1
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Gao X, Zhou P, Li F. The multiple activations in budding yeast S-phase checkpoint are Poisson processes. PNAS NEXUS 2023; 2:pgad342. [PMID: 37941810 PMCID: PMC10629469 DOI: 10.1093/pnasnexus/pgad342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Eukaryotic cells activate the S-phase checkpoint signal transduction pathway in response to DNA replication stress. Affected by the noise in biochemical reactions, such activation process demonstrates cell-to-cell variability. Here, through the analysis of microfluidics-integrated time-lapse imaging, we found multiple S-phase checkpoint activations in a certain budding yeast cell cycle. Yeast cells not only varied in their activation moments but also differed in the number of activations within the cell cycle, resulting in a stochastic multiple activation process. By investigating dynamics at the single-cell level, we showed that stochastic waiting times between consecutive activations are exponentially distributed and independent from each other. Finite DNA replication time provides a robust upper time limit to the duration of multiple activations. The mathematical model, together with further experimental evidence from the mutant strain, revealed that the number of activations under different levels of replication stress agreed well with Poisson distribution. Therefore, the activation events of S-phase checkpoint meet the criterion of Poisson process during DNA replication. In sum, the observed Poisson activation process may provide new insights into the complex stochastic dynamics of signal transduction pathways.
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Affiliation(s)
- Xin Gao
- School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Peijie Zhou
- Department of Mathematics, University of California, Irvine, CA 92697, USA
| | - Fangting Li
- School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
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2
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Gerhardt KP, Rao SD, Olson EJ, Igoshin OA, Tabor JJ. Independent control of mean and noise by convolution of gene expression distributions. Nat Commun 2021; 12:6957. [PMID: 34845228 PMCID: PMC8630168 DOI: 10.1038/s41467-021-27070-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/03/2021] [Indexed: 11/28/2022] Open
Abstract
Gene expression noise can reduce cellular fitness or facilitate processes such as alternative metabolism, antibiotic resistance, and differentiation. Unfortunately, efforts to study the impacts of noise have been hampered by a scaling relationship between noise and expression level from individual promoters. Here, we use theory to demonstrate that mean and noise can be controlled independently by expressing two copies of a gene from separate inducible promoters in the same cell. We engineer low and high noise inducible promoters to validate this result in Escherichia coli, and develop a model that predicts the experimental distributions. Finally, we use our method to reveal that the response of a promoter to a repressor is less sensitive with higher repressor noise and explain this result using a law from probability theory. Our approach can be applied to investigate the effects of noise on diverse biological pathways or program cellular heterogeneity for synthetic biology applications.
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Affiliation(s)
- Karl P Gerhardt
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Satyajit D Rao
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Evan J Olson
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX, 77005, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
- Department of Biosciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA.
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3
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Characterization of the regulatory 5'-flanking region of bovine mucin 2 (MUC2) gene. Mol Cell Biochem 2021; 476:2847-2856. [PMID: 33730299 DOI: 10.1007/s11010-021-04133-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/06/2021] [Indexed: 10/21/2022]
Abstract
Throughout the intestinal epithelium surface there is an intricate polymer network composed by gel-forming mucins, which plays a protective role due to the formation of a physical, chemical and immunological barrier between the organism and the environment. Mucin 2 (MUC2) is the main mucin in the small and large intestine, and it is expressed specifically in the gastrointestinal tract (GIT), which makes its promoter region an important candidate for expression of heterologous genes of biotechnological interest in the GIT of bovine and other ruminants. In order to characterize the bovine MUC2 promoter we designed primers to amplify and isolate a candidate region for this promoter. The amplified sequence was confirmed by sequencing and cloned into a plasmid vector containing the luciferase (LUC) reporter gene. The regulatory sites of the MUC2 promoter already described in the literature were used to find the putative regulatory sites in the bovine MUC2 promoter region. With these data, some deletions were performed in order to find the promoter sequence with greatest expression capacity and specificity. The constructions were tested by transient transfection assays in LoVo cells (human colorectal adenocarcinoma) and bovine fibroblasts. The quantification of the relative expression of the promoter was measured using dual-luciferase assays. Real-time PCR was performed to analyze the expression of endogenous MUC2. The results presented herein prove that the isolated sequence corresponds to the promoter of bovine MUC2 gene, since it was able to induce expression of a reporter gene in an in vitro cell culture experimental platform.
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4
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Guinn MT, Wan Y, Levovitz S, Yang D, Rosner MR, Balázsi G. Observation and Control of Gene Expression Noise: Barrier Crossing Analogies Between Drug Resistance and Metastasis. Front Genet 2020; 11:586726. [PMID: 33193723 PMCID: PMC7662081 DOI: 10.3389/fgene.2020.586726] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/29/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Michael Tyler Guinn
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States.,Stony Brook Medical Scientist Training Program, Stony Brook, NY, United States
| | - Yiming Wan
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States
| | - Sarah Levovitz
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States
| | - Dongbo Yang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, United States
| | - Marsha R Rosner
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, United States
| | - Gábor Balázsi
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, United States
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5
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Zhang Q, Li J, Middleton A, Bhattacharya S, Conolly RB. Bridging the Data Gap From in vitro Toxicity Testing to Chemical Safety Assessment Through Computational Modeling. Front Public Health 2018; 6:261. [PMID: 30255008 PMCID: PMC6141783 DOI: 10.3389/fpubh.2018.00261] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022] Open
Abstract
Chemical toxicity testing is moving steadily toward a human cell and organoid-based in vitro approach for reasons including scientific relevancy, efficiency, cost, and ethical rightfulness. Inferring human health risk from chemical exposure based on in vitro testing data is a challenging task, facing various data gaps along the way. This review identifies these gaps and makes a case for the in silico approach of computational dose-response and extrapolation modeling to address many of the challenges. Mathematical models that can mechanistically describe chemical toxicokinetics (TK) and toxicodynamics (TD), for both in vitro and in vivo conditions, are the founding pieces in this regard. Identifying toxicity pathways and in vitro point of departure (PoD) associated with adverse health outcomes requires an understanding of the molecular key events in the interacting transcriptome, proteome, and metabolome. Such an understanding will in turn help determine the sets of sensitive biomarkers to be measured in vitro and the scope of toxicity pathways to be modeled in silico. In vitro data reporting both pathway perturbation and chemical biokinetics in the culture medium serve to calibrate the toxicity pathway and virtual tissue models, which can then help predict PoDs in response to chemical dosimetry experienced by cells in vivo. Two types of in vitro to in vivo extrapolation (IVIVE) are needed. (1) For toxic effects involving systemic regulations, such as endocrine disruption, organism-level adverse outcome pathway (AOP) models are needed to extrapolate in vitro toxicity pathway perturbation to in vivo PoD. (2) Physiologically-based toxicokinetic (PBTK) modeling is needed to extrapolate in vitro PoD dose metrics into external doses for expected exposure scenarios. Linked PBTK and TD models can explore the parameter space to recapitulate human population variability in response to chemical insults. While challenges remain for applying these modeling tools to support in vitro toxicity testing, they open the door toward population-stratified and personalized risk assessment.
