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Zhuang Z, Li S, Ding R, Yang M, Zheng E, Yang H, Gu T, Xu Z, Cai G, Wu Z, Yang J. Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations. PLoS One 2019; 14:e0218263. [PMID: 31188900 PMCID: PMC6561594 DOI: 10.1371/journal.pone.0218263] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/29/2019] [Indexed: 01/07/2023] Open
Abstract
Loin muscle area (LMA) and loin muscle depth (LMD) are important traits influencing the production performance of breeding pigs. However, the genetic architecture of these two traits is still poorly understood. To discern the genetic architecture of LMA and LMD, a material consisting of 6043 Duroc pigs belonging to two populations with different genetic backgrounds was collected and applied in genome-wide association studies (GWAS) with a genome-wide distributed panel of 50K single nucleotide polymorphisms (SNPs). To improve the power of detection for common SNPs, we conducted a meta-analysis in these two pig populations and uncovered additional significant SNPs. As a result, we identified 75 significant SNPs for LMA and LMD on SSC6, 7, 12, 16, and 18. Among them, 25 common SNPs were associated with LMA and LMD. One pleiotropic quantitative trait locus (QTL), which was located on SSC7 with a 283 kb interval, was identified to affect LMA and LMD. Marker ALGA0040260 is a key SNP for this QTL, explained 1.77% and 2.48% of the phenotypic variance for LMA and LMD, respectively. Another genetic region on SSC16 (709 kb) was detected and displayed prominent association with LMA and the peak SNP, WU_10.2_16_35829257, contributed 1.83% of the phenotypic variance for LMA. Further bioinformatics analysis determined eight promising candidate genes (GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1) with functions in glutathione metabolism, adipose and muscle tissues development and lipid metabolism. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. The findings further advance our understanding and help elucidate the genetic architecture of LMA, LMD and growth-related traits in pigs.
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Affiliation(s)
- Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Shaoyun Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Huaqiang Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
- * E-mail: (JY); (ZW)
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
- * E-mail: (JY); (ZW)
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Song Y, Nahrgang J, Tollefsen KE. Transcriptomic analysis reveals dose-dependent modes of action of benzo(a)pyrene in polar cod (Boreogadus saida). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:176-189. [PMID: 30408666 DOI: 10.1016/j.scitotenv.2018.10.261] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/15/2018] [Accepted: 10/19/2018] [Indexed: 06/08/2023]
Abstract
Polar cod (Boreogadus saida) has been used as a model Arctic species for hazard assessment of environmental stressors such as polycyclic aromatic hydrocarbons (PAHs). However, most of the PAH studies using polar cod rely on targeted biomarker-based analysis thus may not adequately address the complexity of the toxic mechanisms of the stressors. The present study was performed to develop a broad-content transcriptomic platform for polar cod and apply it for understanding the toxic mechanisms of a model PAH, benzo(a)pyrene (BaP). Hepatic transcriptional analysis using a combination of high-density polar cod oligonucleotide microarray and quantitative real-time RT-PCR was conducted to characterize the stress responses in polar cod after 14d repeated dietary exposure to 0.4 (Low) and 20.3 μg/g fish/feeding (High) BaP doses. Bile metabolic analysis was performed to identify the storage of a key BaP hepatic biotransformation product, 3-hydroxybenzo(a)pyrene (3-OH-BaP). The results clearly showed that 3-OH-BaP was detected in the bile of polar cod after both Low and High BaP exposure. Dose-dependent hepatic stress responses were identified, with Low BaP suppressing genes involved in the defense mechanisms and High BaP inducing genes associated with these pathways. The results suggested that activation of the aryl hydrocarbon receptor signaling, induction of oxidative stress, DNA damage and apoptosis were the common modes of action (MoA) of BaP between polar cod or other vertebrates, whereas induction of protein degradation and disturbance of mitochondrial functions were proposed as novel MoAs. Furthermore, conceptual toxicity pathways were proposed for BaP-mediated effects in Arctic fish. The present study has for the first time reported a transcriptome-wide analysis using a polar cod-specific microarray and suggested novel MoAs of BaP. The analytical tools, bioinformatics solutions and mechanistic knowledge generated by this study may facilitate mechanistically-based hazard assessment of environmental stressors in the Arctic using this important fish as a model species.
