1
|
Hardivillé S, Banerjee PS, Selen Alpergin ES, Smith DM, Han G, Ma J, Talbot CC, Hu P, Wolfgang MJ, Hart GW. TATA-Box Binding Protein O-GlcNAcylation at T114 Regulates Formation of the B-TFIID Complex and Is Critical for Metabolic Gene Regulation. Mol Cell 2019; 77:1143-1152.e7. [PMID: 31866147 DOI: 10.1016/j.molcel.2019.11.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/14/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
In eukaryotes, gene expression is performed by three RNA polymerases that are targeted to promoters by molecular complexes. A unique common factor, the TATA-box binding protein (TBP), is thought to serve as a platform to assemble pre-initiation complexes competent for transcription. Here, we describe a novel molecular mechanism of nutrient regulation of gene transcription by dynamic O-GlcNAcylation of TBP. We show that O-GlcNAcylation at T114 of TBP blocks its interaction with BTAF1, hence the formation of the B-TFIID complex, and its dynamic cycling on and off of DNA. Transcriptomic and metabolomic analyses of TBPT114A CRISPR/Cas9-edited cells showed that loss of O-GlcNAcylation at T114 increases TBP binding to BTAF1 and directly impacts expression of 408 genes. Lack of O-GlcNAcylation at T114 is associated with a striking reprogramming of cellular metabolism induced by a profound modification of the transcriptome, leading to gross alterations in lipid storage.
Collapse
Affiliation(s)
- Stéphan Hardivillé
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Partha S Banerjee
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ebru S Selen Alpergin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Danielle M Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guanghui Han
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Junfeng Ma
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ping Hu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael J Wolfgang
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
2
|
Teves SS, An L, Bhargava-Shah A, Xie L, Darzacq X, Tjian R. A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes. eLife 2018; 7:35621. [PMID: 29939130 PMCID: PMC6037474 DOI: 10.7554/elife.35621] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/23/2018] [Indexed: 12/18/2022] Open
Abstract
Maintenance of transcription programs is challenged during mitosis when chromatin becomes condensed and transcription is silenced. How do the daughter cells re-establish the original transcription program? Here, we report that the TATA-binding protein (TBP), a key component of the core transcriptional machinery, remains bound globally to active promoters in mouse embryonic stem cells during mitosis. Using live-cell single-molecule imaging, we observed that TBP mitotic binding is highly stable, with an average residence time of minutes, in stark contrast to typical TFs with residence times of seconds. To test the functional effect of mitotic TBP binding, we used a drug-inducible degron system and found that TBP promotes the association of RNA Polymerase II with mitotic chromosomes, and facilitates transcriptional reactivation following mitosis. These results suggest that the core transcriptional machinery promotes efficient transcription maintenance globally.
Collapse
Affiliation(s)
- Sheila S Teves
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Luye An
- Department of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, United States
| | - Aarohi Bhargava-Shah
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Liangqi Xie
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, Berkeley, United States
| |
Collapse
|
3
|
Johnson SA, Lin JJ, Walkey CJ, Leathers MP, Coarfa C, Johnson DL. Elevated TATA-binding protein expression drives vascular endothelial growth factor expression in colon cancer. Oncotarget 2017; 8:48832-48845. [PMID: 28415573 PMCID: PMC5564728 DOI: 10.18632/oncotarget.16384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/13/2017] [Indexed: 11/26/2022] Open
Abstract
The TATA-binding protein (TBP) plays a central role in eukaryotic gene transcription. Given its key function in transcription initiation, TBP was initially thought to be an invariant protein. However, studies showed that TBP expression is upregulated by oncogenic signaling pathways. Furthermore, depending on the cell type, small increases in cellular TBP amounts can induce changes in cellular growth properties towards a transformed phenotype. Here we sought to identify the specific TBP-regulated gene targets that drive its ability to induce tumorigenesis. Using microarray analysis, our results reveal that increases in cellular TBP concentrations produce selective alterations in gene expression that include an enrichment for genes involved in angiogenesis. Accordingly, we find that TBP levels modulate VEGFA expression, the master regulator of angiogenesis. Increases in cellular TBP amounts induce VEGFA expression and secretion to enhance cell migration and tumor vascularization. TBP mediates changes in VEGFA transcription requiring its recruitment at a hypoxia-insensitive proximal TSS, revealing a mechanism for VEGF regulation under non-stress conditions. The results are clinically relevant as TBP expression is significantly increased in both colon adenocarcinomas as well as adenomas relative to normal tissue. Furthermore, TBP expression is positively correlated with VEGFA expression. Collectively, these studies support the idea that increases in TBP expression contribute to enhanced VEGFA transcription early in colorectal cancer development to drive tumorigenesis.
