morio Matsumoto
- Department of Orthopaedic Surgery, School of Medicine, Keio University, Tokyo, Japan
| | - Ken-Ichi Furukawa
- Department of Pharmacology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yoshiaki Toyama
- Department of Orthopaedic Surgery, School of Medicine, Keio University, Tokyo, Japan
| | | | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
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Novel candidate genes for 46,XY gonadal dysgenesis identified by a customized 1 M array-CGH platform. Eur J Med Genet 2013; 56:661-8. [DOI: 10.1016/j.ejmg.2013.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/03/2013] [Indexed: 12/14/2022]
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Spivak AT, Stormo GD. ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res 2011; 40:D162-8. [PMID: 22140105 PMCID: PMC3245033 DOI: 10.1093/nar/gkr1180] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Saccharomyces cerevisiae is a primary model for studies of transcriptional control, and the specificities of most yeast transcription factors (TFs) have been determined by multiple methods. However, it is unclear which position weight matrices (PWMs) are most useful; for the roughly 200 TFs in yeast, there are over 1200 PWMs in the literature. To address this issue, we created ScerTF, a comprehensive database of 1226 motifs from 11 different sources. We identified a single matrix for each TF that best predicts in vivo data by benchmarking matrices against chromatin immunoprecipitation and TF deletion experiments. We also used in vivo data to optimize thresholds for identifying regulatory sites with each matrix. To correct for biases from different methods, we developed a strategy to combine matrices. These aligned matrices outperform the best available matrix for several TFs. We used the matrices to predict co-occurring regulatory elements in the genome and identified many known TF combinations. In addition, we predict new combinations and provide evidence of combinatorial regulation from gene expression data. The database is available through a web interface at http://ural.wustl.edu/ScerTF. The site allows users to search the database with a regulatory site or matrix to identify the TFs most likely to bind the input sequence.
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Affiliation(s)
- Aaron T Spivak
- Department of Genetics, Washington University Medical School, St Louis, MO, USA
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Nelson TJ, Alkon DL. Protection against beta-amyloid-induced apoptosis by peptides interacting with beta-amyloid. J Biol Chem 2007; 282:31238-49. [PMID: 17761669 DOI: 10.1074/jbc.m705558200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
beta-Amyloid peptide produces apoptosis in neurons at micromolar concentrations, but the mechanism by which beta-amyloid exerts its toxic effect is unknown. The normal biological function of beta-amyloid is also unknown. We used phage display, co-precipitation, and mass spectrometry to examine the protein-protein interactions of beta-amyloid in normal rabbit brain in order to identify the biochemical receptors for beta-amyloid. beta-Amyloid was found to bind primarily to proteins involved in low density lipoprotein and cholesterol transport and metabolism, including sortilin, endoplasmic reticulum-Golgi intermediate compartment 2 (ERGIC2), ERGIC-53, steroid 5alpha-reductase, and apolipoprotein B. beta-Amyloid also bound to the C-reactive protein precursor, a protein involved in inflammation, and to 14-3-3, a protein that regulates glycogen synthase kinase-3beta, the kinase involved in tau phosphorylation. Of eight synthetic peptides identified as targets of beta-amyloid, three were found to be effective blockers of the toxic effect of beta-amyloid on cultured neuronal cells. These peptides bound to the hydrophobic region (residues 17-21) or to the nearby protein kinase C pseudo-phosphorylation site (residues 26-30) of beta-amyloid, suggesting that these may be the most critical regions for beta-amyloid effector action and for aggregation. Peptides or other small molecules that bind to this region may protect against beta-amyloid toxic effect by competitively blocking its ability to bind beta-amyloid effector proteins such as sortilin and 14-3-3.
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Affiliation(s)
- Thomas J Nelson
- Blanchette Rockefeller Neurosciences Institute, Rockville, Maryland 20850, USA.
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11
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Verdone L, Caserta M, Di Mauro E. Role of histone acetylation in the control of gene expression. Biochem Cell Biol 2005; 83:344-53. [PMID: 15959560 DOI: 10.1139/o05-041] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Histone proteins play structural and functional roles in all nuclear processes. They undergo different types of covalent modifications, defined in their ensemble as epigenetic because changes in DNA sequences are not involved. Histone acetylation emerges as a central switch that allows interconversion between permissive and repressive chromatin domains in terms of transcriptional competence. The mechanisms underlying the histone acetylation-dependent control of gene expression include a direct effect on the stability of nucleosomal arrays and the creation of docking sites for the binding of regulatory proteins. Histone acetyltransferases and deacetylases are, respectively, the enzymes devoted to the addition and removal of acetyl groups from lysine residues on the histone N-terminal tails. The enzymes exert fundamental roles in developmental processes and their deregulation has been linked to the progression of diverse human disorders, including cancer.