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Affiliation(s)
- Qiang Zhang
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Jin Li
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, United Kingdom
| | - Alistair Middleton
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, United Kingdom
| | - Sudin Bhattacharya
- Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | - Rory B Conolly
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Durham, NC, United States
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6
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Abstract
Being concerned by the understanding of the mechanism underlying chronic degenerative diseases , we presented in the previous chapter the medical systems biology conceptual framework that we present for that purpose in this volume. More specifically, we argued there the clear advantages offered by a state-space perspective when applied to the systems-level description of the biomolecular machinery that regulates complex degenerative diseases. We also discussed the importance of the dynamical interplay between the risk factors and the network of interdependencies that characterizes the biochemical, cellular, and tissue-level biomolecular reactions that underlie the physiological processes in health and disease. As we pointed out in the previous chapter, the understanding of this interplay (articulated around cellular phenotypic plasticity properties, regulated by specific kinds of gene regulatory networks) is necessary if prevention is chosen as the human-health improvement strategy (potentially involving the modulation of the patient's lifestyle). In this chapter we provide the medical systems biology mathematical and computational modeling tools required for this task.
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Kumari S, Deng W, Gunasekara C, Chiang V, Chen HS, Ma H, Davis X, Wei H. Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes. BMC Bioinformatics 2016; 17:132. [PMID: 26993098 PMCID: PMC4797117 DOI: 10.1186/s12859-016-0981-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/09/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available for directly building ML-hGRNs that regulate biological pathways. RESULTS A bottom-up graphic Gaussian model (GGM) algorithm was developed for constructing ML-hGRN operating above a biological pathway using small- to medium-sized microarray or RNA-seq data sets. The algorithm first placed genes of a pathway at the bottom layer and began to construct a ML-hGRN by evaluating all combined triple genes: two pathway genes and one regulatory gene. The algorithm retained all triple genes where a regulatory gene significantly interfered two paired pathway genes. The regulatory genes with highest interference frequency were kept as the second layer and the number kept is based on an optimization function. Thereafter, the algorithm was used recursively to build a ML-hGRN in layer-by-layer fashion until the defined number of layers was obtained or terminated automatically. CONCLUSIONS We validated the algorithm and demonstrated its high efficiency in constructing ML-hGRNs governing biological pathways. The algorithm is instrumental for biologists to learn the hierarchical regulators associated with a given biological pathway from even small-sized microarray or RNA-seq data sets.
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Affiliation(s)
- Sapna Kumari
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Wenping Deng
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Chathura Gunasekara
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Vincent Chiang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Huann-Sheng Chen
- Statistical Methodology and Applications Branch, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Hao Ma
- NCCWA, USDA ARS, Kearneysville, WV, 25430, USA
| | - Xin Davis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.
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8
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Clewell RA, McMullen PD, Adeleye Y, Carmichael PL, Andersen ME. Pathway Based Toxicology and Fit-for-Purpose Assays. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 856:205-230. [DOI: 10.1007/978-3-319-33826-2_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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9
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Rybakova KN, Bruggeman FJ, Tomaszewska A, Moné MJ, Carlberg C, Westerhoff HV. Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism. PLoS Comput Biol 2015; 11:e1004236. [PMID: 25909187 PMCID: PMC4409292 DOI: 10.1371/journal.pcbi.1004236] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/11/2015] [Indexed: 12/12/2022] Open
Abstract
Activation of eukaryotic transcription is an intricate process that relies on a multitude of regulatory proteins forming complexes on chromatin. Chromatin modifications appear to play a guiding role in protein-complex assembly on chromatin. Together, these processes give rise to stochastic, often bursting, transcriptional activity. Here we present a model of eukaryotic transcription that aims to integrate those mechanisms. We use stochastic and ordinary-differential-equation modeling frameworks to examine various possible mechanisms of gene regulation by multiple transcription factors. We find that the assembly of large transcription factor complexes on chromatin via equilibrium-binding mechanisms is highly inefficient and insensitive to concentration changes of single regulatory proteins. An alternative model that lacks these limitations is a cyclic ratchet mechanism. In this mechanism, small protein complexes assemble sequentially on the promoter. Chromatin modifications mark the completion of a protein complex assembly, and sensitize the local chromatin for the assembly of the next protein complex. In this manner, a strict order of protein complex assemblies is attained. Even though the individual assembly steps are highly stochastic in duration, a sequence of them gives rise to a remarkable precision of the transcription cycle duration. This mechanism explains how transcription activation cycles, lasting for tens of minutes, derive from regulatory proteins residing on chromatin for only tens of seconds. Transcriptional bursts are an inherent feature of such transcription activation cycles. Bursting transcription can cause individual cells to remain in synchrony transiently, offering an explanation of transcriptional cycling as observed in cell populations, both on promoter chromatin status and mRNA levels.
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Affiliation(s)
- Katja N. Rybakova
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands
| | - Aleksandra Tomaszewska
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Martijn J. Moné
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Hans V. Westerhoff
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
- Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom
- Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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10
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Mohr W, Vagner T, Kuypers MMM, Ackermann M, LaRoche J. Resolution of Conflicting Signals at the Single-Cell Level in the Regulation of Cyanobacterial Photosynthesis and Nitrogen Fixation. PLoS One 2013; 8:e66060. [PMID: 23805199 PMCID: PMC3689712 DOI: 10.1371/journal.pone.0066060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/01/2013] [Indexed: 11/19/2022] Open
Abstract
Unicellular, diazotrophic cyanobacteria temporally separate dinitrogen (N2) fixation and photosynthesis to prevent inactivation of the nitrogenase by oxygen. This temporal segregation is regulated by a circadian clock with oscillating activities of N2 fixation in the dark and photosynthesis in the light. On the population level, this separation is not always complete, since the two processes can overlap during transitions from dark to light. How do single cells avoid inactivation of nitrogenase during these periods? One possibility is that phenotypic heterogeneity in populations leads to segregation of the two processes. Here, we measured N2 fixation and photosynthesis of individual cells using nanometer-scale secondary ion mass spectrometry (nanoSIMS) to assess both processes in a culture of the unicellular, diazotrophic cyanobacterium Crocosphaera watsonii during a dark-light and a continuous light phase. We compared single-cell rates with bulk rates and gene expression profiles. During the regular dark and light phases, C. watsonii exhibited the temporal segregation of N2 fixation and photosynthesis commonly observed. However, N2 fixation and photosynthesis were concurrently measurable at the population level during the subjective dark phase in which cells were kept in the light rather than returned to the expected dark phase. At the single-cell level, though, cells discriminated against either one of the two processes. Cells that showed high levels of photosynthesis had low nitrogen fixing activities, and vice versa. These results suggest that, under ambiguous environmental signals, single cells discriminate against either photosynthesis or nitrogen fixation, and thereby might reduce costs associated with running incompatible processes in the same cell.