Collapse
Affiliation(s)
- Sandra A.S. Johnson
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Justin J. Lin
- Zymo Research, Irvine, California, United States of America
| | - Christopher J. Walkey
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael P. Leathers
- Department of Orthopedic Surgery, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, California, United States of America
| | - Cristian Coarfa
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Deborah L. Johnson
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, Texas, United States of America
| |
Collapse
|
4
|
Transient Shifts of Incubation Temperature Reveal Immediate and Long-Term Transcriptional Response in Chicken Breast Muscle Underpinning Resilience and Phenotypic Plasticity. PLoS One 2016; 11:e0162485. [PMID: 27611643 PMCID: PMC5017601 DOI: 10.1371/journal.pone.0162485] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/23/2016] [Indexed: 12/24/2022] Open
Abstract
Variations in egg incubation temperatures can have acute or long-term effects on gene transcription in avian species. Altered gene expression may, in turn, affect muscle traits in poultry and indirectly influence commercial production. To determine how changes in eggshell temperature affect gene expression, incubation temperatures were varied [36.8°C (low), 37.8°C (control), 38.8°C (high)] at specific time periods reflecting two stages of myogenesis [embryonic days (ED) 7-10 and 10-13]. Gene expression was compared between interventions and matching controls by microarrays in broiler breast muscle at ED10 or ED13 and post-hatch at day 35. Early (ED7-10) high incubation temperature (H10ΔC) resulted in 1370 differentially expressed genes (DEGs) in embryos. Ingenuity pathway analysis revealed temporary activation of cell maintenance, organismal development, and survival ability genes, but these effects were not maintained in adults. Late high incubation temperature (ED10-13) (H13ΔC) had slightly negative impacts on development of cellular components in embryos, but a cumulative effect was observed in adults, in which tissue development and nutrition metabolism were affected. Early low incubation temperature (L10ΔC) produced 368 DEGs, most of which were down-regulated and involved in differentiation and formation of muscle cells. In adults, this treatment down-regulated pathways of transcriptional processes, but up-regulated cell proliferation. Late low temperature incubation (L13ΔC) produced 795 DEGs in embryos, and activated organismal survival and post-transcriptional regulation pathways. In adults this treatment activated cellular and organ development, nutrition and small molecule activity, and survival rate, but deactivated size of body and muscle cells. Thermal interventions during incubation initiate immediate and delayed transcriptional responses that are specific for timing and direction of treatment. Interestingly, the transcriptional response to transiently decreased incubation temperature, which did not affect the phenotypes, prompts compensatory effects reflecting resilience. In contrast, higher incubation temperature triggers gene expression and has long-term effects on the phenotype. These mechanisms of considerable phenotypic plasticity contribute to the biodiversity and broaden the basis for managing poultry populations.
Collapse
|
5
|
Relevance of HCN2-expressing human mesenchymal stem cells for the generation of biological pacemakers. Stem Cell Res Ther 2016; 7:67. [PMID: 27137910 PMCID: PMC4853868 DOI: 10.1186/s13287-016-0326-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/29/2016] [Accepted: 04/13/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The transfection of human mesenchymal stem cells (hMSCs) with the hyperpolarization-activated cyclic nucleotide-gated ion channel 2 (HCN2) gene has been demonstrated to provide biological pacing in dogs with complete heart block. The mechanism appears to be the generation of the ion current (If) by the HCN2-expressing hMSCs. However, it is not clear how the transfection process and/or the HCN2 gene affect the growth functions of the hMSCs. Therefore, we investigated survival, proliferation, cell cycle, and growth on a Kapton® scaffold of HCN2-expressing hMSCs. METHODS hMSCs were isolated from the bone marrow of healthy volunteers applying a selective cell adhesion procedure and were identified by their expression of specific surface markers. Cells from passages 2-3 were transfected by electroporation using commercial transfection kits and a pIRES2-EGFP vector carrying the pacemaker gene, mouse HCN2 (mHCN2). Transfection efficiency was confirmed by enhanced green fluorescent protein (EGFP) fluorescence, quantitative real-time polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA). After hMSCs were transfected, their viability, proliferation, If generation, apoptosis, cell cycle, and expression of transcription factors were measured and compared with non-transfected cells and cells transfected with pIRES2-EGFP vector alone. RESULTS Intracellular mHCN2 expression after transfection increased from 22.14 to 62.66 ng/mg protein (p < 0.05). Transfection efficiency was 45 ± 5 %. The viability of mHCN2-transfected cells was 82 ± 5 %; they grew stably for more than 3 weeks and induced If current. mHCN2-transfected cells had low mitotic activity (10.4 ± 1.24 % in G2/M and 83.6 ± 2.5 % in G1 phases) as compared with non-transfected cells (52-53 % in G2/M and 31-35 % in G1 phases). Transfected cells showed increased activation of nine cell cycle-regulating transcription factors: the most prominent upregulation was of AMP-dependent transcription factor ATF3 (7.11-fold, p = 0.00056) which regulates the G1 phase. mHCN2-expressing hMSCs were attached and made anchorage-dependent connection with other cells without transmigration through a 12.7-μm thick Kapton® HN film with micromachined 1-3 μm diameter pores. CONCLUSIONS mHCN2-expressing hMSCs preserved the major cell functions required for the generation of biological pacemakers: high viability, functional activity, but low proliferation rate through the arrest of cell cycle in the G1 phase. mHCN2-expressing hMSCs attached and grew on a Kapton® scaffold without transmigration, confirming the relevance of these cells for the generation of biological pacemakers.