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Affiliation(s)
- You Song
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Gaustadalléen 21, N-0349 Oslo, Norway.
| | - Jasmine Nahrgang
- UiT The Arctic University of Norway, Faculty of Biosciences, Fisheries and Economics, Dept. of Arctic and Marine Biology, N-9037 Tromsø, Norway
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Section of Ecotoxicology and Risk Assessment, Gaustadalléen 21, N-0349 Oslo, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, Dept. for Environmental Sciences, Post box 5003, N-1432 Ås, Norway.
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3
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Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I. Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. eLife 2017; 6:e30395. [PMID: 29111974 PMCID: PMC5690282 DOI: 10.7554/elife.30395] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-interaction domain (CTID) in TAF13, which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
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Affiliation(s)
- Kapil Gupta
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
- European Molecular Biology LaboratoryGrenobleFrance
| | | | - Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Anna L Chambers
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
| | | | - Juan Zou
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Ima Obong-Ebong
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Eaazhisai Kandiah
- European Molecular Biology LaboratoryGrenobleFrance
- Institut de Biologie Structurale IBSGrenobleFrance
| | | | - Adam Round
- European Molecular Biology LaboratoryGrenobleFrance
| | - Eric Forest
- Institut de Biologie Structurale IBSGrenobleFrance
| | - Petr Man
- Institute of MicrobiologyThe Czech Academy of SciencesVestecCzech Republic
- BioCeV - Faculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Ernest D Laue
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Juri Rappsilber
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Carol V Robinson
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Làszlò Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Imre Berger
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
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Wang J, Zhao S, He W, Wei Y, Zhang Y, Pegg H, Shore P, Roberts SGE, Deng W. A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner. J Biol Chem 2017; 292:11873-11885. [PMID: 28539359 DOI: 10.1074/jbc.m116.770412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/23/2017] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase II (pol II) is required for the transcription of all protein-coding genes and as such represents a major enzyme whose activity is tightly regulated. Transcriptional initiation therefore requires numerous general transcriptional factors and cofactors that associate with pol II at the core promoter to form a pre-initiation complex. Transcription factor IIA (TFIIA) is a general cofactor that binds TFIID and stabilizes the TFIID-DNA complex during transcription initiation. Previous studies showed that TFIIA can make contact with the DNA sequence upstream or downstream of the TATA box, and that the region bound by TFIIA could overlap with the elements recognized by another factor, TFIIB, at adenovirus major late core promoter. Whether core promoters contain a DNA motif recognized by TFIIA remains unknown. Here we have identified a core promoter element upstream of the TATA box that is recognized by TFIIA. A search of the human promoter database revealed that many natural promoters contain a TFIIA recognition element (IIARE). We show that the IIARE enhances TFIIA-promoter binding and enhances the activity of TATA-containing promoters, but represses or activates promoters that lack a TATA box. Chromatin immunoprecipitation assays revealed that the IIARE activates transcription by increasing the recruitment of pol II, TFIIA, TAF4, and P300 at TATA-dependent promoters. These findings extend our understanding of the role of TFIIA in transcription, and provide new insights into the regulatory mechanism of core promoter elements in gene transcription by pol II.
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Affiliation(s)
- Juan Wang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Shasha Zhao
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Wei He
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Yun Wei
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Yang Zhang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Henry Pegg
- School of Biological Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Paul Shore
- School of Biological Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Stefan G E Roberts
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom.
| | - Wensheng Deng
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China.