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Affiliation(s)
- Loredana Verdone
- Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, Rome, Italy
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Glusman G, Kaur A, Hood L, Rowen L. An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution. BMC Evol Biol 2004; 4:43. [PMID: 15527507 PMCID: PMC533870 DOI: 10.1186/1471-2148-4-43] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Accepted: 11/04/2004] [Indexed: 11/10/2022] Open
Abstract
Background The runt domain transcription factors are key regulators of developmental processes in bilaterians, involved both in cell proliferation and differentiation, and their disruption usually leads to disease. Three runt domain genes have been described in each vertebrate genome (the RUNX gene family), but only one in other chordates. Therefore, the common ancestor of vertebrates has been thought to have had a single runt domain gene. Results Analysis of the genome draft of the fugu pufferfish (Takifugu rubripes) reveals the existence of a fourth runt domain gene, FrRUNT, in addition to the orthologs of human RUNX1, RUNX2 and RUNX3. The tiny FrRUNT packs six exons and two putative promoters in just 3 kb of genomic sequence. The first exon is located within an intron of FrSUPT3H, the ortholog of human SUPT3H, and the first exon of FrSUPT3H resides within the first intron of FrRUNT. The two gene structures are therefore "interlocked". In the human genome, SUPT3H is instead interlocked with RUNX2. FrRUNT has no detectable ortholog in the genomes of mammals, birds or amphibians. We consider alternative explanations for an apparent contradiction between the phylogenetic data and the comparison of the genomic neighborhoods of human and fugu runt domain genes. We hypothesize that an ancient RUNT locus was lost in the tetrapod lineage, together with FrFSTL6, a member of a novel family of follistatin-like genes. Conclusions Our results suggest that the runt domain family may have started expanding in chordates much earlier than previously thought, and exemplify the importance of detailed analysis of whole-genome draft sequence to provide new insights into gene evolution.
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Affiliation(s)
- Gustavo Glusman
- Institute for Systems Biology, 1441 N 34th St., Seattle, WA 98103, USA
| | - Amardeep Kaur
- Institute for Systems Biology, 1441 N 34th St., Seattle, WA 98103, USA
| | - Leroy Hood
- Institute for Systems Biology, 1441 N 34th St., Seattle, WA 98103, USA
| | - Lee Rowen
- Institute for Systems Biology, 1441 N 34th St., Seattle, WA 98103, USA
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13
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Bhaumik SR, Green MR. Differential requirement of SAGA components for recruitment of TATA-box-binding protein to promoters in vivo. Mol Cell Biol 2002; 22:7365-71. [PMID: 12370284 PMCID: PMC135674 DOI: 10.1128/mcb.22.21.7365-7371.2002] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The multisubunit Saccharomyces cerevisiae SAGA (Spt-Ada-Gcn5-acetyltransferase) complex is required to activate transcription of a subset of RNA polymerase II-dependent genes. However, the contribution of each SAGA component to transcription activation is relatively unknown. Here, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation assay, we have systematically analyzed the role of SAGA components in the recruitment of TATA-box binding protein (TBP) to SAGA-dependent promoters. We show that recruitment of TBP is diminished at a number of SAGA-dependent promoters in ada1delta, spt7delta, and spt20delta null mutants, consistent with previous biochemical data suggesting that these components maintain the integrity of the SAGA complex. We also find that Spt3p is generally required for TBP binding to SAGA-dependent promoters, consistent with biochemical and genetic experiments, suggesting that Spt3p interacts with and recruits TBP to the core promoter. By contrast, Spt8p, which has been proposed to be required for the interaction between Spt3p and TBP, is required for TBP binding at only a subset of SAGA-dependent promoters. Ada2p and Ada3p are both required for TBP recruitment to Gcn5p-dependent promoters, supporting previous biochemical data that Ada2p and Ada3p are required for the histone acetyltransferase activity of Gcn5p. Finally, our results suggest that TBP-associated-factor components of SAGA are differentially required for TBP binding to SAGA-dependent promoters. In summary, we show that SAGA-dependent promoters require different combinations of SAGA components for TBP recruitment, revealing a complex combinatorial network for transcription activation in vivo.
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Affiliation(s)
- Sukesh R Bhaumik
- Howard Hughes Medical Institute, Programs in Gene Expression and Function and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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14
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Abstract
The Saccharomyces cerevisiae SAGA complex is required for the normal transcription of a large number of genes. Complex integrity depends on three core subunits, Spt7, Spt20, and Ada1. We have investigated the role of Spt7 in the assembly and function of SAGA. Our results show that Spt7 is important in controlling the levels of the other core subunits and therefore of SAGA. In addition, partial SAGA complexes containing Spt7 can be assembled in the absence of both Spt20 and Ada1. Through biochemical and genetic analyses of a series of spt7 deletion mutants, we have identified a region of Spt7 required for interaction with the SAGA component Spt8. An adjacent Spt7 domain was found to be required for a processed form of Spt7 that is present in a previously identified altered form of SAGA called SLIK, SAGA(alt), or SALSA. Analysis of an spt7 mutant with greatly reduced levels of SLIK/SAGA(alt)/SALSA suggests a subtle role for this complex in transcription that may be redundant with a subset of SAGA functions.