Collapse
|
6
|
Li L, Martinez SS, Hu W, Liu Z, Tjian R. A specific E3 ligase/deubiquitinase pair modulates TBP protein levels during muscle differentiation. eLife 2015; 4:e08536. [PMID: 26393420 PMCID: PMC4576175 DOI: 10.7554/elife.08536] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/24/2015] [Indexed: 01/23/2023] Open
Abstract
TFIID—a complex of TATA-binding protein (TBP) and TBP-associated factors (TAFs)—is a central component of the Pol II promoter recognition apparatus. Recent studies have revealed significant downregulation of TFIID subunits in terminally differentiated myocytes, hepatocytes and adipocytes. Here, we report that TBP protein levels are tightly regulated by the ubiquitin-proteasome system. Using an in vitro ubiquitination assay coupled with biochemical fractionation, we identified Huwe1 as an E3 ligase targeting TBP for K48-linked ubiquitination and proteasome-mediated degradation. Upregulation of Huwe1 expression during myogenesis induces TBP degradation and myotube differentiation. We found that Huwe1 activity on TBP is antagonized by the deubiquitinase USP10, which protects TBP from degradation. Thus, modulating the levels of both Huwe1 and USP10 appears to fine-tune the requisite degradation of TBP during myogenesis. Together, our study unmasks a previously unknown interplay between an E3 ligase and a deubiquitinating enzyme regulating TBP levels during cellular differentiation. DOI:http://dx.doi.org/10.7554/eLife.08536.001 Most animal cells specialize to perform particular roles that contribute to the survival of the animal in different ways. For example, the cells that form our muscles are able to contract, while other cells in the body are efficient at storing fat. The different types of cells develop from unspecialized cells, but it is not clear what controls this process to form a particular type of cell in the right place at the right time. The TATA-box binding protein (TBP) is one of a group of proteins that helps to activate the expression of genes in animal cells. Recent studies have revealed that TBP is deliberately destroyed by a group of proteins called the proteasome in muscle cells, in a type of liver cell, and in fat cells. Here, Li et al. used biochemical techniques to study the regulation of TBP during the formation of muscle cells from less specialist mouse cells called myoblasts. The experiments show that an enzyme called Huwe1 selectively adds a tag to TBP that marks TBP for destruction by the proteasome. Another protein called USP10 acts to remove the tags to prevent TBP from being destroyed. Therefore, it appears that changes in the levels of Huwe1 and USP10 fine-tune the amount of TBP that is degraded during the formation of muscle cells. Li et al.'s findings suggest that other proteins that are also involved in activating gene expression may also be destroyed as muscle cells form. The next step is to understand how important the degradation of these proteins is to the formation of other types of specialist cells. DOI:http://dx.doi.org/10.7554/eLife.08536.002
Collapse
Affiliation(s)
- Li Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | | | - Wenxin Hu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Zhe Liu
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Robert Tjian
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| |
Collapse
|
7
|
R. Lambert J, K. Nordeen S. A role for the non-conserved N-terminal domain of the TATA-binding protein in the crosstalk between cell signaling pathways and steroid receptors. AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.2.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
8
|
Akhtar W, Veenstra GJC. TBP-related factors: a paradigm of diversity in transcription initiation. Cell Biosci 2011; 1:23. [PMID: 21711503 PMCID: PMC3142196 DOI: 10.1186/2045-3701-1-23] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/27/2011] [Indexed: 01/24/2023] Open
Abstract
TATA binding protein (TBP) is a key component of the eukaryotic transcription initiation machinery. It functions in several complexes involved in core promoter recognition and assembly of the pre-initiation complex. Through gene duplication eukaryotes have expanded their repertoire of TATA binding proteins, leading to a variable composition of the transcription machinery. In vertebrates this repertoire consists of TBP, TBP-like factor (TLF, also known as TBPL1, TRF2) and TBP2 (also known as TBPL2, TRF3). All three factors are essential, with TLF and TBP2 playing important roles in development and differentiation, in particular gametogenesis and early embryonic development, whereas TBP dominates somatic cell transcription. TBP-related factors may compete for promoters when co-expressed, but also show preferential interactions with subsets of promoters. Initiation factor switching occurs on account of differential expression of these proteins in gametes, embryos and somatic cells. Paralogs of TFIIA and TAF subunits account for additional variation in the transcription initiation complex. This variation in core promoter recognition accommodates the expanded regulatory capacity and specificity required for germ cells and embryonic development in higher eukaryotes.
Collapse
Affiliation(s)
- Waseem Akhtar
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.
| | | |
Collapse
|
9
|
Increased interaction of proteins in nuclear extract from mouse liver and lung tumors with TATA-containing oligonucleotide. Bull Exp Biol Med 2008; 145:93-5. [PMID: 19024013 DOI: 10.1007/s10517-008-0037-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Increased TATA-binding activity of proteins in nuclear extracts from murine hepatocarcinoma HA-1 and murine Lewis lung adenocarcinoma was demonstrated. The dependence of the amount of formed complexes on protein concentration, displacement of labeled 32P-TATA-containing oligonucleotide by its unlabeled analog, and weak interaction with an oligonucleotide containing damaged TATA box confirm specificity of the formed complexes.
Collapse
|
10
|
Epidermal growth factor receptor 1 (EGFR1) and its variant EGFRvIII regulate TATA-binding protein expression through distinct pathways. Mol Cell Biol 2008; 28:6483-95. [PMID: 18710943 DOI: 10.1128/mcb.00288-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The epidermal growth factor receptor (EGFR) family regulates essential biological processes. Various epithelial tumors are linked to EGFR overexpression or expression of variant forms, such as the EGFR1 variant, EGFRvIII. Perturbations in expression of the transcription initiation factor, TATA-binding protein (TBP), alter cellular growth properties. Here we demonstrate that EGFR1 and EGFRvIII, but not HER2, induce TBP expression at a transcriptional level through distinct mechanisms. EGFR1 enhances the phosphorylation and function of Elk-1, recruiting it to the TBP promoter. In contrast, EGFRvIII robustly induces c-jun expression, stimulating recruitment of c-fos/c-jun to an overlapping AP-1 site. Enhancing c-jun expression alone induces TBP promoter activity through the AP-1 site. To determine the underlying mechanism for differences in Elk-1 function and c-jun expression by these receptors, we inhibited the internalization of EGFR1. Persistent EGFR1 cell surface occupancy mimics EGFRvIII-mediated effects on Elk-1 and c-jun and switches the requirement of Elk-1 to AP-1 for TBP promoter induction. Together, these studies define a new molecular mechanism for the regulation of TBP expression. In addition, we identify distinct molecular targets of EGFR1 and EGFRvIII and demonstrate the importance of receptor internalization in distinguishing their specific functions.