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5
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Genetic code expansion for multiprotein complex engineering. Nat Methods 2016; 13:997-1000. [DOI: 10.1038/nmeth.4032] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 09/02/2016] [Indexed: 12/21/2022]
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Feigerle JT, Weil PA. The C Terminus of the RNA Polymerase II Transcription Factor IID (TFIID) Subunit Taf2 Mediates Stable Association of Subunit Taf14 into the Yeast TFIID Complex. J Biol Chem 2016; 291:22721-22740. [PMID: 27587401 DOI: 10.1074/jbc.m116.751107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/31/2016] [Indexed: 12/22/2022] Open
Abstract
The evolutionarily conserved RNA polymerase II transcription factor D (TFIID) complex is composed of TATA box-binding protein (TBP) and 13 TBP-associated factors (Tafs). The mechanisms by which many Taf subunits contribute to the essential function of TFIID are only poorly understood. To address this gap in knowledge, we present the results of a molecular genetic dissection of the TFIID subunit Taf2. Through systematic site-directed mutagenesis, we have discovered 12 taf2 temperature-sensitive (ts) alleles. Two of these alleles display growth defects that can be strongly suppressed by overexpression of the yeast-specific TFIID subunit TAF14 but not by overexpression of any other TFIID subunit. In Saccharomyces cerevisiae, Taf14 is also a constituent of six other transcription-related complexes, making interpretation of its role in each of these complexes difficult. Although Taf14 is not conserved as a TFIID subunit in metazoans, it is conserved through its chromatin-binding YEATS domain. Based on the Taf2-Taf14 genetic interaction, we demonstrate that Taf2 and Taf14 directly interact and mapped the Taf2-Taf14 interaction domains. We used this information to identify a Taf2 separation-of-function variant (Taf2-ΔC). Although Taf2-ΔC no longer interacts with Taf14 in vivo or in vitro, it stably incorporates into the TFIID complex. In addition, purified Taf2-ΔC mutant TFIID is devoid of Taf14, making this variant a powerful reagent for determining the role of Taf14 in TFIID function. Furthermore, we characterized the mechanism through which Taf14 suppresses taf2ts alleles, shedding light on how Taf2-Taf14 interaction contributes to TFIID complex organization and identifying a potential role for Taf14 in mediating TFIID-chromatin interactions.
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Affiliation(s)
- Jordan T Feigerle
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615
| | - P Anthony Weil
- From the Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615
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7
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Hložková K, Matěnová M, Žáčková P, Strnad H, Hršelová H, Hroudová M, Kotrba P. Characterization of three distinct metallothionein genes of the Ag-hyperaccumulating ectomycorrhizal fungus Amanita strobiliformis. Fungal Biol 2016; 120:358-69. [DOI: 10.1016/j.funbio.2015.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/19/2015] [Accepted: 11/12/2015] [Indexed: 01/07/2023]
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8
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Layer JH, Weil PA. Direct TFIIA-TFIID protein contacts drive budding yeast ribosomal protein gene transcription. J Biol Chem 2013; 288:23273-94. [PMID: 23814059 DOI: 10.1074/jbc.m113.486829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have previously shown that yeast TFIID provides coactivator function on the promoters of ribosomal protein-encoding genes (RPGs) by making direct contact with the transactivator repressor activator protein 1 (Rap1). Further, our structural studies of assemblies generated with purified Rap1, TFIID, and TFIIA on RPG enhancer-promoter DNA indicate that Rap1-TFIID interaction induces dramatic conformational rearrangements of enhancer-promoter DNA and TFIID-bound TFIIA. These data indicate a previously unknown yet critical role for yeast TFIIA in the integration of activator-TFIID contacts with promoter conformation and downstream preinitiation complex formation and/or function. Here we describe the use of systematic mutagenesis to define how specific TFIIA contacts contribute to these processes. We have verified that TFIIA is required for RPG transcription in vivo and in vitro, consistent with the existence of a critical Rap1-TFIIA-TFIID interaction network. We also identified essential points of contact for TFIIA and Rap1 within the Rap1 binding domain of the Taf4 subunit of TFIID. These data suggest a mechanism for how interactions between TFIID, TFIIA, and Rap1 contribute to the high rate of transcription initiation seen on RPGs in vivo.