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Affiliation(s)
- Wiebke Mohr
- Department of Biogeochemistry, Helmholtz Centre for Ocean Research (GEOMAR), Kiel, Germany
- * E-mail:
| | - Tomas Vagner
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcel M. M. Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Martin Ackermann
- Department of Environmental Systems Science, Swiss Federal Institute of Technology, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | - Julie LaRoche
- Department of Biogeochemistry, Helmholtz Centre for Ocean Research (GEOMAR), Kiel, Germany
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11
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Abstract
Both microbes and multicellular organisms actively regulate their cell fate determination to cope with changing environments or to ensure proper development. Here, we use synthetic biology approaches to engineer bistable gene networks to demonstrate that stochastic and permanent cell fate determination can be achieved through initializing gene regulatory networks (GRNs) at the boundary between dynamic attractors. We realize this experimentally by linking a synthetic GRN to a natural output of galactose metabolism regulation in yeast. Combining mathematical modeling and flow cytometry, we show that our engineered systems are bistable and that inherent gene expression stochasticity does not induce spontaneous state transitioning at steady state. Mathematical analysis predicts that stochastic cell fate determination in this case can only be realized when gene expression fluctuation occurs on or near attractor basin boundaries (the points of instability). Guided by numerical simulations, experiments are designed and performed with quantitatively diverse gene networks to test model predictions, which are verified by both flow cytometry and single-cell microscopy. By interfacing rationally designed synthetic GRNs with background gene regulation mechanisms, this work investigates intricate properties of networks that illuminate possible regulatory mechanisms for cell differentiation and development that can be initiated from points of instability.
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12
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Zhang Q, Kline DE, Bhattacharya S, Crawford RB, Conolly RB, Thomas RS, Andersen ME, Kaminski NE. All-or-none suppression of B cell terminal differentiation by environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Appl Pharmacol 2013; 268:17-26. [PMID: 23357550 DOI: 10.1016/j.taap.2013.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/21/2012] [Accepted: 01/18/2013] [Indexed: 10/27/2022]
Abstract
Many environmental contaminants can disrupt the adaptive immune response. Exposure to the ubiquitous aryl hydrocarbon receptor (AhR) ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other agonists suppresses the antibody response. The underlying pathway mechanism by which TCDD alters B cell function is not well understood. The present study investigated the mechanism of AhR-mediated pathways and mode of suppression by which TCDD perturbs terminal differentiation of B cells to plasma cells and thereby impairs antibody production. An integrated approach combining computational pathway modeling and in vitro assays with primary mouse B cells activated by lipopolysaccharide was employed. We demonstrated that suppression of the IgM response by TCDD occurs in an all-or-none (binary) rather than graded mode: i.e., it reduces the number of IgM-secreting cells in a concentration-dependent manner without affecting the IgM content in individual plasma cells. The mathematical model of the gene regulatory circuit underpinning B cell differentiation revealed that two previously identified AhR-regulated pathways, inhibition of signaling protein AP-1 and activation of transcription factor Bach2, could account for the all-or-none mode of suppression. Both pathways disrupt the operation of a bistable-switch circuit that contains transcription factors Bcl6, Prdm1, Pax5, and Bach2 and regulates B cell fate. The model further predicted that by transcriptionally activating Bach2, TCDD might delay B cell differentiation and increase the likelihood of isotype switching, thereby altering the antibody repertoire. In conclusion, the present study revealed the mode and specific pathway mechanisms by which the environmental immunosuppressant TCDD suppresses B cell differentiation.
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Affiliation(s)
- Qiang Zhang
- Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences, NC 27709, USA.
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13
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Tong P, Chen Y, Su X, Coombes KR. SIBER: systematic identification of bimodally expressed genes using RNAseq data. ACTA ACUST UNITED AC 2013; 29:605-13. [PMID: 23303507 DOI: 10.1093/bioinformatics/bts713] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Identification of bimodally expressed genes is an important task, as genes with bimodal expression play important roles in cell differentiation, signalling and disease progression. Several useful algorithms have been developed to identify bimodal genes from microarray data. Currently, no method can deal with data from next-generation sequencing, which is emerging as a replacement technology for microarrays. RESULTS We present SIBER (systematic identification of bimodally expressed genes using RNAseq data) for effectively identifying bimodally expressed genes from next-generation RNAseq data. We evaluate several candidate methods for modelling RNAseq count data and compare their performance in identifying bimodal genes through both simulation and real data analysis. We show that the lognormal mixture model performs best in terms of power and robustness under various scenarios. We also compare our method with alternative approaches, including profile analysis using clustering and kurtosis (PACK) and cancer outlier profile analysis (COPA). Our method is robust, powerful, invariant to shifting and scaling, has no blind spots and has a sample-size-free interpretation. AVAILABILITY The R package SIBER is available at the website http://bioinformatics.mdanderson.org/main/OOMPA:Overview.
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Affiliation(s)
- Pan Tong
- Department of Bioinformatics and Computational Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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14
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Babiskin AH, Smolke CD. Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity. Nucleic Acids Res 2011; 39:8651-64. [PMID: 21737428 PMCID: PMC3201855 DOI: 10.1093/nar/gkr445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The design of synthetic gene networks requires an extensive genetic toolbox to control the activities and levels of protein components to achieve desired cellular functions. Recently, a novel class of RNA-based control modules, which act through post-transcriptional processing of transcripts by directed RNase III (Rnt1p) cleavage, were shown to provide predictable control over gene expression and unique properties for manipulating biological networks. Here, we increase the regulatory range of the Rnt1p control elements, by modifying a critical region for enzyme binding to its hairpin substrates, the binding stability box (BSB). We used a high throughput, cell-based selection strategy to screen a BSB library for sequences that exhibit low fluorescence and thus high Rnt1p processing efficiencies. Sixteen unique BSBs were identified that cover a range of protein expression levels, due to the ability of the sequences to affect the hairpin cleavage rate and to form active cleavable complexes with Rnt1p. We further demonstrated that the activity of synthetic Rnt1p hairpins can be rationally programmed by combining the synthetic BSBs with a set of sequences located within a different region of the hairpin that directly modulate cleavage rates, providing a modular assembly strategy for this class of RNA-based control elements.
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Affiliation(s)
- Andrew H Babiskin
- Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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15
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A synthetic library of RNA control modules for predictable tuning of gene expression in yeast. Mol Syst Biol 2011; 7:471. [PMID: 21364573 PMCID: PMC3094065 DOI: 10.1038/msb.2011.4] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 01/18/2011] [Indexed: 01/28/2023] Open
Abstract
The authors describe a library of synthetic RNA control elements that provide programmable post-transcriptional regulation of gene expression in yeast. This toolkit is then used to study endogenous regulation of the ergosterol biosynthetic pathway.