Collapse
|
11
|
Johnson SAS, Dubeau L, Johnson DL. Enhanced RNA polymerase III-dependent transcription is required for oncogenic transformation. J Biol Chem 2008; 283:19184-91. [PMID: 18456653 DOI: 10.1074/jbc.m802872200] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
RNA polymerase (pol) III transcription, responsible for the synthesis of various stable RNAs, including 5 S rRNAs and tRNAs, is regulated by oncogenic proteins and tumor suppressors. Although it is well established that RNA pol III-dependent transcription is deregulated in transformed cells and malignant tumors, it has not been determined whether this represents a cause or consequence of these processes. We show that Rat1a fibroblasts undergoing oncogenic transformation by the TATA-binding protein or c-Myc display enhanced RNA pol III transcription. Decreased expression of the RNA pol III-specific transcription factor Brf1 prevented this increase in RNA pol III transcription. Although the overall proliferation rates of these cells remained unchanged, the ability of cells to grow in an anchorage-independent manner and form tumors in mice was markedly reduced. Although overexpression of Brf1 modestly stimulated RNA pol III transcription, expression of a phosphomimic, Brf1-T145D, more significantly induced transcription. However, these increases in transcription were not sufficient to promote cellular transformation. Together, these results demonstrate that enhanced RNA pol III transcription is essential for anchorage-independent growth and tumorigenesis and that these events can be uncoupled from effects on anchorage-dependent proliferation.
Collapse
Affiliation(s)
- Sandra A S Johnson
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, California 90089, USA
| | | | | |
Collapse
|
12
|
Variations in intracellular levels of TATA binding protein can affect specific genes by different mechanisms. Mol Cell Biol 2007; 28:83-92. [PMID: 17954564 DOI: 10.1128/mcb.00809-07] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously showed that reduced intracellular levels of the TATA binding protein (TBP), brought about by tbp heterozygosity in DT40 cells, resulted in a mitotic delay reflecting reduced expression of the mitotic regulator cdc25B but did not significantly affect overall transcription. Here we extend these findings in several ways. We first provide evidence that the decrease in cdc25B expression reflects reduced activity of the cdc25B core promoter in the heterozygous (TBP-het) cells. Strikingly, mutations in a previously described repressor element that overlaps the TATA box restored promoter activity in TBP-het cells, supporting the idea that the sensitivity of this promoter to TBP levels reflects a competition between TBP and the repressor for DNA binding. To determine whether cells might have mechanisms to compensate for fluctuations in TBP levels, we next examined expression of the two known vertebrate TBP homologues, TLP and TBP2. Significantly, mRNAs encoding both were significantly overexpressed relative to levels observed in wild-type cells. In the case of TLP, this was shown to reflect regulation of the core promoter by both TBP and TLP. Together, our results indicate that variations in TBP levels can affect the transcription of specific promoters in distinct ways, but overall transcription may be buffered by corresponding alterations in the expression of TBP homologues.
Collapse
|
13
|
Johnson SS, Zhang C, Fromm J, Willis IM, Johnson DL. Mammalian Maf1 is a negative regulator of transcription by all three nuclear RNA polymerases. Mol Cell 2007; 26:367-79. [PMID: 17499043 DOI: 10.1016/j.molcel.2007.03.021] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 02/22/2007] [Accepted: 03/28/2007] [Indexed: 11/23/2022]
Abstract
Most eukaryotic transcriptional regulators act in an RNA polymerase (Pol)-selective manner. Here we show that the human Maf1 protein negatively regulates transcription by all three nuclear Pols. Changes in Maf1 expression affect Pol I- and Pol III-dependent transcription in human glioblastoma lines. These effects are mediated, in part, through the ability of Maf1 to repress transcription of the TATA binding protein, TBP. Maf1 targets an Elk-1-binding site in the TBP promoter, and its occupancy of this region is reciprocal with that of Elk-1. Similarly, Maf1 occupancy of Pol III genes is inversely correlated with that of the initiation factor TFIIIB and Pol III. The phenotypic consequences of reducing Maf1 expression include changes in cell morphology and the accumulation of actin stress fibers, whereas Maf1 overexpression suppresses anchorage-independent growth. Together with the ability of Maf1 to reduce biosynthetic capacity, these findings support the idea that Maf1 regulates the transformation state of cells.
Collapse
Affiliation(s)
- Sandra S Johnson
- Department of Biochemistry and Molecular Biology, Keck School of Medicine and the Norris Comprehensive Cancer Center, University of Southern California, 2011 Zonal Avenue, Los Angeles, CA 90033, USA
| | | | | | | | | |
Collapse
|
14
|
Zhong S, Fromm J, Johnson DL. TBP is differentially regulated by c-Jun N-terminal kinase 1 (JNK1) and JNK2 through Elk-1, controlling c-Jun expression and cell proliferation. Mol Cell Biol 2006; 27:54-64. [PMID: 17074809 PMCID: PMC1800663 DOI: 10.1128/mcb.01365-06] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence supports the idea that the c-Jun N-terminal kinases (JNKs) possess overlapping but distinct functions. The potential roles of the ubiquitously expressed JNK1 and JNK2 in regulating expression of the central transcription initiation factor, TATA-binding protein (TBP), were examined. Relative to wild-type fibroblasts, TBP was decreased in Jnk1(-/-) cells and increased in Jnk2(-/-) cells. Similarly, reduction of JNK1 in human hepatoma cells decreased TBP expression, whereas reduction of JNK2 enhanced it. JNK-mediated regulation of TBP expression occurs at the transcriptional level through their ability to target Elk-1, which directly regulates the TBP promoter in response to epidermal growth factor stimulation. JNK1 increases, whereas JNK2 decreases, the phosphorylation state of Elk-1, which differentially affects Elk-1 occupancy at a defined site within the TBP promoter. These JNK-mediated alterations in TBP expression, alone, serve to regulate c-Jun expression and fibroblast proliferation rates. These studies uncovered several new molecular events that distinguish the functions of JNK1 and JNK2 that are critical for their regulation of cellular proliferation.