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Affiliation(s)
- Justin H Layer
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232-0615, USA
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Gentile A, Da Cruz P, Tavares RG, Krug-Baldacin MG, Menossi M. Molecular characterization of ScTFIIAgamma, encoding the putative TFIIA small subunit from sugarcane. PLANT CELL REPORTS 2010; 29:857-864. [PMID: 20480367 DOI: 10.1007/s00299-010-0871-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/27/2010] [Accepted: 05/05/2010] [Indexed: 05/29/2023]
Abstract
Transcription mediated by RNA polymerase II depends on a set of different transcription factors to form the pre-initiation complex. TFIIA is involved in the construction of this complex and increases the affinity of TBP for the DNA union region in vitro. In this study, we characterized the ScTFIIAgamma gene, which encodes a homolog of the smaller subunit (gamma) of transcription factor TFIIA in sugarcane. RNA blot analysis showed that ScTFIIAgamma transcripts accumulate in all tissues evaluated, with higher levels in leaf roll and flowers. In situ hybridization showed that ScTFIIAgamma was expressed in different cells of the reproductive meristem. In sugarcane plantlets, methyl jasmonate and absicic acid treatments as well as phosphate starvation had no influence on ScTFIIAgamma transcript accumulation. The subcelullar localization assay demonstrates that ScTFIIAgamma protein is directed to the cell nucleus. The phylogenetic analysis, the expression in several tissues and under different treatments and the nuclear localization are in line with the putative role of ScTFIIAgamma as a subunit of basal transcription factor.
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Affiliation(s)
- Agustina Gentile
- Laboratório de Genoma Funcional, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, 13083-875 Campinas, São Paulo 6109, Brazil
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Ohtsuki K, Kasahara K, Shirahige K, Kokubo T. Genome-wide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters. Nucleic Acids Res 2009; 38:1805-20. [PMID: 20026583 PMCID: PMC2847235 DOI: 10.1093/nar/gkp1172] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In Saccharomyces cerevisiae, TFIID and SAGA principally mediate transcription of constitutive housekeeping genes and stress-inducible genes, respectively, by delivering TBP to the core promoter. Both are multi-protein complexes composed of 15 and 20 subunits, respectively, five of which are common and which may constitute a core sub-module in each complex. Although genome-wide gene expression studies have been conducted extensively in several TFIID and/or SAGA mutants, there are only a limited number of studies investigating genome-wide localization of the components of these two complexes. Specifically, there are no previous reports on localization of a complete set of Tafs and the effects of taf mutations on localization. Here, we examine the localization profiles of a complete set of Tafs, Gcn5, Bur6/Ncb2, Sua7, Tfa2, Tfg1, Tfb3 and Rpb1, on chromosomes III, IV and V by chromatin immunoprecipitation (ChIP)-chip analysis in wild-type and taf1-T657K mutant strains. In addition, we conducted conventional and sequential ChIP analysis of several ribosomal protein genes (RPGs) and non-RPGs. Intriguingly, the results revealed a novel relationship between TFIIB and NC2, simultaneous co-localization of SAGA and TFIID on RPG promoters, specific effects of taf1 mutation on Taf2 occupancy, and an indirect evidence for the existence of different TFIID conformations.
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Affiliation(s)
- Kazushige Ohtsuki
- Division of Molecular and Cellular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan
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Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations. Psychiatr Genet 2009; 19:64-71. [PMID: 19672138 DOI: 10.1097/ypg.0b013e3283207ff6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
OBJECTIVES Genomic copy number variations (CNVs) are a major form of variation in the human genome and play an etiologic role in several neuropsychiatric diseases. Tandem repeats, particularly with long (>50 bp) repeat units, are a relatively common yet underexplored type of CNV that may significantly contribute to human genomic variation and disease risk. We therefore carried out a pilot experiment to explore the potential role of long tandem repeats as risk factors in psychiatric disorders. METHODS A bacterial artificial chromosome-based array comparative genomic hybridization (aCGH) platform was used to examine CNVs in genomic DNA from 34 probands with schizophrenia or schizoaffective disorder. RESULTS The aCGH screen detected an apparent deletion on 5p15.1 in two probands, caused by the presence in each proband of two low copy number (short) alleles of a tandem repeat that ranges in length from fewer than 10 to greater than 50 3.4 kb units in the population examined. Short alleles partially segregate with schizophrenia in a small number of families, though linkage was not significant. An association study showed no significant difference in repeat length between 406 schizophrenia cases and 392 controls. CONCLUSION Although we did not demonstrate a relationship between the 5p15.1 repeat and schizophrenia, our results illustrate that long tandem repeats represent an intriguing type of genetic variation that have not been studied in earlier connection with psychiatric illness. aCGH can detect a small subset of these repeats, but systematic investigation will require the development of specific arrays and improved analytical methods.