Rnt1p hairpins can act as effective posttranscriptional gene regulatory elements in the yeast Saccharomyces cerevisiae. Modification of the cleavage efficiency box (CEB) region of an Rnt1p hairpin can modulate Rnt1p cleavage rates, and thus the resulting gene regulatory activities of the hairpin control elements. A library of Rnt1p hairpins can act as a set of synthetic control modules that provide predictable tuning of gene expression over a wide range of expression levels. The Rnt1p-based control elements can be combined with any promoter to support titration of regulatory strategies encoded in transcriptional regulators, including feedback control around endogenous proteins.
The design of complex biological systems encoding desired functions require the development of genetic tools for the precise control of protein levels in cells (Elowitz and Leibler, 2000; Gardner et al, 2000; Basu et al, 2004). For example, in the design of engineered metabolic networks, the tuning of enzyme levels is often critical for overcoming metabolic burden (Jones et al, 2000; Jin et al, 2003), the accumulation of toxic intermediates (Zhu et al, 2001; Pfleger et al, 2006) and detrimental consequences associated with the redirection of cellular resources from native pathways (Alper et al, 2005b; Paradise et al, 2008). Various examples of libraries of genetic control modules have been described that have been generated through the randomization of well-characterized gene expression control elements (Basu et al, 2004; Pfleger et al, 2006; Anderson et al, 2007). However, most of these studies have been conducted in Escherichia coli such that there is a lack of similar tools for other cellular chassis. The budding yeast, Saccharomyces cerevisiae, is a relevant organism in industrial processes, including biosynthesis and biomanufacturing strategies (Ostergaard et al, 2000; Szczebara et al, 2003; Nguyen et al, 2004; Veen and Lang, 2004; Ro et al, 2006; Hawkins and Smolke, 2008). The majority of existing methods for tuning gene expression in yeast are through transcriptional control mechanisms in the form of inducible and constitutive promoter systems (Hawkins and Smolke, 2006; Nevoigt et al, 2006; Nevoigt et al, 2007). RNA-based control modules based on posttranscriptional mechanisms may offer an advantage in that they can be coupled to any promoter of choice, providing for enhanced control strategies and finer resolution tuning of protein expression levels. Although posttranscriptional control elements, such as internal ribosome entry sites and AU-rich elements, have been applied to regulate heterologous gene expression in yeast (Vasudevan and Peltz, 2001; Zhou et al, 2001; Lautz et al, 2010), these control elements have exhibited substantial variability in activity and have not been engineered as synthetic libraries exhibiting a wide range of predictable gene regulatory activities. RNase III enzymes are a class of enzymes that cleave double-stranded RNA. The S. cerevisiae RNase III enzyme, Rnt1p, exhibits a number of unique features that allow it to recognize very specific RNA hairpin substrates that harbor a consensus AGNN tetraloop sequence. Despite extensive characterization of this enzyme and its demonstrated role in processing non-coding RNA and mRNA, neither natural nor synthetic Rnt1p substrates have been used to control gene expression levels in yeast. Therefore, we developed a genetic control system based on directed Rnt1p processing of a target transcript. Specifically, Rnt1p hairpins were immediately flanked by a clamp sequence (that insulates the hairpin structure from surrounding sequences) and placed downstream of a gene of interest, where they direct cleavage and thus inactivate the transcript, resulting in rapid transcript degradation. We validated this Rnt1p-based control system with two Rnt1p hairpins based on previous in vitro studies and demonstrated that Rnt1p hairpins can act as gene control modules in yeast. Previous in vitro studies had identified three key regions in Rnt1p hairpins: the cleavage efficiency box (CEB), the binding stability box and the initial binding and positioning box (Lamontagne et al, 2003). The CEB region affects the processing of the hairpin stem by Rnt1p, such that nucleotide (nt) modifications in this region are expected to specifically modulate the cleavage rate. We created an Rnt1p hairpin library by randomizing the CEB region (12 nt). This library was placed downstream of a fluorescent reporter protein and a cell-based screening assay was used to identify functional members of the library that resulted in lowered fluorescence levels. The functional Rnt1p hairpin library comprises 16 unique sequences that span a large gene regulatory range—from 8 to 85% (Figure 3A)—and are fairly evenly distributed across this range. The negative controls for each sequence (constructed by mutating the required consensus tetraloop sequence) demonstrated that the majority of gene knockdown observed from each hairpin is due to Rnt1p processing (Figure 3B). A correlation analysis on the transcript and protein levels for each library hairpin construct indicated a strong positive correlation and a strong preservation of rank order between the two in vivo regulatory measurements (Figure 3C). Characterization of the hairpin library in a different genetic context supported the broader utility of these control modules for providing predictable gene control. We applied the Rnt1p control modules to titrating a key enzyme component of the endogenous ergosterol biosynthesis network—the ERG9 genetic target. Squalene synthase, encoded by the ERG9 gene, is responsible for catalyzing the conversion of two molecules of farnesyl pyrophosphate to squalene, the first precursor in the ergosterol biosynthetic pathway in S. cerevisiae (Poulter and Rilling, 1981; Figure 6A). We integrated several members of the Rnt1p hairpin library downstream of the native ERG9 gene to cover the regulatory range of the library (Figure 6B). A strong positive correlation and preservation of rank order was observed between the ERG9 transcript levels and their yEGFP3 counterparts (Figure 6C). However, ERG9 expression levels did not fall below ∼40%, regardless of the Rnt1p hairpin strength, indicating that a previously identified endogenous feedback mechanism associated with the native ERG9 promoter acts to maintain ERG9 expression levels at that threshold value. In addition, most strains exhibited high relative ergosterol levels and growth rates, except for two strains harboring synthetic Rnt1p hairpins that resulted in the lowest expression levels, which exhibited a significant reduction in the amount of ergosterol produced and growth rate (Figure 6D and E). Our studies indicate that the endogenous feedback mechanism can be acting to increase ERG9 expression levels to the desired set point in the slow-growing strains, but the perturbations introduced in these strains may result in other impacts on the pathway that inhibit the endogenous control systems from restoring cellular growth to wild-type rates. These studies support the unique ability of the synthetic Rnt1p hairpin library to systematically titrate pathway enzyme levels by introducing precise perturbations around major control points while maintaining native cellular control strategies acting through transcriptional mechanisms. Advances in synthetic biology have resulted in the development of genetic tools that support the design of complex biological systems encoding desired functions. The majority of efforts have focused on the development of regulatory tools in bacteria, whereas fewer tools exist for the tuning of expression levels in eukaryotic organisms. Here, we describe a novel class of RNA-based control modules that provide predictable tuning of expression levels in the yeast Saccharomyces cerevisiae. A library of synthetic control modules that act through posttranscriptional RNase cleavage mechanisms was generated through an in vivo screen, in which structural engineering methods were applied to enhance the insulation and modularity of the resulting components. This new class of control elements can be combined with any promoter to support titration of regulatory strategies encoded in transcriptional regulators and thus more sophisticated control schemes. We applied these synthetic controllers to the systematic titration of flux through the ergosterol biosynthesis pathway, providing insight into endogenous control strategies and highlighting the utility of this control module library for manipulating and probing biological systems.