Collapse
Affiliation(s)
- Shuping Zhong
- Department of Biochemistry and Molecular Biology, University of Southern California, 2011 Zonal Ave., Los Angeles, CA 90033, USA
| | | | | |
Collapse
|
15
|
Howe ML, Mehmud ZF, Saha S, Buratovich M, Stutius EA, Schmidt HD, Lenon AL, Reddicks C, Ivanov GS, Przyborski SA, Ozer JS. Transcription Factor IIA tau is associated with undifferentiated cells and its gene expression is repressed in primary neurons at the chromatin level in vivo. Stem Cells Dev 2006; 15:175-90. [PMID: 16646664 DOI: 10.1089/scd.2006.15.175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The levels of General Transcription Factor (TF) IIA were examined during mammalian brain development and in rat embryo fibroblasts and transformed cell lines. The large TFIIA subunit paralogues alphabeta and tau are largely produced in unsynchronized cell lines, yet only TFIIA alphabeta is observed in a number of differentiated tissue extracts. Steady-state protein levels of the TFIIA tau, alphabeta, and gamma subunits were significantly reduced when human embryonal (ec) and hepatic carcinoma cell lines were stimulated to differentiate with either all-trans-retinoic acid (ATRA) or sodium butyrate. ATRA-treated NT2-ec cells required replating to induce a neuronal phenotype and loss of detectable TFIIA tau and gamma proteins. High levels of TFIIA tau, alphabeta, and gamma and Sp factors were identified in extracts from human fetal and rat embryonic day-18 brains, but not in human and rat adult brain extracts. A high histone H3 Lys9/Lys4 methylation ratio was observed in the TFIIA tau promoter of primary hippocampal neurons from day-18 rat embryos, suggesting that repressive epigenetic marks of chromatin prevent TFIIA tau from being transcribed in neurons. We conclude that TFIIA tau is associated with undifferentiated cells during development, yet is down-regulated at the chromatin level upon cellular differentiation.
Collapse
Affiliation(s)
- Mariko L Howe
- Department of Pharmacology and Experimental Therpeutics, Boston University School of Medicine, MA 02118, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Buenz EJ, Howe CL. Picornaviruses and cell death. Trends Microbiol 2005; 14:28-36. [PMID: 16337385 DOI: 10.1016/j.tim.2005.11.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 10/07/2005] [Accepted: 11/21/2005] [Indexed: 11/21/2022]
Abstract
Members of the picornavirus family, including poliovirus and foot-and-mouth disease virus, are widespread pathogens of humans and domestic animals. Recent global developments in the resurgence of poliovirus infection and in the control of foot-and-mouth disease infection highlight the problems caused by the ability of picornaviruses to alter the apoptotic machinery of host cells and establish persistent infections. Despite the medical, economic and social impact of this family of viruses, little information exists that integrates the mechanisms of cell death and damage induced by related family members. Fortunately, examination of the reported roles and functions of individual viral proteins from multiple picornaviruses makes it possible to surmise canonical functions for these proteins. This review analyzes the canonical function of picornavirus proteins involved in the alteration of apoptotic homeostasis in infected host cells.
Collapse
Affiliation(s)
- Eric J Buenz
- Molecular Neuroscience Program, Department of Neurology, Department of Neuroscience, RO_GU_04_12_NR, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | | |
Collapse
|
17
|
Kieffer-Kwon P, Martianov I, Davidson I. Cell-specific nucleolar localization of TBP-related factor 2. Mol Biol Cell 2004; 15:4356-68. [PMID: 15269281 PMCID: PMC519132 DOI: 10.1091/mbc.e04-02-0138] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Revised: 06/09/2004] [Accepted: 06/30/2004] [Indexed: 01/05/2023] Open
Abstract
TATA-binding protein (TBP)-related factor 2 (TRF2) is one of four closely related RNA polymerase II transcription factors. We compared the intracellular localizations of TBP and TRF2 during the cell cycle and mitosis in HeLa cells. We show that during interphase, endogenous or exogenously expressed TRF2 is located almost exclusively in the nucleolus in HeLa or Cos cells. TRF2 localization is not affected by stress or mitotic stimuli, but TRF2 is rapidly released from the nucleolus upon inhibition of pol I transcription or treatment by RNase. These results suggest that localization of HeLa TRF2 requires a nucleolar-associated RNA species. In contrast, in 3T3 fibroblast cells, exogenously expressed TRF2 localizes to the nucleoplasm. Constitutive expression of ectopic TRF2 in 3T3 cells leads to a prolonged S phase of the cell cycle and reduced proliferation. Together with previous data, our results highlight the cell-specific localization and functions of TRF2. Furthermore, we show that during cell division, HeLa TRF2 and TBP are localized in the mitotic cytoplasm and TRF2 relocalizes into the nascent nucleoli immediately after mitosis, whereas TBP reassociates with the chromatin. Although partially contradictory results have been reported, our data are consistent with a model where only small proportion of the cellular TBP remains associated with specific promoter loci during mitosis.
Collapse
Affiliation(s)
- Philippe Kieffer-Kwon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur, 67404 Illkirch Cédex, France
| | | | | |
Collapse
|
18
|
Abstract
The TATA binding protein (TBP) is a subunit of several macromolecular complexes required for transcription by the three nuclear RNA polymerases. This observation led to the idea that TBP is a "universal" transcription factor. The discovery of three TBP-related factors and a macromolecular complex which lacks TBP but can support RNA polymerase II transcription in vitro has led to a reappraisal of the universal character of TBP. Several in vivo studies have rather shown that TBP plays a specific role in the activation of a subset of cellular genes controlling the cell cycle. In mammals, the aminoterminal region of TBP plays a highly selective role in the maternal immunotolerance of pregnancy.
