scholarly journals Coordinated transcriptional regulation of two key genes in the lignin branch pathway - CAD and CCR - is mediated through MYB- binding sites

2010 ◽  
Vol 10 (1) ◽  
pp. 130 ◽  
Author(s):  
Anjanirina Rahantamalala ◽  
Philippe Rech ◽  
Yves Martinez ◽  
Nicole Chaubet-Gigot ◽  
Jacqueline Grima-Pettenati ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Binding Sites ◽  
Key Genes

scholarly journals The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis

2018 ◽  
Author(s):  
E. Shannon Torres ◽  
Roger B. Deal
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Binding Sites ◽  
Transcriptional Repression ◽  
Nucleosome Positioning ◽  
Chromatin Organization ◽  
Histone H2a ◽  
Nucleosome Dynamics ◽  
Environmentally Responsive ◽  
Context Specific

ABSTRACTPlants adapt to changes in their environment by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM act both cooperatively and antagonistically to contribute directly to transcriptional repression and activation of genes involved in development and response to environmental stimuli. We identified 8 classes of genes that show distinct relationships between H2A.Z and BRM and their roles in transcription. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes and/or repositions flanking nucleosomes. H2A.Z and BRM contribute to +1 nucleosome destabilization, especially where they coordinately regulate transcription. We also found that at genes regulated by both BRM and H2A.Z, both factors overlap with the binding sites of light-regulated transcription factors PIF4, PIF5, and FRS9, and that some of the FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated their interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context-specific roles within diverse chromatin environments than previously assumed.

scholarly journals Transcriptional Regulation of sitABCD of Salmonella enterica Serovar Typhimurium by MntR and Fur

2005 ◽  
Vol 187 (3) ◽  
pp. 912-922 ◽  
Author(s):  
Jack S. Ikeda ◽  
Anuradha Janakiraman ◽  
David G. Kehres ◽  
Michael E. Maguire ◽  
James M. Slauch
Keyword(s):  
Transcriptional Regulation ◽  
Binding Sites ◽  
Transcriptional Repression ◽  
Salmonella Enterica ◽  
Transcriptional Control ◽  
Natural Resistance ◽  
Transport Systems ◽  
Transcriptional Level ◽  
Promoter Regions ◽  
Serovar Typhimurium

ABSTRACT Salmonella enterica serovar Typhimurium has two manganese transport systems, MntH and SitABCD. MntH is a bacterial homolog of the eukaryotic natural resistance-associated macrophage protein 1 (Nramp1), and SitABCD is an ABC-type transporter. Previously we showed that mntH is negatively controlled at the transcriptional level by the trans-acting regulatory factors, MntR and Fur. In this study, we examined the transcriptional regulation of sitABCD and compared it to the transcriptional regulation of mntH by constructing lacZ fusions to the promoter regions with and without mutations in putative MntR and/or Fur binding sites. The presence of Mn caused transcriptional repression of the sitABCD and mntH promoters primarily via MntR, but Fur was also capable of some repression in response to Mn. Likewise, Fe in the medium repressed transcription of both sit and mntH primarily via Fur, although MntR was also involved in this response. Transcriptional control by MntR and Fur was disrupted by site-specific mutations in the putative MntR and Fur binding sites, respectively. Transcription of the sit operon was also affected by the oxygen level and growth phase, but the increased expression observed under high oxygen conditions and higher cell densities is consistent with decreased availability of metals required for repression by the metalloregulatory proteins.

scholarly journals Transcriptional regulation of human and murine 17β-hydroxysteroid dehydrogenase type-7 confers its participation in cholesterol biosynthesis

2006 ◽  
Vol 37 (1) ◽  
pp. 185-197 ◽  
Author(s):  
Thomas Ohnesorg ◽  
Brigitte Keller ◽  
Martin Hrabé de Angelis ◽  
Jerzy Adamski
Keyword(s):  
Transcriptional Regulation ◽  
Binding Sites ◽  
Sequence Similarity ◽  
Regulatory Element ◽  
Cholesterol Biosynthesis ◽  
Hydroxysteroid Dehydrogenase ◽  
Site Directed Mutagenesis ◽  
Mobility Shift ◽  
Mobility Shift Assay

