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Likhoshvai VA, Golubyatnikov VP, Khlebodarova TM. Limit cycles in models of circular gene networks regulated by negative feedback loops. BMC Bioinformatics 2020; 21:255. [PMID: 32921311 PMCID: PMC7488683 DOI: 10.1186/s12859-020-03598-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal reception and its implementation, provide natural conditions for complicated dynamic regimes in these systems. The delay phenomenon at the intracellular level is a consequence of the matrix principle of data transmission, implemented through the rather complex processes of transcription and translation.However, the rules of the influence of system structure on system dynamics are not clearly understood. Knowledge of these rules is particularly important for construction of synthetic gene networks with predetermined properties. RESULTS We study dynamical properties of models of simplest circular gene networks regulated by negative feedback mechanisms. We have shown existence and stability of oscillating trajectories (cycles) in these models. Two algorithms of construction and localization of these cycles have been proposed. For one of these models, we have solved an inverse problem of parameters identification. CONCLUSIONS The modeling results demonstrate that non-stationary dynamics in the models of circular gene networks with negative feedback loops is achieved by a high degree of non-linearity of the mechanism of the autorepressor influence on its own expression, by the presence of regulatory signal delay, the value of which must exceed a certain critical value, and transcription/translation should be initiated from a sufficiently strong promoter/Shine-Dalgarno site. We believe that the identified patterns are key elements of the oscillating construction design.
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Affiliation(s)
- Vitaly A Likhoshvai
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch RAS, Novosibirsk, Russia
| | - Vladimir P Golubyatnikov
- Laboratory of Inverse Problems of Mathematical Physics, Sobolev Institute of Mathematics Siberian Branch RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | - Tamara M Khlebodarova
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Khlebodarova TM, Kogai VV, Fadeev SI, Likhoshvai VA. Chaos and hyperchaos in simple gene network with negative feedback and time delays. J Bioinform Comput Biol 2016; 15:1650042. [PMID: 28052708 DOI: 10.1142/s0219720016500426] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Today there are examples that prove the existence of chaotic dynamics at all levels of organization of living systems, except intracellular, although such a possibility has been theoretically predicted. The lack of experimental evidence of chaos generation at the intracellular level in vivo may indicate that during evolution the cell got rid of chaos. This work allows the hypothesis that one of the possible mechanisms for avoiding chaos in gene networks can be a negative evolutionary selection, which prevents fixation or realization of regulatory circuits, creating too mild, from the biological point of view, conditions for the emergence of chaos. It has been shown that one of such circuits may be a combination of negative autoregulation of expression of transcription factors at the level of their synthesis and degradation. The presence of such a circuit results in formation of multiple branches of chaotic solutions as well as formation of hyperchaos with equal and sufficiently low values of the delayed argument that can be implemented not only in eukaryotic, but in prokaryotic cells.
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Affiliation(s)
- Tamara M Khlebodarova
- * Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr., Lavrentieva 10, Novosibirsk, 630090, Russia
| | - Vladislav V Kogai
- † Sobolev Institute of Mathematics, Siberian Branch, Russian Academy of Sciences, Prospect Koptyuga 4, Novosibirsk, 630090, Russia
| | - Stanislav I Fadeev
- † Sobolev Institute of Mathematics, Siberian Branch, Russian Academy of Sciences, Prospect Koptyuga 4, Novosibirsk, 630090, Russia
| | - Vitaly A Likhoshvai
- * Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr., Lavrentieva 10, Novosibirsk, 630090, Russia.,‡ Novosibirsk State University, av. Pirogova 2, Novosibirsk, 630090, Russia
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Likhoshvai VA, Kogai VV, Fadeev SI, Khlebodarova TM. Alternative splicing can lead to chaos. J Bioinform Comput Biol 2015; 13:1540003. [PMID: 25556917 DOI: 10.1142/s021972001540003x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Alternative splicing is a widespread phenomenon in higher eukaryotes, where it serves as a mechanism to increase the functional diversity of proteins. This phenomenon has been described for different classes of proteins, including transcription regulatory proteins. We demonstrated that in the simplest genetic system model the formation of the alternatively spliced isoforms with opposite functions (activators and repressors) could be a cause of transition to chaotic dynamics. Under the simplest genetic system we understand a system consisting of a single gene encoding the structure of a transcription regulatory protein whose expression is regulated by a feedback mechanism. As demonstrated by numerical analysis of the models, if the synthesized isoforms regulate the expression of their own gene acting through different sites and independently of each other, for the generation of chaotic dynamics it is sufficient that the regulatory proteins have a dimeric structure. If regulatory proteins act through one site, the chaotic dynamics is generated in the system only when the repressor protein is either a tetrameric or a higher-dimensional multimer. In this case the activator can be a dimer. It was also demonstrated that if the transcription factor isoforms exhibit either activating or inhibiting activity and are lower-dimensional multimers (< 4), independently of the regulation type the model demonstrates either cyclic or stationary trajectories.