Collapse
Affiliation(s)
- Irwin Davidson
- Institut de génétique et de biologie moléculaire et cellulaire, 1, rue Laurent Fries, 67404 Illkirch, France.
| | | | | |
Collapse
|
19
|
Zhong S, Zhang C, Johnson DL. Epidermal growth factor enhances cellular TATA binding protein levels and induces RNA polymerase I- and III-dependent gene activity. Mol Cell Biol 2004; 24:5119-29. [PMID: 15169879 PMCID: PMC419868 DOI: 10.1128/mcb.24.12.5119-5129.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
TATA binding protein (TBP) is a central transcription factor used by all three cellular RNA polymerases. Changes in the levels of TBP have been shown to have selective effects on gene activity. Overexpression of TBP has been recently shown to contribute to cellular transformation, and elevated levels of TBP occur in a clinically significant proportion of human colon tumors relative to matched normal tissue. To understand the mechanisms by which TBP is regulated, we have analyzed whether activation of the epidermal growth factor receptor (EGFR), a membrane-bound tyrosine receptor kinase that is activated in a large number of human cancers, can serve to regulate cellular TBP. We show that treatment of mouse epidermal cells with EGF produces an increase in TBP levels, which can be blocked with an EGFR-specific inhibitor. In contrast, TBP levels remain unchanged after EGF treatment of EGFR null cells. EGF-mediated increases in TBP are regulated at the transcriptional level, as transient expression of the human TBP promoter is induced with EGF. This regulatory event is dependent upon the downstream activation of Ras and requires the activation of p38, JNK, and ERK mitogen-activated protein kinases. The consequence of elevated TBP on gene expression was further determined. Transcription by RNA polymerase (Pol) I and III was induced by EGF. Directly overexpressing TBP also stimulated transcription from these promoters. Thus, we have identified a new and important target of EGFR signaling, TBP, that contributes to EGF-mediated stimulation of RNA Pol I- and III-dependent gene activity. Since the cellular levels of the products of these genes, tRNAs and rRNAs, determine the translational capacity of cells, this event may be an important contributor to the transforming function of EGF.
Collapse
Affiliation(s)
- Shuping Zhong
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, 90033, USA
| | | | | |
Collapse
|
20
|
Trachtulec Z, Vlcek C, Mihola O, Forejt J. Comparative analysis of the PDCD2–TBP–PSMB1 region in vertebrates. Gene 2004; 335:151-7. [PMID: 15194198 DOI: 10.1016/j.gene.2004.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Revised: 02/25/2004] [Accepted: 03/18/2004] [Indexed: 10/26/2022]
Abstract
Three orthologous genes encoding programmed cell death 2 (PDCD2), TATA-binding protein (TBP), and proteasomal subunit C5 (PSMB1) proteins have been shown previously to be nonrandomly distributed in both mammalian and invertebrate genomes. Here we analyze a conserved synteny of the PDCD2, TBP, and PSMB1 orthologs in four nonmammalian vertebrates. Homologous genes of the chicken, zebrafish, fugu, and Tetraodon nigroviridis were identified. A chicken cosmid harboring the orthologs of these three genes was completely sequenced. The fish genes were analyzed in silico. In all seven vertebrates thus far investigated, the PDCD2 and TBP genes are located tail-to-tail. In six tested species but the zebrafish, the PSMB1 gene mapped head-to-head or in the close vicinity to the TBP, but even in the zebrafish, all three genes were syntenic. In contrast, a three times reused synteny breakpoint in the 5'-region from PDCD2 was detected. A comparative analysis revealed the distribution of putative matrix-attached regions (MARs), which may affect the synteny conservation.
Collapse
Affiliation(s)
- Zdenek Trachtulec
- Center for Integrated Genomics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | | | | | | |
Collapse
|
21
|
Chen Z, Manley JL. In vivo functional analysis of the histone 3-like TAF9 and a TAF9-related factor, TAF9L. J Biol Chem 2003; 278:35172-83. [PMID: 12837753 DOI: 10.1074/jbc.m304241200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The majority of the TATA-binding protein (TBP)-associated factors (TAFs) that constitute transcription factor II D (TFIID) contain histone fold motifs (HFMs). Our previous results utilizing DT40 cells containing a conditional TAF9 allele indicated that the histone 3-like TAF9 is essential for cell viability but largely dispensable for general transcription. In this study, we investigated further the role of TAF9 structural domains in TFIID integrity and cell growth and the functions of a TAF9-related factor, TAF9L. We first show that TAF9 depletion severely disrupts TFIID, indicating that the observed ongoing transcription is initiated with at least partially TAF-free TATA-binding protein. We also provide evidence for specific roles of TAF HFMs, highlighting the functional significance of HFM specificity observed in vitro and, importantly, of the TAF9-histone 3 similarity. Although we provide evidence that TAF9 and TAF9L are partly redundant, RNA interference experiments suggest that TAF9L is essential for HeLa cell growth. Strikingly, we provide evidence that TAF9L plays a role in transcriptional repression and/or silencing.
Collapse
Affiliation(s)
- Zheng Chen
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | |
Collapse
|
22
|
Affiliation(s)
- Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch Cédex, France.
| |
Collapse
|
23
|
Shimada M, Nakadai T, Tamura TA. TATA-binding protein-like protein (TLP/TRF2/TLF) negatively regulates cell cycle progression and is required for the stress-mediated G(2) checkpoint. Mol Cell Biol 2003; 23:4107-20. [PMID: 12773555 PMCID: PMC156134 DOI: 10.1128/mcb.23.12.4107-4120.2003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2002] [Revised: 11/13/2002] [Accepted: 03/19/2003] [Indexed: 11/20/2022] Open
Abstract
The TATA-binding protein (TBP) is a universal transcription factor required for all of the eukaryotic RNA polymerases. In addition to TBP, metazoans commonly express a distantly TBP-related protein referred to as TBP-like protein (TLP/TRF2/TLF). Although the function of TLP in transcriptional regulation is not clear, it is known that TLP is required for embryogenesis and spermiogenesis. In the present study, we investigated the cellular functions of TLP by using TLP knockout chicken DT40 cells. TLP was found to be dispensable for cell growth. Unexpectedly, TLP-null cells exhibited a 20% elevated cell cycle progression rate that was attributed to shortening of the G(2) phase. This indicates that TLP functions as a negative regulator of cell growth. Moreover, we found that TLP mainly existed in the cytoplasm and was translocated to the nucleus restrictedly at the G(2) phase. Ectopic expression of nuclear localization signal-carrying TLP resulted in an increase (1.5-fold) in the proportion of cells remaining in the G(2)/M phase and apoptotic state. Notably, TLP-null cells showed an insufficient G(2) checkpoint when the cells were exposed to stresses such as UV light and methyl methanesulfonate, and the population of apoptotic cells after stresses decreased to 40%. These phenomena in G(2) checkpoint regulation are suggested to be p53 independent because p53 does not function in DT40 cells. Moreover, TLP was transiently translocated to the nucleus shortly (15 min) after stress treatment. The expression of several stress response and cell cycle regulatory genes drifted in a both TLP- and stress-dependent manner. Nucleus-translocating TLP is therefore thought to work by checking cell integrity through its transcription regulatory ability. TLP is considered to be a signal-transducing transcription factor in cell cycle regulation and stress response.