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16
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Tabaka M, Hołyst R. Binary and graded evolution in time in a simple model of gene induction. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:052902. [PMID: 21230531 DOI: 10.1103/physreve.82.052902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Indexed: 05/30/2023]
Abstract
We solve analytically the model of gene expression induction which consists of three steps: gene activation, gene products synthesis, and product degradation. The solution is given as a time-dependent probability distribution for gene products. Following the distribution in time from the inactive state of the gene to the stationary state we observe binary or graded response depending solely on the ratio r of the gene activation rate to the rate of the gene product degradation. If r << 1 the response is binary and the continuous transition from binary to graded response occurs between r=0.1 and r=1. Therefore, if binary response is observed during relaxation to steady state, then the activation rate constant must be smaller than the degradation rate constant.
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Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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17
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Zhuravel D, Fraser D, St-Pierre S, Tepliakova L, Pang WL, Hasty J, Kærn M. Phenotypic impact of regulatory noise in cellular stress-response pathways. SYSTEMS AND SYNTHETIC BIOLOGY 2010; 4:105-16. [PMID: 20805931 PMCID: PMC2923296 DOI: 10.1007/s11693-010-9055-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 04/02/2010] [Indexed: 11/25/2022]
Abstract
Recent studies indicate that intrinsic promoter-mediated gene expression noise can confer a selective advantage under acute environmental stress by providing beneficial phenotypic diversity within cell populations. To investigate how extrinsic gene expression noise impacts the fitness of cell populations under stress, we engineered two nearly isogenic budding yeast strains; one carrying a two-step regulatory cascade that allows for precise control of the noise transmitted from a transcriptional regulator to a downstream stress-inducing gene, and one carrying a network with low constant upstream noise. The fitness and gene expression of these strains were compared under acute and prolonged stress exposure. Using a phenomenological modeling approach, we predicted that increased noise should confer a fitness advantage under high stress conditions, but reciprocally reduce the resistance of the population to low stress. The model also predicted that extrinsic noise might serve as a basis for phenotypic plasticity whereby gene expression distributions are modulated in response to prolonged stress. Experimentally, we confirmed the predicted differential fitness advantage of extrinsic noise under acute stress, as well as the predicted modulation of gene expression under prolonged stress. However, contrary to model predictions, strains with low and high extrinsic noise showed very similar adaptive responses to prolonged stress. This suggests that while phenotypic heterogeneity generated by noise in regulatory signals can confer increased robustness to acute stress, it is not a requirement for the observed long-term phenotypic plasticity.
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Affiliation(s)
- Daniil Zhuravel
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
| | - Dawn Fraser
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5 Canada
| | - Simon St-Pierre
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
| | - Lioudmila Tepliakova
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
| | - Wyming L. Pang
- Department of Bioengineering and Institute for Nonlinear Science, University of California at San Diego, 500 Gilman Drive, La Jolla, CA 92093 USA
- Institute for Systems Biology, Seattle, WA 98103 USA
| | - Jeff Hasty
- Department of Bioengineering and Institute for Nonlinear Science, University of California at San Diego, 500 Gilman Drive, La Jolla, CA 92093 USA
| | - Mads Kærn
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5 Canada
- Department of Physics, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario K1N 6N5 Canada
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18
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Kimmig S, Baumgrass R. [Biological switches: the 'all-or-none' principle in T-cell activation]. Z Rheumatol 2009; 68:560, 562-5. [PMID: 19585132 DOI: 10.1007/s00393-009-0495-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
T helper lymphocytes (Th cells) play a central role in cellular defence against pathogens as well as in cellular self tolerance. The activation of Th cells is a crucial process determining the course of a protective immune response. Dysregulated activation processes can lead to pathologic immune reactions and may induce autoimmune diseases. Thus, for example, chronic activation of Th cells can trigger autoimmune diseases such as rheumatoid arthritis. One fundamental feature of antigen-specific T-cell activation is the synthesis of cytokines, e.g. Interleukin- (IL-)2. Here we present results of our working group indicating for the first time that, at the level of the individual cell, IL-2 is expressed in a binary fashion, i.e. according to an all-or-none principle. The identification and characterization of such intracellular switches may provide new options to manipulate the fate of T cells and develop novel therapeutic strategies.
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Affiliation(s)
- S Kimmig
- Deutsches Rheuma-Forschungszentrum, Charitéplatz 1, 10117, Berlin, Deutschland
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19
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A role for the transcriptional repressor Blimp-1 in CD8(+) T cell exhaustion during chronic viral infection. Immunity 2009; 31:309-20. [PMID: 19664943 DOI: 10.1016/j.immuni.2009.06.019] [Citation(s) in RCA: 376] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/15/2009] [Accepted: 06/29/2009] [Indexed: 01/01/2023]
Abstract
T cell exhaustion is common during chronic infections and can prevent optimal immunity. Although recent studies have demonstrated the importance of inhibitory receptors and other pathways in T cell exhaustion, the underlying transcriptional mechanisms are unknown. Here, we define a role for the transcription factor Blimp-1 in CD8(+) T cell exhaustion during chronic viral infection. Blimp-1 repressed key aspects of normal memory CD8(+) T cell differentiation and promoted high expression of inhibitory receptors during chronic infection. These cardinal features of CD8(+) T cell exhaustion were corrected by conditionally deleting Blimp-1. Although high expression of Blimp-1 fostered aspects of CD8(+) T cell exhaustion, haploinsufficiency indicated that moderate Blimp-1 expression sustained some effector function during chronic viral infection. Thus, we identify Blimp-1 as a transcriptional regulator of CD8(+) T cell exhaustion during chronic viral infection and propose that Blimp-1 acts as a transcriptional rheostat balancing effector function and T cell exhaustion.
