Basal transcription machinery: role in regulation of stress response in eukaryotes

Sadhale, Parag P.; Verma, Jiyoti; Naorem, Aruna

doi:10.1007/s12038-007-0056-6

Cited by 12 publications

(9 citation statements)

References 66 publications

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“…Similar accumulation of the TATA box has been observed in plants (Yamamoto et al 2011 ). A TATA box is a core element of the basal transcriptional machinery that regulates genes in conjunction with other cis -elements (Sadhale et al 2007 ). Consistent with these reports, our data demonstrated that TATA-box motifs affect the response to Fe deficiency in rice by collaborating with Fe deficiency-specific transcription factors.…”

Section: Resultsmentioning

confidence: 99%

“…Downstream core elements (DCEs) were reported in yeast and mammalians downstream of TSSs, and are known to collaborate with the TATA box (Sadhale et al 2007 ). Some TATA box-binding protein (TBP)-associated factors (TAFs) bind to DCEs (Sadhale et al 2007 ). Our results showed that the DCEp1 (Figure 2 H) motif was commonly found immediately downstream of TSSs of Fe deficiency-inducible genes.…”

Section: Resultsmentioning

confidence: 99%

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Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice

Kakei

Ogo

Itai

et al. 2013

Rice

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BackgroundCis-acting elements are essential genomic sequences that control gene expression. In higher eukaryotes, a series of cis-elements function cooperatively. However, further studies are required to examine the co-regulation of multiple cis-elements on a promoter. The aim of this study was to propose a model of cis-element networks that cooperatively regulate gene expression in rice under iron (Fe) deficiency.ResultsWe developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. Based on sequences of Oryza sativa genes upregulated by Fe deficiency, MAMA returned experimentally identified cis-elements responsible for Fe deficiency in O. sativa. When this method was applied to O. sativa subjected to zinc deficiency and Arabidopsis thaliana subjected to salt stress, several novel candidate cis-acting elements that overlap with known cis-acting elements, such as ZDRE, ABRE, and DRE, were identified. After optimization, MAMA accurately simulated more than 87% of gene expression. Predicted motifs strongly co-localized in the upstream regions of regulated genes and sequences around transcription start sites. Furthermore, in many cases, the separation (in bp) between co-localized motifs was conserved, suggesting that predicted motifs and the separation between them were important in the co-regulation of gene expression.ConclusionsOur results are suggestive of a typical sequence model for Fe deficiency-responsive promoters and some strong candidate cis-elements that function cooperatively with known cis-elements.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-22) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice

Kakei

Ogo

Itai

et al. 2013

Rice

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“…This core promoter region is often transcriptionally silent and with additional activating elements forms the minimal promoter for transcriptional efficiency. [Adapted from Smale and Kadonaga, 2003; Deng and Roberts 2006; Thomas and Chiang, 2006; and Sadhale et al, 2007. ]…”

Section: Figuresmentioning

confidence: 99%

The regulation of neuronal gene expression by alcohol

Pignataro

Varodayan

Tannenholz

et al. 2009

Pharmacology & Therapeutics

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In recent years there has been an explosion of interest in how genes regulate alcohol drinking and contribute to alcoholism. This work has been stimulated by the completion of the human and mouse genome projects and the resulting availability of gene microarrays. Most of this work has been performed in drinking animals, and has utilized the extensive genetic variation among different mouse strains. At the same time, a much smaller amount of effort has gone into the in vitro study of the mechanisms underlying the regulation of individual genes by alcohol. These studies at the cellular and sub-cellular level are beginning to reveal the ways in which alcohol can interact with the transcriptional, translational and post-translational events inside the cell. Detailed studies of the promoter regions within several individual alcohol-responsive genes (ARGs) have been performed and this work has uncovered intricate signaling pathways that may be generalized to larger groups of ARGs. In the last few years several distinct ARGs have been identified from 35,000 mouse genes, by both the “top-down” approach (ex vivo gene arrays) and the “bottom-up” methods (in vitro promoter analysis). These divergent methodologies have converged on a surprisingly small number of genes encoding ion channels, receptors, transcription factors and proteins involved in synaptic function and remodeling. In this review we will describe some of the most interesting cellular and microarray work in the field, and will outline specific examples of genes for which the mechanisms of regulation by alcohol are now somewhat understood.

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“…GTFs are involved in formation of the pre-initiation complex that binds to the promoter region of DNA and regulates the basal transcriptional regulation [6]. On the other hand, GSTFs bind to sequences specific to certain genes and thus contribute to differential gene expression [7, 8].…”

Section: Introductionmentioning

confidence: 99%

Transcription Factors in Heart: Promising Therapeutic Targets in Cardiac Hypertrophy

Kohli

Ahuja²,

Rani³

2012

CCR

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Regulation of gene expression is central to cell growth, differentiation and diseases. Context specific and signal dependent regulation of gene expression is achieved to a large part by transcription factors. Cardiac transcription factors regulate heart development and are also involved in stress regulation of the adult heart, which may lead to cardiac hypertrophy. Hypertrophy of cardiac myocytes is an outcome of the imbalance between prohypertrophic factors and anti-hypertrophic factors. This is initially a compensatory mechanism but sustained hypertrophy may lead to heart failure. The growing knowledge of transcriptional control mechanisms is helpful in the development of novel therapies. This review summarizes the role of cardiac transcription factors in cardiac hypertrophy, emphasizing their potential as attractive therapeutic targets to prevent the onset of heart failure and sudden death as they can be converging targets for current therapy.

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Basal transcription machinery: role in regulation of stress response in eukaryotes

Cited by 12 publications

References 66 publications

Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice

Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice

The regulation of neuronal gene expression by alcohol

Transcription Factors in Heart: Promising Therapeutic Targets in Cardiac Hypertrophy

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