Collapse
Affiliation(s)
- Miho Shimada
- Faculty of Science, Chiba University, Inage-ku, Chiba 263-8522, Japan
| | | | | |
Collapse
|
24
|
Johnson SAS, Dubeau L, Kawalek M, Dervan A, Schönthal AH, Dang CV, Johnson DL. Increased expression of TATA-binding protein, the central transcription factor, can contribute to oncogenesis. Mol Cell Biol 2003; 23:3043-51. [PMID: 12697807 PMCID: PMC153209 DOI: 10.1128/mcb.23.9.3043-3051.2003] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the central role of TATA-binding protein (TBP) in transcription, changes in cellular TBP concentration produce selective effects on gene expression. Moreover, TBP is up-regulated by oncogenic signaling pathways. These findings suggest that TBP could be a nexus in pathways that regulate cell proliferation and that genetic lesions that result in cellular transformation may produce their effects at least in part through TBP. We provide evidence consistent with this hypothesis, demonstrating that increases in TBP expression contribute to cellular transformation. A Ras-mediated increase in TBP expression is required for full Ras transforming activity. TBP overexpression induces cells to grow in an anchorage-independent manner and to form tumors in athymic mice. These effects on cellular transformation require changes in RNA polymerase II-dependent transcription and on the selective recruitment of TBP to promoters via its DNA binding activity. TBP expression is elevated in human colon carcinomas relative to normal colon epithelium. Both Ras-dependent and Ras-independent mechanisms mediate increases in TBP expression in colon carcinoma cell lines. We conclude that TBP may be a critical component in dysregulated signaling that occurs downstream of genetic lesions that cause tumors.
Collapse
Affiliation(s)
- Sandra A S Johnson
- Department of Biochemistry and Molecular Biology, Keck School of Medicine and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA
| | | | | | | | | | | | | |
Collapse
|
25
|
Yamazaki K, Aso T, Ohnishi Y, Ohno M, Tamura K, Shuin T, Kitajima S, Nakabeppu Y. Mammalian elongin A is not essential for cell viability but is required for proper cell cycle progression with limited alteration of gene expression. J Biol Chem 2003; 278:13585-9. [PMID: 12604609 DOI: 10.1074/jbc.c300047200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elongin A is a transcription elongation factor that increases the overall rate of mRNA chain elongation by RNA polymerase II. To investigate the function of Elongin A in vivo, the two alleles of the Elongin A gene have been disrupted by homologous recombination in murine embryonic stem (ES) cells. The Elongin A-deficient ES cells are viable, but show a slow growth phenotype because they undergo a delayed mitosis. The cDNA microarray and RNase protection assay using the wild-type and Elongin A-deficient ES cells indicate that the expression of only a small subset of genes is affected in the mutant cells. Taken together, our results suggest that Elongin A regulates transcription of a subset but not all of genes and reveal a linkage between Elongin A function and cell cycle progression.
Collapse
Affiliation(s)
- Katsuhisa Yamazaki
- Medical Institute of Bioregulation, Kyushu University, and CREST, Japan Science and Technology Corporation, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Schmidt EE, Bondareva AA, Radke JR, Capecchi MR. Fundamental cellular processes do not require vertebrate-specific sequences within the TATA-binding protein. J Biol Chem 2003; 278:6168-74. [PMID: 12471023 DOI: 10.1074/jbc.m211205200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 180-amino acid core of the TATA-binding protein (TBPcore) is conserved from Archae bacteria to man. Vertebrate TBPs contain, in addition, a large and highly conserved N-terminal region that is not found in other phyla. We have generated a line of mice in which the tbp allele is replaced with a version, tbp(Delta N), which lacks 111 of 135 N-terminal amino acid residues. Most tbp(Delta N/Delta N) fetuses die in midgestation. To test whether a disruption of general cellular processes contributed to this fetal loss, primary fibroblast cultures were established from +/+, Delta N/+, and Delta N/Delta N fetuses. The cultures exhibited no genotype-dependent differences in proliferation or in expression of the proliferative markers dihydrofolate reductase (DHFR) mRNA (S phase-specific) and cdc25B mRNA (G(2)-specific). The mutation had no effect on transcription initiation site fidelity by either RNA polymerase II (pol II) or pol III. Moreover, the mutation did not cause differences in levels of U6 RNA, a pol III-dependent component of the splicing machinery, in mRNA splicing efficiency, in expression of housekeeping genes from either TATA-containing or TATA-less promoters, or in global gene expression. Our results indicated that general eukaryotic cell functions are unaffected by deletion of these vertebrate-specific sequences from TBP. Thus, all activities of this polypeptide domain must either be compensated for by redundant activities or be restricted to situations that are not represented by primary fibroblasts.