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20
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Jordan JJ, Menendez D, Inga A, Nourredine M, Bell D, Resnick MA. Noncanonical DNA motifs as transactivation targets by wild type and mutant p53. PLoS Genet 2008; 4:e1000104. [PMID: 18714371 PMCID: PMC2518093 DOI: 10.1371/journal.pgen.1000104] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2008] [Accepted: 05/22/2008] [Indexed: 12/31/2022] Open
Abstract
Sequence-specific binding by the human p53 master regulator is critical to its tumor suppressor activity in response to environmental stresses. p53 binds as a tetramer to two decameric half-sites separated by 0–13 nucleotides (nt), originally defined by the consensus RRRCWWGYYY (n = 0–13) RRRCWWGYYY. To better understand the role of sequence, organization, and level of p53 on transactivation at target response elements (REs) by wild type (WT) and mutant p53, we deconstructed the functional p53 canonical consensus sequence using budding yeast and human cell systems. Contrary to early reports on binding in vitro, small increases in distance between decamer half-sites greatly reduces p53 transactivation, as demonstrated for the natural TIGER RE. This was confirmed with human cell extracts using a newly developed, semi–in vitro microsphere binding assay. These results contrast with the synergistic increase in transactivation from a pair of weak, full-site REs in the MDM2 promoter that are separated by an evolutionary conserved 17 bp spacer. Surprisingly, there can be substantial transactivation at noncanonical ½-(a single decamer) and ¾-sites, some of which were originally classified as biologically relevant canonical consensus sequences including PIDD and Apaf-1. p53 family members p63 and p73 yielded similar results. Efficient transactivation from noncanonical elements requires tetrameric p53, and the presence of the carboxy terminal, non-specific DNA binding domain enhanced transactivation from noncanonical sequences. Our findings demonstrate that RE sequence, organization, and level of p53 can strongly impact p53-mediated transactivation, thereby changing the view of what constitutes a functional p53 target. Importantly, inclusion of ½- and ¾-site REs greatly expands the p53 master regulatory network. Within human cells, the tumor suppressor p53 is the central node of regulation required to elicit multiple biological responses that include cell cycle arrest and death in response to stress or DNA damage, where mutations in p53 are a hallmark of cancer. As a master regulatory gene, p53 controls the action of target genes within its network by directly interacting with a widely accepted consensus DNA binding sequence, composed of two decamer ½-sites that can be separated by up to 13 bases. While mismatches from consensus sequence are frequent, the canonical consensus sequence places a limitation upon the organization and number of target genes within the p53 transcriptional network. Using yeast and human cell systems, our goal was to further understand how the DNA sequence, DNA organization, and level of p53 expression might influence the inclusion of genes within the p53 regulatory network. We found that increases in spacer beyond a few bases greatly reduce responsiveness to p53. Importantly, we established that p53 can function from noncanonical sequences comprising only a decamer ½-site or a ¾-site. These findings further define and expand the universe of potential downstream target genes which may be regulated by p53 and bring further diversity into the p53 regulatory network.
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Affiliation(s)
- Jennifer J. Jordan
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel Menendez
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
| | - Alberto Inga
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
- Unit of Molecular Mutagenesis and DNA Repair, National Institute for Cancer Research, IST, Genoa, Italy
| | - Maher Nourredine
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
| | - Douglas Bell
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
| | - Michael A. Resnick
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina, United States of America
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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21
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Abstract
Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model.
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Affiliation(s)
- Thomas Schlitt
- Department of Medical and Molecular Genetics, King's College London School of Medicine, 8floor Guy's Tower, London SE1 9RT, UK
| | - Alvis Brazma
- European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
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22
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Podtschaske M, Benary U, Zwinger S, Höfer T, Radbruch A, Baumgrass R. Digital NFATc2 activation per cell transforms graded T cell receptor activation into an all-or-none IL-2 expression. PLoS One 2007; 2:e935. [PMID: 17895976 PMCID: PMC1978524 DOI: 10.1371/journal.pone.0000935] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 08/30/2007] [Indexed: 11/19/2022] Open
Abstract
The expression of interleukin-2 (IL-2) is a key event in T helper (Th) lymphocyte activation, controlling both, the expansion and differentiation of effector Th cells as well as the activation of regulatory T cells. We demonstrate that the strength of TCR stimulation is translated into the frequency of memory Th cells expressing IL-2 but not into the amount of IL-2 per cell. This molecular switch decision for IL-2 expression per cell is located downstream of the cytosolic Ca2+ level. Here we show that in a single activated Th cell, NFATc2 activation is digital but NF-κB activation is graded after graded T cell receptor (TCR) signaling. Subsequently, NFATc2 translocates into the nucleus in an all-or-none fashion per cell, transforming the strength of TCR-stimulation into the number of nuclei positive for NFATc2 and IL-2 transcription. Thus, the described NFATc2 switch regulates the number of Th cells actively participating in an immune response.
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MESH Headings
- Active Transport, Cell Nucleus/drug effects
- Antigens, CD/metabolism
- Antigens, Differentiation, T-Lymphocyte/metabolism
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/metabolism
- Calcineurin/pharmacology
- Calcium/metabolism
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Cells, Cultured
- Flow Cytometry
- Humans
- Interferon-gamma/metabolism
- Interleukin-2/genetics
- Interleukin-2/metabolism
- Ionomycin/pharmacology
- Lectins, C-Type
- Lymphocyte Activation/drug effects
- Models, Theoretical
- NF-kappa B/metabolism
- NFATC Transcription Factors/genetics
- NFATC Transcription Factors/metabolism
- Phosphorylation
- Receptors, Antigen, T-Cell/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- T-Lymphocytes, Helper-Inducer/drug effects
- T-Lymphocytes, Helper-Inducer/metabolism
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Affiliation(s)
| | - Uwe Benary
- German Rheumatism Research Centre, Berlin, Germany
| | - Sandra Zwinger
- Institute of Medical Immunology, Charité, Humboldt-University Berlin, Berlin, Germany
| | - Thomas Höfer
- Department of Theoretical Biophysics, Humboldt-University Berlin, Berlin, Germany
| | | | - Ria Baumgrass
- German Rheumatism Research Centre, Berlin, Germany
- * To whom correspondence should be addressed. E-mail:
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23
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Shi YY, Miller GA, Qian H, Bomsztyk K. Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences. Proc Natl Acad Sci U S A 2006; 103:11527-32. [PMID: 16861299 PMCID: PMC1544203 DOI: 10.1073/pnas.0604316103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Major advances in large-scale yeast two-hybrid screening have provided a global view of binary protein-protein interactions across species as dissimilar as human, yeast, and bacteria. Remarkably, these analyses have revealed that all species studied have a degree distribution of protein-protein binding that is approximately scale-free (varies as a power law) even though their evolutionary divergence times differ by billions of years. The universal power law shows only the surface of the rich information harbored by these high-throughput data. We develop a detailed mathematical model of the protein-protein interaction network based on association free energy, the biochemical quantity that determines protein-protein interaction strength. This model reproduces the degree distribution of all of the large-scale yeast two-hybrid data sets available and allows us to extract the distribution of free energy, the likelihood that a pair of proteins of a given species will bind. We find that across-species interactomes have significant differences that reflect the strengths of the protein-protein interaction. Our results identify a global evolutionary shift: more evolved organisms have weaker binary protein-protein binding. This result is consistent with the evolution of increased protein unfoldedness and challenges the dogma that only specific protein-protein interactions can be biologically functional.
