scholarly journals Calculation of Free Energy Consumption in Gene Transcription with Complex Promoter Structure

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Lifang Huang ◽  
Peijiang Liu ◽  
Kunwen Wen ◽  
Jianshe Yu
Keyword(s):  
Free Energy ◽  
Energy Consumption ◽  
Gene Transcription ◽  
Core Promoter ◽  
Fano Factor ◽  
Dependent Manner ◽  
Nonequilibrium Processes ◽  
Promoter Structure ◽  
Transcription Process ◽  
Energy Dependent

From the viewpoint of thermodynamics, gene transcription necessarily consumes free energy due to nonequilibrium processes. On the other hand, regulatory molecules present on the core promoter of a gene interact often in a dynamic, highly combinatorial, and possibly energy-dependent manner, leading to a complex promoter structure. This raises the question of how gene transcription with general promoter topology consumes free energy. We propose a biophysically intuitive approach to calculate energy consumption (quantified by the production rate of entropy) of a gene transcription process. Then, we show that the numbers of the ON and OFF states of a promoter can reduce energy consumption of the gene system and the Fano factor of mRNA, and in contrast to other regulatory ways, the cooperative binding of transcription factors to DNA sites always reduces energy consumption but amplifies the mRNA noise. While our proposed approach is general, our obtained qualitative results can in turn be used to the inference of complex promoter structure.

Modeling and analytical solution of free energy of complex promoter structure

2021 ◽  
Vol 71 ◽  
pp. 151-158
Author(s):  
Lifang Huang ◽  
Peijiang Liu ◽  
Kunwen Wen
Keyword(s):  
Free Energy ◽  
Analytical Solution ◽  
Promoter Structure

Correlated Firing Improves Stimulus Discrimination in a Retinal Model

2004 ◽  
Vol 16 (11) ◽  
pp. 2261-2291 ◽  
Author(s):  
Garrett T. Kenyon ◽  
James Theiler ◽  
John S. George ◽  
Bryan J. Travis ◽  
David W. Marshak
Keyword(s):  
Stimulus Intensity ◽  
Ganglion Cells ◽  
Fano Factor ◽  
Spike Trains ◽  
Dependent Manner ◽  
Common Input ◽  
Threshold Detector ◽  
Synchronous Firing ◽  
Inhibitory Feedback ◽  
Synchronous Oscillations

Synchronous firing limits the amount of information that can be extracted by averaging the firing rates of similarly tuned neurons. Here, we show that the loss of such rate-coded information due to synchronous oscillations between retinal ganglion cells can be overcome by exploiting the information encoded by the correlations themselves. Two very different models, one based on axon-mediated inhibitory feedback and the other on oscillatory common input, were used to generate artificial spike trains whose synchronous oscillations were similar to those measured experimentally. Pooled spike trains were summed into a threshold detector whose output was classified using Bayesian discrimination. For a threshold detector with short summation times, realistic oscillatory input yielded superior discrimination of stimulus intensity compared to rate-matched Poisson controls. Even for summation times too long to resolve synchronous inputs, gamma band oscillations still contributed to improved discrimination by reducing the total spike count variability, or Fano factor. In separate experiments in which neurons were synchronized in a stimulus-dependent manner without attendant oscillations, the Fano factor increased markedly with stimulus intensity, implying that stimulus-dependent oscillations can offset the increased variability due to synchrony alone.

scholarly journals CREPT/RPRD1B promotes tumorigenesis through STAT3-driven gene transcription in a p300-dependent manner

2021 ◽  
Author(s):  
Wanli Zhai ◽  
Xiongjun Ye ◽  
Yinyin Wang ◽  
Yarui Feng ◽  
Ying Wang ◽  
...  
Keyword(s):  
Gene Transcription ◽  
Dependent Manner

Direct interaction of the tau 1 transactivation domain of the human glucocorticoid receptor with the basal transcriptional machinery