Collapse
Affiliation(s)
- Edward E Schmidt
- Department of Veterinary Molecular Biology, Marsh Laboratories, Montana State University, Bozeman, Montana 59717, USA.
| | | | | | | |
Collapse
|
27
|
Martianov I, Viville S, Davidson I. RNA polymerase II transcription in murine cells lacking the TATA binding protein. Science 2002; 298:1036-9. [PMID: 12411709 DOI: 10.1126/science.1076327] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Inactivation of the murine TATA binding protein (TBP) gene by homologous recombination leads to growth arrest and apoptosis at the embryonic blastocyst stage. However, after loss of TBP, RNA polymerase II (pol II) remains in a transcriptionally active phosphorylation state, and in situ run-on experiments showed high levels of pol II transcription comparable to those of wild-type cells. In contrast, pol I and pol III transcription was arrested. Our results show a differential dependency of the RNA polymerases on TBP and provide evidence for TBP-independent pol II transcriptional mechanisms that allow reinitiation and maintenance of gene transcription in vivo.
Collapse
Affiliation(s)
- Igor Martianov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, B.P. 163, 67404 Illkirch Cédex, Communauté Urbaine de Strasbourg, France
| | | | | |
Collapse
|
28
|
Swamynathan SK, Varma BR, Weber KT, Guntaka RV. Targeted disruption of one allele of the Y-box protein gene, Chk-YB-1b, in DT40 cells results in major defects in cell cycle. Biochem Biophys Res Commun 2002; 296:451-7. [PMID: 12163040 DOI: 10.1016/s0006-291x(02)00875-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Y-box or inverted CCAAT box-binding proteins are multifunctional regulators of transcription and translation of several genes. Although YB-1 has been shown to play a key role in cell cycle, to date, there is no direct evidence. We disrupted one allele of Chk-YB-1b in a chicken pre-B lymphocyte cell line, DT40. Compared to wild-type DT40 cells, these heterozygous DT40YB1b(+/-) cells with one copy of the wild-type Chk-YB-1b allele showed multiple abnormalities, which include slower rate of growth, abnormal cell morphology, increased cell size, and increased genomic DNA content. These phenotypic defects resemble those cells that have a block in G2 and/or mitosis (G2/M). In addition, we have observed that a fraction of these heterozygous DT40YB1b(+/-) cells undergo apoptosis. In conclusion, we have discovered major defects in the G2/M phase of cell cycle in YB-1 knocked-out heterozygous mutant cells, providing for the first time direct evidence establishing a crucial role for YB-1 in cell proliferation.
Collapse
Affiliation(s)
- Shivalingappa K Swamynathan
- Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine, Columbia, MO, USA
| | | | | | | |
Collapse
|
29
|
Buerstedde JM, Arakawa H, Watahiki A, Carninci PP, Hayashizaki YY, Korn B, Plachy J. The DT40 web site: sampling and connecting the genes of a B cell line. Nucleic Acids Res 2002; 30:230-1. [PMID: 11752301 PMCID: PMC99062 DOI: 10.1093/nar/30.1.230] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Thousands of new vertebrate genes have been discovered and genetic systems are needed to address their functions at the cellular level. The chicken B cell line DT40 allows efficient gene disruptions due to its high homologous recombination activity. However, cloning the gene of interest is often cumbersome, since relatively few chicken cDNA sequences are present in the public databases. In addition, the accumulation of multiple mutations within the same cell clone is limited by the consumption of one drug-resistance marker for each transfection. Here, we present the DT40 web site (http://genetics.hpi.uni-hamburg.de/dt40.html), which includes a comprehensive database of chicken bursal ESTs to identify disruption candidate genes and recyclable marker cassettes based on the loxP system. These freely available resources greatly facilitate the analysis of genes and genetic networks.
Collapse
Affiliation(s)
- Jean-Marie Buerstedde
- Department of Cellular Immunology, Heinrich-Pette-Institute, Martinistrasse 52, 20251 Hamburg, Germany.
| | | | | | | | | | | | | |
Collapse
|
30
|
Kroll SL, Barth-Baus D, Hensold JO. The carboxyl-terminal domain of the granulocyte colony-stimulating factor receptor uncouples ribosomal biogenesis from cell cycle progression in differentiating 32D myeloid cells. J Biol Chem 2001; 276:49410-8. [PMID: 11598144 DOI: 10.1074/jbc.m109577200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Translational regulation plays an important role in development. In terminally differentiating cells a decrease in translation rate is common, although the regulatory mechanisms are unknown. We utilized 32Dcl3 myeloblast cells to investigate translational regulation during granulocyte colony-stimulating factor (G-CSF)-induced differentiation. G-CSF causes a significant decrease in translation rate compared with interleukin-3, which is a mitogen for these cells. Although these two cytokines exhibit modest differences in their effect on translation factor phosphorylation, they exhibit dramatic differences in their effect on ribosomal abundance and ribosomal DNA transcription. However, because both cytokines stimulate cell cycling, G-CSF induces a dissociation of ribosomal biogenesis from cell cycle progression. This uncoupling of ribosomal biogenesis from cell cycle progression appears to be closely related to the transmission of a differentiation signal, because it is not observed in cells expressing a carboxyl-terminally truncated G-CSF receptor, which supports proliferation but not differentiation of these cells. Because a similar event occurs early in differentiation of murine erythroleukemic cells, this suggests that ribosomal content is a common target of differentiating agents.
Collapse
Affiliation(s)
- S L Kroll
- Department of Medicine & University/Ireland Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | | | | |
Collapse
|
31
|
Abstract
Innumerable transcription factors integrate cellular and intercellular signals to generate a profile of expressed genes that is characteristic of the biochemical and cellular properties of the cell. This profile of expressed genes changes dynamically along with the developmental stage and differentiation state of the cell. The biochemical machinery upon which transcription factors integrate their signals is referred to as the general transcription machinery. However, this machinery is not of universal composition, and variants of the general transcription factors play specific roles in embryonic development, reflecting the constraints and requirements of developmental gene regulation.
Collapse
Affiliation(s)
- G J Veenstra
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
| | | |
Collapse
|