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Affiliation(s)
| | | | | | - Karol Bomsztyk
- Medicine, University of Washington, Seattle, WA 98195
- To whom correspondence should be addressed at:
University of Washington, Box 358050, Seattle, WA 98109. E-mail:
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24
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Schlitt T, Brazma A. Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos Trans R Soc Lond B Biol Sci 2006; 361:483-94. [PMID: 16524837 PMCID: PMC1609346 DOI: 10.1098/rstb.2005.1806] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Approaches to describe gene regulation networks can be categorized by increasing detail, as network parts lists, network topology models, network control logic models or dynamic models. We discuss the current state of the art for each of these approaches. We study the relationship between different topology models, and give examples how they can be used to infer functional annotations for genes of unknown function. We introduce a new simple way of describing dynamic models called finite state linear model (FSLM). We discuss the gap between the parts list and topology models on one hand, and network logic and dynamic models, on the other hand. The first two classes of models have reached a genome-wide scale, while for the other model classes high-throughput technologies are yet to make a major impact.
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Affiliation(s)
- Thomas Schlitt
- European Bioinformatics Institute, Wellcome Trust Genome CampusEMBL-EBI, Cambridge CB10 1SD, UK
- British Antarctic Survey, National Environment Research CouncilHigh Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Alvis Brazma
- European Bioinformatics Institute, Wellcome Trust Genome CampusEMBL-EBI, Cambridge CB10 1SD, UK
- Author for correspondence ()
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25
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Zhang Q, Andersen ME, Conolly RB. Binary gene induction and protein expression in individual cells. Theor Biol Med Model 2006; 3:18. [PMID: 16597340 PMCID: PMC1488830 DOI: 10.1186/1742-4682-3-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 04/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eukaryotic gene transcription is believed to occur in either a binary or a graded fashion. With binary induction, a transcription activator (TA) regulates the probability with which a gene template is switched from the inactive to the active state without affecting the rate at which RNA molecules are produced from the template. With graded, also called rheostat-like, induction the gene template has continuously varying levels of transcriptional activity, and the TA regulates the rate of RNA production. Support for each of these two mechanisms arises primarily from experimental studies measuring reporter proteins in individual cells, rather than from direct measurement of induction events at the gene template. METHODS AND RESULTS In this paper, using a computational model of stochastic gene expression, we have studied the biological and experimental conditions under which a binary induction mode operating at the gene template can give rise to differentially expressed "phenotypes" (i.e., binary, hybrid or graded) at the protein level. We have also investigated whether the choice of reporter genes plays a significant role in determining the observed protein expression patterns in individual cells, given the diverse properties of commonly-used reporter genes. Our simulation confirmed early findings that the lifetimes of active/inactive promoters and half-lives of downstream mRNA/protein products are important determinants of various protein expression patterns, but showed that the induction time and the sensitivity with which the expressed genes are detected are also important experimental variables. Using parameter conditions representative of reporter genes including green fluorescence protein (GFP) and beta-galactosidase, we also demonstrated that graded gene expression is more likely to be observed with GFP, a longer-lived protein with low detection sensitivity. CONCLUSION The choice of reporter genes may determine whether protein expression is binary, graded or hybrid, even though gene induction itself operates in an all-or-none fashion.
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Affiliation(s)
- Qiang Zhang
- Division of Computational Biology, CIIT Centers for Health Research, Research Triangle Park, NC 27709, USA
| | - Melvin E Andersen
- Division of Computational Biology, CIIT Centers for Health Research, Research Triangle Park, NC 27709, USA
| | - Rory B Conolly
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
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26
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Hawkins KM, Smolke CD. The regulatory roles of the galactose permease and kinase in the induction response of the GAL network in Saccharomyces cerevisiae. J Biol Chem 2006; 281:13485-13492. [PMID: 16524886 DOI: 10.1074/jbc.m512317200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The GAL genetic switch of Saccharomyces cerevisiae exhibits an ultrasensitive response to the inducer galactose as well as the "all-or-none" behavior characteristic of many eukaryotic regulatory networks. We have constructed a strain that allows intermediate levels of gene expression from a tunable GAL1 promoter at both the population and the single cell level by altering the regulation of the galactose permease Gal2p. Similar modifications to other feedback loops regulating the Gal80p repressor and the Gal3p signaling protein did not result in similarly tuned responses, indicating that the level of inducer transport is unique in its ability to control the switch response of the network. In addition, removal of the Gal1p galactokinase from the network resulted in a regimed response due to the dual role of this enzyme in galactose catabolism and transport. These two activities have competing effects on the response of the network to galactose such that the transport effects of Gal1p are dominant at low galactose concentrations, whereas its catabolic effects are dominant at high galactose concentrations. In addition, flow cytometry analysis revealed the unexpected phenomenon of multiple populations in the gal1delta strains, which were not present in the isogenic GAL1 background. This result indicates that Gal1p may play a previously undescribed role in the stability of the GAL network response.
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Affiliation(s)
- Kristy M Hawkins
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Christina D Smolke
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125.
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27
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Andersen ME, Lutz RW, Liao KH, Lutz WK. Dose-Incidence Modeling: Consequences of Linking Quantal Measures of Response to Depletion of Critical Tissue Targets. Toxicol Sci 2005; 89:331-7. [PMID: 16237194 DOI: 10.1093/toxsci/kfj024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In developing mechanistic PK-PD models, incidence of toxic responses in a population has to be described in relation to measures of biologically effective dose (BED). We have developed a simple dose-incidence model that links incidence with BED for compounds that cause toxicity by depleting critical cellular target molecules. The BED in this model was the proportion of target molecule adducted by the dose of toxic compound. Our modeling approach first estimated the proportion depleted for each dose and then calculated the tolerance distribution for toxicity in relation to either administered dose or log of administered dose. We first examined cases where the mean of the tolerance distribution for toxicity occurred when a significant proportion of target had been adducted (i.e., more than half). When a normal distribution was assumed to exist for the relationship of incidence and BED, the tolerance distribution based on administered dose for these cases becomes asymmetrical and logarithmic transformations of the administered dose axis lead to a more symmetrical distribution. These linked PK-PD models for tissue reactivity, consistent with conclusions from other work for receptor binding models (Lutz et al., 2005), indicate that log normal distributions with administered dose may arise from normal distributions for BED and nonlinear kinetics between BED and administered dose. These conclusions are important for developing biologically based dose response (BBDR) models that link incidences of toxicity or other biological responses to measures of BED.
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Affiliation(s)
- Melvin E Andersen
- CIIT Centers for Health Research, Research Triangle Park, North Carolina 27709-2137, USA.