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Masson P, Leimgruber E, Creton S, Collart MA. The dual control of TFIIB recruitment by NC2 is gene specific. Nucleic Acids Res 2007; 36:539-49. [PMID: 18048413 PMCID: PMC2241854 DOI: 10.1093/nar/gkm1078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Negative co-factor 2 (NC2) is a conserved eukaryotic complex composed of two subunits, NC2alpha (Drap1) and NC2beta (Dr1) that associate through a histone-fold motif. In this work, we generated mutants of NC2, characterized target genes for these mutants and studied the assembly of NC2 and general transcription factors on target promoters. We determined that the two NC2 subunits mostly function together to be recruited to DNA and regulate gene expression. We found that NC2 strongly controls promoter association of TFIIB, both negatively and positively. We could attribute the gene-specific repressor effect of NC2 on TFIIB to the C-terminal domain of NC2beta, and define that it requires ORF sequences of the target gene. In contrast, the positive function of NC2 on TFIIB targets is more general and requires adequate levels of the NC2 histone-fold heterodimer on promoters. Finally, we determined that NC2 becomes limiting for TATA-binding protein (TBP) association with a heat inducible promoter under heat stress. This study demonstrates an important positive role of NC2 for formation of the pre-initiation complex on promoters, under normal conditions through control of TFIIB, or upon activation by stress via control of TBP.
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Affiliation(s)
- Patrick Masson
- Department of Microbiology and Molecular Medicine, CMU, 1 rue Michel Servet 1211, Geneva 4, Switzerland
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Iyer-Pascuzzi AS, McCouch SR. Recessive resistance genes and the Oryza sativa-Xanthomonas oryzae pv. oryzae pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:731-9. [PMID: 17601161 DOI: 10.1094/mpmi-20-7-0731] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Though recessive resistance is well-studied in viral systems, little is understood regarding the phenomenon in plant-bacterial interactions. The Oryza sativa-Xanthomonas oryzae pv. orzyae pathosystem provides an excellent opportunity to examine recessive resistance in plant-bacterial interactions, in which nine of 30 documented resistance (R) genes are recessively inherited. Infestations of X. oryzae pv. oryzae, the causal agent of bacterial blight, result in significant crop loss and damage throughout South and Southeast Asia. Two recently cloned novel recessive R genes, xa5 and xa13, have yielded insights to this system. Like their viral counterparts, these bacterial recessive R gene products do not conform to the five commonly described classes of R proteins. New findings suggest that such genes may more aptly be viewed as mutations in dominant susceptibility alleles and may also function in a gene-for-gene manner. In this review, we discuss recent accomplishments in the understanding of recessively inherited R genes in the rice-bacterial blight pathosystem and suggest a new model for the function of recessive resistance in plant-bacterial interactions.
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Fossey SC, Vnencak-Jones CL, Olsen NJ, Sriram S, Garrison G, Deng X, Crooke PS, Aune TM. Identification of molecular biomarkers for multiple sclerosis. J Mol Diagn 2007; 9:197-204. [PMID: 17384211 PMCID: PMC1867435 DOI: 10.2353/jmoldx.2007.060147] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multiple sclerosis is a demyelinating disease of the central nervous system with a presumed autoimmune etiology. Previous microarray analyses identified conserved gene expression signatures in peripheral blood mononuclear cells of patients with autoimmune diseases. We used quantitative real-time polymerase chain reaction analysis to identify a minimum number of genes of which transcript levels discriminated multiple sclerosis patients from patients with other chronic diseases and from controls. We used a computer program to search quantitative transcript levels to identify optimum ratios that distinguished among the different categories. A combination of a 4-ratio equation using expression levels of five genes segregated the multiple sclerosis cohort (n=55) from the control cohort (n=49) with a sensitivity of 91% and specificity of 98%. When autoimmune and other chronic disease groups were included (n=78), this discriminator still performed with a sensitivity of 79% and a specificity of 87%. This approach may have diagnostic utility not only for multiple sclerosis but also for other clinically complex autoimmune diseases.