1993 ◽  
Vol 13 (1) ◽  
pp. 399-407
Author(s):  
I J McEwan ◽  
A P Wright ◽  
K Dahlman-Wright ◽  
J Carlstedt-Duke ◽  
J A Gustafsson
Keyword(s):  
Glucocorticoid Receptor ◽  
Protein Interactions ◽  
Core Promoter ◽  
Specific Interaction ◽  
Direct Interaction ◽  
Dependent Manner ◽  
Transactivation Domain ◽  
Yeast Saccharomyces Cerevisiae ◽  
Concentration Dependent Manner

We have used a yeast (Saccharomyces cerevisiae) cell free transcription system to study protein-protein interactions involving the tau 1 transactivation domain of the human glucocorticoid receptor that are important for transcriptional transactivation by the receptor. Purified tau 1 specifically inhibited transcription from a basal promoter derived from the CYC1 gene and from the adenovirus 2 major late core promoter in a concentration-dependent manner. This inhibition or squelching was correlated with the transactivation activity of tau 1. Recombinant yeast TATA-binding protein (yTFIID), although active in vitro, did not specifically reverse the inhibitory effect of tau 1. In addition, no specific interaction between tau 1 and yTFIID could be shown in vitro by affinity chromatography. Taken together, these results indicate that the tau 1 transactivation domain of the human glucocorticoid receptor interacts directly with the general transcriptional apparatus through some target protein(s) that is distinct from the TATA-binding factor. Furthermore, this assay can be used to identify interacting factors, since after phosphocellulose chromatography of a whole-cell yeast extract, a fraction that contained an activity which selectively counteracted the squelching effect of tau 1 was found.

Nuclear import of glycoconjugates is distinct from the classical NLS pathway

1995 ◽  
Vol 108 (4) ◽  
pp. 1325-1332 ◽  
Author(s):  
E. Duverger ◽  
C. Pellerin-Mendes ◽  
R. Mayer ◽  
A.C. Roche ◽  
M. Monsigny
Keyword(s):  
Nuclear Localization ◽  
Nuclear Import ◽  
Nuclear Localization Signal ◽  
Peptide Sequence ◽  
Nuclear Pore ◽  
Dependent Manner ◽  
Permeabilized Cells ◽  
Localization Signal ◽  
Energy Dependent ◽  
Cytosolic Factors

The nuclear import of many proteins depends on a short peptide sequence called the nuclear localization signal. However, glycosylated proteins, which lack such a nuclear localization signal, upon their injection into the cytosol by electroporation, enter the nucleus in a sugar-dependent manner. This paper brings new insights on the mechanism of this process, based on a study of neoglycoprotein nuclear uptake by digitonin-permeabilized cells. The nuclear import of neoglycoproteins is energy dependent: it does not occur when cells are maintained at 4 degrees C or when cells are ATP-depleted by treatment with apyrase. The nuclear import of neoglycoproteins occurs through the nuclear pore: it is inhibited by preincubation of cells with wheat germ agglutinin, a lectin which binds the nuclear pore glycoproteins and blocks the translocation step of nuclear localization signal bearing proteins through the nuclear pore. Furthermore, the nuclear import of neoglycoproteins does not use the pathway of nuclear localization signal bearing proteins: nuclear import of nuclear localization signal bearing proteins depends on cytosolic factors and is inhibited by treatment of cells with N-ethylmaleimide, while the nuclear import of neoglycoproteins neither requires added cytosolic factors nor is sensitive to alkylation by N-ethylmaleimide. In addition, upon incubation in the presence of a large excess of nuclear localization signal bearing protein, the nuclear import of neoglycoproteins is not inhibited.

scholarly journals A Novel Transcriptional Repression Domain Mediates p21WAF1/CIP1 Induction of p300 Transactivation

2000 ◽  
Vol 20 (8) ◽  
pp. 2676-2686 ◽  
Author(s):  
Andrew W. Snowden ◽  
Lisa A. Anderson ◽  
Gill A. Webster ◽  
Neil D. Perkins
Keyword(s):  
Cell Cycle ◽  
Transcriptional Activation ◽  
Transcriptional Repression ◽  
Kinase Inhibitor ◽  
Core Promoter ◽  
Dependent Manner ◽  
Creb Binding Protein ◽  
Cycle Dependent ◽  
Repression Domain