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Affiliation(s)
- Vitaly A Likhoshvai
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, pr. Lavrentieva 10, Novosibirsk 630090, Russia , Novosibirsk State University, av. Pirogova 2, Novosibirsk 630090, Russia
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Algamas-Dimantov A, Davidovsky D, Ben-Ari J, Kang JX, Peri I, Hertz R, Bar-Tana J, Schwartz B. Amelioration of diabesity-induced colorectal ontogenesis by omega-3 fatty acids in mice. J Lipid Res 2012; 53:1056-70. [PMID: 22357704 DOI: 10.1194/jlr.m021949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Postnatal intestinal ontogenesis in an animal model of diabesity may recapitulate morphological and transduction features of diabesity-induced intestinal dysplasia and its amelioration by endogenous (n-3) polyunsaturated fatty acids (PUFA). Proliferation, differentiation, and transduction aspects of intestinal ontogenesis have been studied here in obese, insulin-resistant db/db mice, in fat-1 transgene coding for desaturation of (n-6) PUFA into (n-3) PUFA, in db/db crossed with fat-1 mice, and in control mice. Diabesity resulted in increased colonic proliferation and dedifferentiation of epithelial colonocytes and goblet cells, with increased colonic β-catenin and hepatocyte nuclear factor (HNF)-4α transcriptional activities accompanied by enrichment in HNF-4α-bound (n-6) PUFA. In contrast, in fat-1 mice, colonic proliferation was restrained, accompanied by differentiation of crypt stem cells into epithelial colonocytes and goblet cells and by decrease in colonic β-catenin and HNF-4α transcriptional activities, with concomitant enrichment in HNF-4α-bound (n-3) PUFA at the expense of (n-6) PUFA. Colonic proliferation and differentiation, the profile of β-catenin and HNF-4α-responsive genes, and the composition of HNF-4α-bound PUFA of db/db mice reverted to wild-type by introducing the fat-1 gene into the db/db context. Suppression of intestinal HNF-4α activity by (n-3) PUFA may ameliorate diabesity-induced intestinal ontogenesis and offer an effective preventive modality for colorectal cancer.
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Affiliation(s)
- Anna Algamas-Dimantov
- Institute of Biochemistry, Food Science, and Nutrition and Interdepartmental Equipment Facility, Hebrew University of Jerusalem, Jerusalem, Israel
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Bailly A, Briançon N, Weiss MC. Characterization of glucocorticoid receptor and hepatocyte nuclear factor 4alpha (HNF4alpha) binding to the hnf4alpha gene in the liver. Biochimie 2009; 91:1095-103. [PMID: 19540905 DOI: 10.1016/j.biochi.2009.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 06/12/2009] [Indexed: 11/15/2022]
Abstract
Hepatocyte nuclear factor 4alpha (HNF4alpha) plays a crucial role in hepatocyte differentiation, liver organogenesis and regulation of liver functions. In mouse liver, HNF4alpha is expressed from two promoters, P1 and P2, the latter being very weakly active and only in the embryo. Previously, using transfection assays we identified an enhancer upstream of P1 that mediates both HNF4alpha transactivation and glucocorticoid induction and showed that HNF4alpha1, originated from P1, represses activity of the P2 promoter, possibly through its indirect recruitment to the promoter. However, glucocorticoid receptor (GR) binding to the enhancer was not shown and HNF4alpha binding to P2, first reported in isolated human hepatocytes, was not confirmed in mouse liver. Here, to analyse glucocorticoid inducibility and auto-regulation of the hnf4alpha gene in the liver, we accurately mapped and quantitatively assessed GR and HNF4alpha binding to enhancer and HNF4alpha recruitment to the P2 promoter using chromatin immunoprecipitation (ChIP) and real-time PCR. We proved that GR binds to enhancer from embryonic day (E) 17.5 onward and HNF4alpha even earlier. We showed that HNF4alpha binds to P2 independently of the activation function (AF) 1 domain in adult liver. We mapped the binding region between -400 and -200 bp upstream of the transcription start site. Although Sp1 binds within this region in vitro, we did not find evidence of a role of this factor in HNF4alpha recruitment. Our results suggest that, in the liver, HNF4alpha expression may be induced by glucocorticoids around birth and positive auto-regulation of the gene may take place early in development. They support a model of P2 repression involving HNF4alpha recruitment to promoter, possibly through interaction with several promoter-bound factors.