In both humans and mice, 17β-hydroxysteroid dehydrogenase type-7 (HSD17B7) was described as possessing dual enzymatic functionality. The enzyme was first shown to be able to convert estrone to estradiol in vitro. Later involvement of this enzyme in postsqualene cholesterol biosynthesis was postulated (conversion of zymosterone to zymosterol) and could be proven in vitro. In this work, we performed a detailed analysis of the transcriptional regulation of both the human and murine genes. Despite relatively low sequence similarity, both promoters contain similar contexts of transcription factor-binding sites. The participation of these sites in transcriptional regulation of HSD17B7 was proven by electro-mobility shift assay and site-directed mutagenesis of the corresponding binding sites. We describe novel involvement of vitamin D receptor/retinoid X receptor and provide new information on the regulation of HSD17B7 expression by sterol regulatory element-binding protein and hepatocyte nuclear factor 4, the latter known from other genes of cholesterogenic enzymes. The results of our study provide unequivocal evidence for a role of HSD17B7 in cholesterol biosynthesis.

scholarly journals Ehrlichia chaffeensis TRP120 Binds a G+C-Rich Motif in Host Cell DNA and Exhibits Eukaryotic Transcriptional Activator Function

2011 ◽  
Vol 79 (11) ◽  
pp. 4370-4381 ◽  
Author(s):  
Bing Zhu ◽  
Jeeba A. Kuriakose ◽  
Tian Luo ◽  
Efren Ballesteros ◽  
Sharu Gupta ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Dna Binding ◽  
Host Cell ◽  
High Throughput ◽  
Tandem Repeat ◽  
Binding Sites ◽  
Host Gene ◽  
Host Cells ◽  
Ehrlichia Chaffeensis ◽  
Content Type

ABSTRACTEhrlichia chaffeensisis an obligately intracellular bacterium that modulates host cell gene transcription in the mononuclear phagocyte, but the host gene targets and mechanisms involved in transcriptional modulation are not well-defined. In this study, we identified a novel tandem repeat DNA-binding domain in theE. chaffeensis120-kDa tandem repeat protein (TRP120) that directly binds host cell DNA. TRP120 was observed by immunofluorescent microscopy in the nucleus ofE. chaffeensis-infected host cells and was detected in nuclear extracts by Western immunoblotting with TRP120-specific antibody. The TRP120 binding sites and associated host cell target genes were identified using high-throughput deep sequencing (Illumina) of immunoprecipitated DNA (chromatin immunoprecipitation and high-throughput DNA sequencing). Multiple em motif elicitation (MEME) analysis of the most highly enriched TRP120-bound sequences revealed a G+C-rich DNA motif, and recombinant TRP120 specifically bound synthetic oligonucleotides containing the motif. TRP120 target gene binding sites were mapped most frequently to intersecting regions (intron/exon; 49%) but were also identified in upstream regulatory regions (25%) and downstream locations (26%). Genes targeted by TRP120 were most frequently associated with transcriptional regulation, signal transduction, and apoptosis. TRP120 targeted inflammatory chemokine genes, CCL2, CCL20, and CXCL11, which were strongly upregulated duringE. chaffeensisinfection and were also upregulated by direct transfection with recombinant TRP120. This study reveals that TRP120 is a novel DNA-binding protein that is involved in a host gene transcriptional regulation strategy.

scholarly journals Novel Mechanism of Positive versus Negative Regulation by Thyroid Hormone Receptor β1 (TRβ1) Identified by Genome-wide Profiling of Binding Sites in Mouse Liver

2013 ◽  
Vol 289 (3) ◽  
pp. 1313-1328 ◽  
Author(s):  
Preeti Ramadoss ◽  
Brian J. Abraham ◽  
Linus Tsai ◽  
Yiming Zhou ◽  
Ricardo H. Costa-e-Sousa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Thyroid Hormone ◽  
Binding Sites ◽  
Hormone Receptor ◽  
Target Genes ◽  
Thyroid Hormone Receptor ◽  
Negative Regulation ◽  
Genome Wide

Triiodothyronine (T3) regulates key metabolic processes in the liver through the thyroid hormone receptor, TRβ1. However, the number of known target genes directly regulated by TRβ1 is limited, and the mechanisms by which positive and especially negative transcriptional regulation occur are not well understood. To characterize the TRβ1 cistrome in vivo, we expressed a biotinylated TRβ1 in hypo- and hyperthyroid mouse livers, used ChIP-seq to identify genomic TRβ1 targets, and correlated these data with gene expression changes. As with other nuclear receptors, the majority of TRβ1 binding sites were not in proximal promoters but in the gene body of known genes. Remarkably, T3 can dictate changes in TRβ1 binding, with strong correlation to T3-induced gene expression changes, suggesting that differential TRβ1 binding regulates transcriptional outcome. Additionally, DR-4 and DR-0 motifs were significantly enriched at binding sites where T3 induced an increase or decrease in TRβ1 binding, respectively, leading to either positive or negative regulation by T3. Taken together, the results of this study provide new insights into the mechanisms of transcriptional regulation by TRβ1 in vivo.