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Affiliation(s)
- Sallyanne C Fossey
- Department of Pathology, Vanderbilt University School of Medicine, Nashvill, Tennessee, USA
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15
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Kraemer SM, Goldstrohm DA, Berger A, Hankey S, Rovinsky SA, Scott Moye-Rowley W, Stargell LA. TFIIA plays a role in the response to oxidative stress. EUKARYOTIC CELL 2006; 5:1081-90. [PMID: 16835452 PMCID: PMC1489289 DOI: 10.1128/ec.00071-06] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To characterize the role of the general transcription factor TFIIA in the regulation of gene expression by RNA polymerase II, we examined the transcriptional profiles of TFIIA mutants of Saccharomyces cerevisiae using DNA microarrays. Whole-genome expression profiles were determined for three different mutants with mutations in the gene coding for the small subunit of TFIIA, TOA2. Depending on the particular mutant strain, approximately 11 to 27% of the expressed genes exhibit altered message levels. A search for common motifs in the upstream regions of the pool of genes decreased in all three mutants yielded the binding site for Yap1, the transcription factor that regulates the response to oxidative stress. Consistent with a TFIIA-Yap1 connection, the TFIIA mutants are unable to grow under conditions that require the oxidative stress response. Underexpression of Yap1-regulated genes in the TFIIA mutant strains is not the result of decreased expression of Yap1 protein, since immunoblot analysis indicates similar amounts of Yap1 in the wild-type and mutant strains. In addition, intracellular localization studies indicate that both the wild-type and mutant strains localize Yap1 indistinguishably in response to oxidative stress. As such, the decrease in transcription of Yap1-dependent genes in the TFIIA mutant strains appears to reflect a compromised interaction between Yap1 and TFIIA. This hypothesis is supported by the observations that Yap1 and TFIIA interact both in vivo and in vitro. Taken together, these studies demonstrate a dependence of Yap1 on TFIIA function and highlight a new role for TFIIA in the cellular mechanism of defense against reactive oxygen species.
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Affiliation(s)
- Susan M Kraemer
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA
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Abstract
In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.
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Affiliation(s)
- Mary C Thomas
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4935, USA
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Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, Wu LF. Systems-level analyses identify extensive coupling among gene expression machines. Mol Syst Biol 2006; 2:2006.0003. [PMID: 16738550 PMCID: PMC1681477 DOI: 10.1038/msb4100045] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Accepted: 12/06/2005] [Indexed: 01/30/2023] Open
Abstract
Here, we develop computational methods to assess and consolidate large, diverse protein interaction data sets, with the objective of identifying proteins involved in the coupling of multicomponent complexes within the yeast gene expression pathway. From among approximately 43 000 total interactions and 2100 proteins, our methods identify known structural complexes, such as the spliceosome and SAGA, and functional modules, such as the DEAD-box helicases, within the interaction network of proteins involved in gene expression. Our process identifies and ranks instances of three distinct, biologically motivated motifs, or patterns of coupling among distinct machineries involved in different subprocesses of gene expression. Our results confirm known coupling among transcription, RNA processing, and export, and predict further coupling with translation and nonsense-mediated decay. We systematically corroborate our analysis with two independent, comprehensive experimental data sets. The methods presented here may be generalized to other biological processes and organisms to generate principled, systems-level network models that provide experimentally testable hypotheses for coupling among biological machines.
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Affiliation(s)
- Karolina Maciag
- Bauer Center for Genomics Research, Harvard University, Cambridge, MA, USA
| | - Steven J Altschuler
- Department of Pharmacology and Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael D Slack
- Department of Pharmacology and Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nevan J Krogan
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Emili
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Jack F Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
| | - Tom Maniatis
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Lani F Wu
- Department of Pharmacology and Green Comprehensive Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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