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Affiliation(s)
- Alain Bailly
- Unité de Génétique de la Différenciation, URA 2578 du CNRS, Département de Biologie du Développement, Institut Pasteur, 75724 Paris Cedex 15, France.
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Schwartz B, Algamas-Dimantov A, Hertz R, Nataf J, Kerman A, Peri I, Bar-Tana J. Inhibition of colorectal cancer by targeting hepatocyte nuclear factor-4alpha. Int J Cancer 2009; 124:1081-9. [PMID: 19048623 DOI: 10.1002/ijc.24041] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Hepatocyte nuclear factor-4alpha (HNF-4alpha) serves as target for fatty acid nutrients and xenobiotic amphipathic carboxylates and may account for the differential effects of dietary fatty acids on colorectal cancer (CRC). The putative role played by HNF-4alpha in CRC has been verified here by evaluating the effect of HNF-4alpha antagonists and HNF-4alpha siRNA on CRC growth and proliferation in cultured CRC cells and xenotransplanted nude mice in vivo. HNF-4alpha ligand antagonists of the MEDICA series, namely, beta,beta'-tetramethylhexadecanedioic acid (M16betabeta) and gamma,gamma'-tetramethyloctadocanedioic acid (M18gammagamma) as well as HNF-4alpha siRNA are shown here to inhibit growth and proliferation of HT29 and Caco2 CRC cells, accompanied by increased subG1 cell population, downregulated PCNA, activation of caspase-3, upregulation of Bak and cytoplasmic cytochrome-c, and downregulation of Bcl-2 resulting in apoptotic death. Inhibition of CRC growth with concomitant apoptosis was further confirmed in nude mice xenotransplanted with HT29 CRC cells. CRC suppression by HNF-4alpha ligand antagonists and by HNF-4alpha siRNA was accounted for by suppression of HNF-4alpha transcription and protein expression. alpha,alpha'-tetrachlorotetradecanedioic acid (Cl-DICA), a MEDICA analogue that fails to suppress HNF-4alpha, was ineffective in suppressing growth of cultured or xenotransplanted HT29 CRC cells. Hence, increased transcriptional activity of HNF-4alpha converging onto genes coding for antiapoptotic oncogenes and cytokines may promote CRC development. Suppression of HNF-4alpha activity by natural or xenobiotic HNF-4alpha ligand antagonists or by HNF-4alpha siRNA may offer a treatment mode for CRC.
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Affiliation(s)
- Betty Schwartz
- The Institute of Biochemistry, Food Science and Nutrition, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Banerjee S, Bose I. Functional characteristics of a double positive feedback loop coupled with autorepression. Phys Biol 2008; 5:046008. [DOI: 10.1088/1478-3975/5/4/046008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Lazarevich NL, Alpern DV. Hepatocyte nuclear factor 4 in epithelial development and carcinogenesis. Mol Biol 2008. [DOI: 10.1134/s0026893308050075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Goodyer CG, Rhani Z, Zheng H. Expression of the hepatic specific V1 messenger ribonucleic acid of the human growth hormone receptor gene is regulated by hepatic nuclear factor (HNF)-4alpha2 and HNF-4alpha8. Mol Endocrinol 2007; 22:485-500. [PMID: 17991764 DOI: 10.1210/me.2007-0387] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Human (h) GH plays an essential role in growth and metabolism, and its effectiveness is modulated by the availability of its specific receptor [hGH receptor (hGHR)] on target cells. The hGHR gene has a complex 5'-regulatory region containing multiple first exons. Seven are clustered within two small regions: V2,V3,V9 (module A) and V1,V4,V7,V8 (module B). Module A-derived mRNAs are ubiquitously expressed whereas those from module B are only found in postnatal liver, suggesting developmental- and liver-specific regulation of module B hGHR gene expression. To characterize the elements regulating module B activity, we studied a 1.8-kb promoter of the highest expressing exon in liver, V1. This promoter was repressed in transfection assays; however, either 5'- or 3'-deletions relieved this, suggesting the presence of multiple negative regulatory elements. Six putative hepatic nuclear factor 4 (HNF-4) response elements were identified. We determined that HNF-4alpha is developmentally regulated in the human liver: HNF-4alpha2 and HNF-4alpha8 are expressed in fetal hepatocytes but only HNF-4alpha2 is expressed in postnatal liver. Transient transfection assays demonstrated that HNF-4alpha2 and HNF-4alpha8 have a similar dual effect on V1 transcription: activation via site 1 in the proximal promoter and repression through site 6, approximately 1.7 kb upstream. EMSA/electrophoretic mobility supershift assays and chromatin immunoprecipitation analyses confirmed these two sites are bound by HNF-4alpha. Based on these data, we speculate there are multiple regions working together to repress the expression of V1 hGHR transcripts in tissues other than the normal postnatal liver, and that HNF-4alpha is a good candidate for regulating V1 hGHR expression in the human hepatocyte.