ABSTRACT The transcriptional coactivators p300 and CREB binding protein (CBP) are important regulators of the cell cycle, differentiation, and tumorigenesis. Both p300 and CBP are targeted by viral oncoproteins, are mutated in certain forms of cancer, are phosphorylated in a cell cycle-dependent manner, interact with transcription factors such as p53 and E2F, and can be found complexed with cyclinE-Cdk2 in vivo. Moreover, p300-deficient cells show defects in proliferation. Here we demonstrate that transcriptional activation by both p300 and CBP is stimulated by coexpression of the cyclin-dependent kinase inhibitor p21WAF/CIP1. Significantly this stimulation is independent of both the inherent histone acetyltransferase (HAT) activity of p300 and CBP and of the previously reported carboxyl-terminal binding site for cyclinE-Cdk2. Rather, we describe a previously uncharacterized transcriptional repression domain (CRD1) within p300. p300 transactivation is stimulated through derepression of CRD1 by p21. Significantly p21 regulation of CRD1 is dependent on the nature of the core promoter. We suggest that CRD1 provides a novel mechanism through which p300 and CBP can switch activities between the promoters of genes that stimulate growth and those that enhance cell cycle arrest.

scholarly journals ZBTB24 regulates gene transcription by recognizing the core promoter of CDCA7

2019 ◽  
Vol 75 (a1) ◽  
pp. a279-a280
Author(s):  
Ren Ren ◽  
John R. Horton ◽  
Xing Zhang ◽  
Taiping Chen ◽  
Xiaodong Cheng
Keyword(s):  
Gene Transcription ◽  
Core Promoter ◽  
The Core

scholarly journals Adeno-Associated Virus Major Rep78 Protein Disrupts Binding of TATA-Binding Protein to the p97 Promoter of Human Papillomavirus Type 16

2000 ◽  
Vol 74 (5) ◽  
pp. 2459-2465 ◽  
Author(s):  
Pei-Fen Su ◽  
Shu-Yuan Chiang ◽  
Cheng-Wen Wu ◽  
Felicia Y.-H. Wu
Keyword(s):  
Human Papillomavirus ◽  
Binding Protein ◽  
Core Promoter ◽  
Tata Binding Protein ◽  
Tata Box ◽  
Dependent Manner ◽  
Hpv 16 ◽  
Adeno Associated Virus ◽  
Human Papillomavirus Type 16 ◽  
E6 And E7

ABSTRACT Adeno-associated virus type 2 (AAV) is known to inhibit the promoter activities of several oncogenes and viral genes, including the human papillomavirus type 16 (HPV-16) E6 and E7 transforming genes. However, the target elements of AAV on the long control region (LCR) upstream of E6 and E7 oncogenes are elusive. A chloramphenicol acetyltransferase assay was performed to study the effect of AAV on the transcription activity of the HPV-16 LCR in SiHa (HPV-positive) and C-33A (HPV-negative) cells. The results reveal that (i) AAV inhibited HPV-16 LCR activity in a dose-dependent manner, (ii) AAV-mediated inhibition did not require the HPV gene products, and (iii) the AAV replication gene product Rep78 was involved in the inhibition. Deletion mutation analyses of the HPV-16 LCR showed that regulatory elements outside the core promoter region of the LCR may not be direct targets of AAV-mediated inhibition. Further study with the electrophoretic mobility shift assay demonstrated that Rep78 interfered with the binding of TATA-binding protein (TBP) to the TATA box of the p97 core promoter more significantly than it disrupted the preformed TBP-TATA complex. These data thus suggest that Rep78 may inhibit transcription initiation of the HPV-16 LCR by disrupting the interaction between TBP and the TATA box of the p97 core promoter.

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