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Affiliation(s)
- Pei-Yun Jenny Wu
- Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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15
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Laprade L, Boyartchuk VL, Dietrich WF, Winston F. Spt3 plays opposite roles in filamentous growth in Saccharomyces cerevisiae and Candida albicans and is required for C. albicans virulence. Genetics 2002; 161:509-19. [PMID: 12072450 PMCID: PMC1462142 DOI: 10.1093/genetics/161.2.509] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spt3 of Saccharomyces cerevisiae is required for the normal transcription of many genes in vivo. Past studies have shown that Spt3 is required for both mating and sporulation, two events that initiate when cells are at G(1)/START. We now show that Spt3 is needed for two other events that begin at G(1)/START, diploid filamentous growth and haploid invasive growth. In addition, Spt3 is required for normal expression of FLO11, a gene required for filamentous growth, although this defect is not the sole cause of the spt3Delta/spt3Delta filamentous growth defect. To extend our studies of Spt3's role in filamentous growth to the pathogenic yeast Candida albicans, we have identified the C. albicans SPT3 gene and have studied its role in C. albicans filamentous growth and virulence. Surprisingly, C. albicans spt3Delta/spt3Delta mutants are hyperfilamentous, the opposite phenotype observed for S. cerevisiae spt3Delta/spt3Delta mutants. Furthermore, C. albicans spt3Delta/spt3Delta mutants are avirulent in mice. These experiments demonstrate that Spt3 plays important but opposite roles in filamentous growth in S. cerevisiae and C. albicans.
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Affiliation(s)
- Lisa Laprade
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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16
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Larschan E, Winston F. The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev 2001; 15:1946-56. [PMID: 11485989 PMCID: PMC312753 DOI: 10.1101/gad.911501] [Citation(s) in RCA: 251] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Previous studies demonstrated that the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex facilitates the binding of TATA-binding protein (TBP) during transcriptional activation of the GAL1 gene of Saccharomyces cerevisiae. TBP binding was shown to require the SAGA components Spt3 and Spt20/Ada5, but not the SAGA component Gcn5. We have now examined whether SAGA is directly required as a coactivator in vivo by using chromatin immunoprecipitation analysis. Our results demonstrate that SAGA is physically recruited in vivo to the upstream activation sequence (UAS) regions of the galactose-inducible GAL genes. This recruitment is dependent on both induction by galactose and the Gal4 activation domain. Furthermore, we demonstrate that another well-characterized activator, Gal4-VP16, also recruits SAGA in vivo. Finally, we provide evidence that a specific interaction between Spt3 and TBP in vivo is important for Gal4 transcriptional activation at a step after SAGA recruitment. These results, taken together with previous studies, demonstrate a dependent pathway for the recruitment of TBP to GAL gene promoters consisting of the recruitment of SAGA by Gal4 and the subsequent recruitment of TBP by SAGA.
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Affiliation(s)
- E Larschan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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17
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Abstract
The state of chromatin (the packaging of DNA in eukaryotes) has long been recognized to have major effects on levels of gene expression, and numerous chromatin-altering strategies-including ATP-dependent remodeling and histone modification-are employed in the cell to bring about transcriptional regulation. Of these, histone acetylation is one of the best characterized, as recent years have seen the identification and further study of many histone acetyltransferase (HAT) proteins and their associated complexes. Interestingly, most of these proteins were previously shown to have coactivator or other transcription-related functions. Confirmed and putative HAT proteins have been identified from various organisms from yeast to humans, and they include Gcn5-related N-acetyltransferase (GNAT) superfamily members Gcn5, PCAF, Elp3, Hpa2, and Hat1: MYST proteins Sas2, Sas3, Esa1, MOF, Tip60, MOZ, MORF, and HBO1; global coactivators p300 and CREB-binding protein; nuclear receptor coactivators SRC-1, ACTR, and TIF2; TATA-binding protein-associated factor TAF(II)250 and its homologs; and subunits of RNA polymerase III general factor TFIIIC. The acetylation and transcriptional functions of these HATs and the native complexes containing them (such as yeast SAGA, NuA4, and possibly analogous human complexes) are discussed. In addition, some of these HATs are also known to modify certain nonhistone transcription-related proteins, including high-mobility-group chromatin proteins, activators such as p53, coactivators, and general factors. Thus, we also detail these known factor acetyltransferase (FAT) substrates and the demonstrated or potential roles of their acetylation in transcriptional processes.
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Affiliation(s)
- D E Sterner
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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18
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Winston F, Sudarsanam P. The SAGA of Spt proteins and transcriptional analysis in yeast: past, present, and future. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:553-61. [PMID: 10384320 DOI: 10.1101/sqb.1998.63.553] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- F Winston
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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