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Broccardo CJ, Billings RE, Andersen ME, Hanneman WH. Probing the Control Elements of the CYP1A1 Switching Module in H4IIE Hepatoma Cells. Toxicol Sci 2005; 88:82-94. [PMID: 16081525 DOI: 10.1093/toxsci/kfi271] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Previous research from our laboratory has shown a switch-like response to PCB 126 mediated CYP1A1 induction in primary rat hepatocytes and in H4IIE rat hepatoma cells. On a single cell level, cells appear to be either "on" or "off" for CYP1A1 induction at a given dose; some cells never respond to PCB 126. These cells represent a non-responding population. Cells that are switched "on" by PCB 126 display varying levels of induction, much like the dimmer on a light switch. The goal of the present research is to begin to uncover the mechanism for this switch-like response to CYP1A1 induction in H4IIE rat hepatoma cells. The AhR pathway is modulated by multiple co-activators and by phosphorylation. This research focuses on the phosphorylation cascades initiated by PCB 126 and the role they play in CYP1A1 induction. Our research reveals a likely role for protein kinase C (PKC) in this switch response. Inhibition of PKC by H-7 dramatically reduced the percent of cells that express CYP1A1 in response to PCB 126 treatment, as determined by flow cytometry. The effect of H-7 was concentration dependent, decreasing the number of cells expressing CYP1A1 rather than decreasing the level of CYP1A1 in all cells. This finding provides further evidence for the switch-like behavior of CYP1A1 induction and implicates PKC in this response to PCB126. The protein kinase inhibitor, HA-1004, had only a minor effect on CYP1A1 induction. A high-throughput immunoblot screen for 40 proteins revealed the regulation of several proteins/phosphoproteins by PCB 126. Most importantly, two proteins containing phosphoserine/phoshothreonine residues were increased by PCB126 treatment. However, PKC translocation studies and activity studies failed to verify that PCB126 activates PKC. It is possible that constitutive PKC activity is sufficient to maintain phosphorylation of critical components of the AhR pathway. Immunoblotting studies showed that MAP kinases ERK and JNK are not activated by PCB 126 in H4IIE cells and the ERK inhibitor U0126 did not impair CYP1A1 induction. Additional studies are planned to further investigate the role of PKC in the switch-like response to PCB 126.
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Affiliation(s)
- Carolyn J Broccardo
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523-1680, USA
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Abstract
Bistable and hysteretic switches, enabling cells to adopt multiple internal expression states in response to a single external input signal, have a pivotal impact on biological systems, ranging from cell-fate decisions to cell-cycle control. We have designed a synthetic hysteretic mammalian transcription network. A positive feedback loop, consisting of a transgene and transactivator (TA) cotranscribed by TA's cognate promoter, is repressed by constitutive expression of a macrolide-dependent transcriptional silencer, whose activity is modulated by the macrolide antibiotic erythromycin. The antibiotic concentration, at which a quasi-discontinuous switch of transgene expression occurs, depends on the history of the synthetic transcription circuitry. If the network components are imbalanced, a graded rather than a quasi-discontinuous signal integration takes place. These findings are consistent with a mathematical model. Synthetic gene networks, which are able to emulate natural gene expression behavior, may foster progress in future gene therapy and tissue engineering initiatives.
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Affiliation(s)
- Beat P Kramer
- Institute for Chemical and Bio-Engineering, Swiss Federal Institute of Technology, Eidgenössische Technische Hochschule Hoenggerberg, HCI F115, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
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Blais A, Dynlacht BD. Hitting their targets: an emerging picture of E2F and cell cycle control. Curr Opin Genet Dev 2005; 14:527-32. [PMID: 15380244 DOI: 10.1016/j.gde.2004.07.003] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Understanding the role of transcription factors in governing cell-cycle progression in mammalian cells has been hindered until recently by a relative lack of genetic and genomic approaches. New approaches that harness the power of ChIP and combine this technique with DNA microarrays and bioinformatics have identified direct, physiological targets and have significantly altered our view of the E2F transcription factor that is known to play a role in regulation of cell-cycle progression. Further, the identification of additional E2F family members and factors that function in concert with E2F have considerably expanded our picture of the genetic programs that are governed by this essential regulatory factor.
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Affiliation(s)
- Alexandre Blais
- Department of Pathology, MSB 504, New York University School of Medicine and NYU Cancer Institute, 550 First Avenue, New York, New York 10016, USA.
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French CT, Hanneman WH, Chubb LS, Billings RE, Andersen ME. Induction of CYP1A1 in primary rat hepatocytes by 3,3',4,4',5-pentachlorobiphenyl: evidence for a switch circuit element. Toxicol Sci 2004; 78:276-86. [PMID: 15014209 DOI: 10.1093/toxsci/kfh105] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In vivo induction of CYP1A1 in hepatocytes by aryl hydrocarbon receptor agonists is heterogeneous. Using immunohistochemistry, cells appear to be either induced or not induced as if the response of an individual cell is better represented as a switch. We have examined induction of CYP1A1 in vitro in primary rat hepatocytes to distinguish the responses of populations of cells and responses of individual cells. Cells were treated with various concentrations of the aryl hydrocarbon receptor agonist, 3,3',4,4',5-pentachlorobiphenyl. Concentration-response and time-course responses were determined for the population of cells by Western blotting for CYP1A1 protein and by real-time RT-PCR for CYP1A1 mRNA. Individual cell responses were visualized by immunocytochemistry (ICC) for protein and by in situ hybridization (ISH) for mRNA. CYP1A1 mRNA was quantified by frequency distribution analysis of grains observed on the ISH slides. Population responses showed time- and concentration-related increases in induction. Single cell responses appeared as all-or-none in the field, with cells appearing to be induced and others appearing to be not induced. Even at the highest concentrations (2.5 x 10(-7) M), some hepatocytes remained unresponsive. Distribution frequencies of single cell induction were more consistent with a switch with variable levels of induction in cells depending on treatment concentration. Combined with the reports from in vivo studies, our results support a switch with rheostat behavior for individual hepatocytes. Mechanistic studies in liver cell lines that are confirmed to exhibit switch-like induction of single cells will be necessary to assess the molecular pathways of this circuit element.
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Affiliation(s)
- C Tenley French
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
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Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature 2004; 427:737-40. [PMID: 14973486 DOI: 10.1038/nature02298] [Citation(s) in RCA: 642] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2003] [Accepted: 12/16/2003] [Indexed: 11/09/2022]
Abstract
Multistability, the capacity to achieve multiple internal states in response to a single set of external inputs, is the defining characteristic of a switch. Biological switches are essential for the determination of cell fate in multicellular organisms, the regulation of cell-cycle oscillations during mitosis and the maintenance of epigenetic traits in microbes. The multistability of several natural and synthetic systems has been attributed to positive feedback loops in their regulatory networks. However, feedback alone does not guarantee multistability. The phase diagram of a multistable system, a concise description of internal states as key parameters are varied, reveals the conditions required to produce a functional switch. Here we present the phase diagram of the bistable lactose utilization network of Escherichia coli. We use this phase diagram, coupled with a mathematical model of the network, to quantitatively investigate processes such as sugar uptake and transcriptional regulation in vivo. We then show how the hysteretic response of the wild-type system can be converted to an ultrasensitive graded response. The phase diagram thus serves as a sensitive probe of molecular interactions and as a powerful tool for rational network design.
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Affiliation(s)
- Ertugrul M Ozbudak
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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