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Affiliation(s)
- Cynthia Gates Goodyer
- McGill University Health Centre-Montreal Children's Hospital Research Institute, 4060 St Catherine West, Montreal, Quebec, Canada.
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Hwang-Verslues WW, Sladek FM. Nuclear receptor hepatocyte nuclear factor 4alpha1 competes with oncoprotein c-Myc for control of the p21/WAF1 promoter. Mol Endocrinol 2007; 22:78-90. [PMID: 17885207 PMCID: PMC2194635 DOI: 10.1210/me.2007-0298] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The dichotomy between cellular differentiation and proliferation is a fundamental aspect of both normal development and tumor progression; however, the molecular basis of this opposition is not well understood. To address this issue, we investigated the mechanism by which the nuclear receptor hepatocyte nuclear factor 4alpha1 (HNF4alpha1) regulates the expression of the human cyclin-dependent kinase inhibitor gene p21/WAF1 (CDKN1A). We found that HNF4alpha1, a transcription factor that plays a central role in differentiation in the liver, pancreas, and intestine, activates the expression of p21 primarily by interacting with promoter-bound Sp1 at both the proximal promoter region and at newly identified sites in a distal region (-2.4 kb). Although HNF4alpha1 also binds two additional regions containing putative HNF4alpha binding sites, HNF4alpha1 mutants deficient in DNA binding activate the p21 promoter to the same extent as wild-type HNF4alpha1, indicating that direct DNA binding by HNF4alpha1 is not necessary for p21 activation. We also observed an in vitro and in vivo interaction between HNF4alpha1 and c-Myc as well as a competition between these two transcription factors for interaction with promoter-bound Sp1 and regulation of p21. Finally, we show that c-Myc competes with HNF4alpha1 for control of apolipoprotein C3 (APOC3), a gene associated with the differentiated hepatic phenotype. These results suggest a general model by which a differentiation factor (HNF4alpha1) and a proliferation factor (c-Myc) may compete for control of genes involved in cell proliferation and differentiation.
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Affiliation(s)
- Wendy W Hwang-Verslues
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, USA
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Leng S, Lu S, Yao Y, Kan Z, Morris GS, Stair BR, Cherny MA, Black DD. Hepatocyte nuclear factor-4 mediates apolipoprotein A-IV transcriptional regulation by fatty acid in newborn swine enterocytes. Am J Physiol Gastrointest Liver Physiol 2007; 293:G475-83. [PMID: 17556588 DOI: 10.1152/ajpgi.00072.2007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Hepatocyte nuclear factor-4alpha (HNF-4alpha) regulates transcription of several genes involved in lipid metabolism, including that of apolipoprotein (apo) A-IV, which is tightly regulated by lipid absorption and enhances enterocyte chylomicron secretion. Studies were performed to define the role of HNF-4alpha in the regulation of apo A-IV gene transcription by dietary fatty acid in neonatal swine small intestine. HNF-4alpha mRNA was expressed in liver > intestine > kidney in suckling, weanling, and weaned pigs. Jejunal HNF-4alpha mRNA and protein and apo A-IV and swine microsomal triglyceride transfer protein (MTP) large subunit mRNA expression were induced in parallel in 2-day-old swine by a 24-h high-fat intraduodenal infusion. In IPEC-1 cells, incubation with oleic acid (OA) resulted in coordinate induction of both HNF-4alpha, apo A-IV, and MTP mRNA, similar to that observed in vivo. When HNF-4alpha expression was driven by doxycycline by using the TET-On system in the absence of OA to observe the effect of HNF-4alpha directly on apo A-IV and MTP mRNA levels in the absence of other factors that might be concomitantly induced by fatty acid absorption, apo A-IV and MTP expression were increased. In luciferase reporter gene assays in IPEC-1 cells using apo A-IV/C-III intergenic region constructs, TET-On-regulated HNF-4alpha expression without OA increased luciferase activity, and incubation with OA did not further increase activity. These data suggest that acute induction of the apo A-IV and MTP genes by dietary lipid in newborn intestine occurs, at least in part, via ligand-independent transactivation by HNF-4alpha that is itself induced by a lipid-mediated mechanism.
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Affiliation(s)
- Shuangying Leng
- Children's Foundation Research Center of Memphis, Le Bonheur Children's Medical Center, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
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