scholarly journals Fixed differences in the 3′UTR of buffalo PRNP gene provide binding sites for miRNAs post-transcriptional regulation

Oncotarget ◽  
2017 ◽  
Vol 8 (28) ◽  
pp. 46006-46019 ◽  
Author(s):  
Hui Zhao ◽  
Siqi Wang ◽  
Lixia Guo ◽  
Yanli Du ◽  
Linlin Liu ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Binding Sites ◽  
Prnp Gene ◽  
Post Transcriptional Regulation

scholarly journals Transcriptional Regulation in the G1-S Cell Cycle Stage in Fungi: Insights through Computational Analysis

2012 ◽  
Vol 6 (1) ◽  
pp. 43-54
Author(s):  
Viktor Martyanov ◽  
Robert H. Gross
Keyword(s):  
Cell Cycle ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Dna Sequences ◽  
Binding Sites ◽  
Positional Distribution ◽  
Upstream Sequence ◽  
Regulatory Pathways ◽  
Binding Factor

The transcription factor complexes Mlu1-box binding factor (MBF) and Swi4/6 cell cycle box binding factor (SBF) regulate the cell cycle in Saccharomyces cerevisiae. They activate hundreds of genes and are responsible for nor-mal cell cycle progression from G1 to S phase. We investigated the conservation of MBF and SBF binding sites during fungal evolution. Orthologs of S. cerevisiae targets of these transcription factors were identified in 37 fungal species and their upstream regions were analyzed for putative transcription factor binding sites. Both groups displayed enrichment in specific putative regulatory DNA sequences in their upstream regions and showed different preferred upstream motif loca-tions, variable patterns of evolutionary conservation of the motifs and enrichment in unique biological functions for the regulated genes. The results indicate that despite high sequence similarity of upstream DNA motifs putatively associated with G1-S transcriptional regulation by MBF and SBF transcription factors, there are important upstream sequence feature differences that may help differentiate the two seemingly similar regulatory modes. The incorporation of upstream motif sequence comparison, positional distribution and evolutionary variability of the motif can complement functional infor-mation about roles of the respective gene products and help elucidate transcriptional regulatory pathways and functions.

scholarly journals Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression

2019 ◽  
Vol 48 (1) ◽  
pp. 121-163 ◽  
Author(s):  
Rob Phillips ◽  
Nathan M. Belliveau ◽  
Griffin Chure ◽  
Hernan G. Garcia ◽  
Manuel Razo-Mejia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Dna Sequences ◽  
Binding Sites ◽  
Regulatory Sequence ◽  
Theoretical Predictions ◽  
Domains Of Life ◽  
History Of ◽  
Predictive Understanding ◽  
The Many

It is tempting to believe that we now own the genome. The ability to read and rewrite it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles’ heel exposed by all of the genomic data that has accrued: We still do not know how to interpret them. Many genes are subject to sophisticated programs of transcriptional regulation, mediated by DNA sequences that harbor binding sites for transcription factors, which can up- or down-regulate gene expression depending upon environmental conditions. This gives rise to an input–output function describing how the level of expression depends upon the parameters of the regulated gene—for instance, on the number and type of binding sites in its regulatory sequence. In recent years, the ability to make precision measurements of expression, coupled with the ability to make increasingly sophisticated theoretical predictions, has enabled an explicit dialogue between theory and experiment that holds the promise of covering this genomic Achilles’ heel. The goal is to reach a predictive understanding of transcriptional regulation that makes it possible to calculate gene expression levels from DNA regulatory sequence. This review focuses on the canonical simple repression motif to ask how well the models that have been used to characterize it actually work. We consider a hierarchy of increasingly sophisticated experiments in which the minimal parameter set learned at one level is applied to make quantitative predictions at the next. We show that these careful quantitative dissections provide a template for a predictive understanding of the many more complex regulatory arrangements found across all domains of life.

Sign in / Sign up

Export Citation Format

Share Document