Activation of the Human Aldehyde Oxidase (hAOX1) Promoter by Tandem Cooperative Sp1/Sp3 Binding Sites: Identification of Complex Architecture in thehAOX Upstream DNA that Includes a Proximal Promoter, Distal Activation Sites, and a Silencer Element

2000 ◽  
Vol 19 (8) ◽  
pp. 459-474 ◽  
Author(s):  
Richard M. Wright ◽  
Mary G. Riley ◽  
Laura K. Weigel ◽  
Lisa A. Ginger ◽  
David A. Costantino ◽  
...  
2008 ◽  
Vol 2008 ◽  
pp. 1-9 ◽  
Author(s):  
J. Sunil Rao ◽  
Suresh Karanam ◽  
Colleen D. McCabe ◽  
Carlos S. Moreno

Background. The computational identification of functional transcription factor binding sites (TFBSs) remains a major challenge of computational biology. Results. We have analyzed the conserved promoter sequences for the complete set of human RefSeq genes using our conserved transcription factor binding site (CONFAC) software. CONFAC identified 16296 human-mouse ortholog gene pairs, and of those pairs, 9107 genes contained conserved TFBS in the 3 kb proximal promoter and first intron. To attempt to predict in vivo occupancy of transcription factor binding sites, we developed a novel marginal effect isolator algorithm that builds upon Bayesian methods for multigroup TFBS filtering and predicted the in vivo occupancy of two transcription factors with an overall accuracy of 84%. Conclusion. Our analyses show that integration of chromatin immunoprecipitation data with conserved TFBS analysis can be used to generate accurate predictions of functional TFBS. They also show that TFBS cooccurrence can be used to predict transcription factor binding to promoters in vivo.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3567-3567
Author(s):  
Gabriela andres-Antonio ◽  
Jesus Rangel-Santiago ◽  
Ana B Tirado-Rodriguez ◽  
Elisa Dorantes-Acosta ◽  
Mario I Vega ◽  
...  

Abstract Abstract 3567 Leukemia is the most common cancer among children under the age of 15 years in the United States and many developed countries. In recent years, there has been the emergence of novel therapeutic drugs for this disease. However, the development of drug resistance by the tumor cells remains the most important obstacle in the treatment of leukemia. A widely studied mechanism of tumor resistance to chemotherapeutic drugs is through the expression of the multi-drug resistance (MDR) genes. P-glycoprotein 170 (gp-170) is an MDR1 gene product which serves as an ATP-dependent cell membrane transporter; it facilitates the efflux of xenobiotics (including chemotherapeutic drugs) from the cells to prevent damage for prolonged drug activity, including chemotherapeutics agents. In addition to MDR1, several reports in different cancers have indicated that the transcription factor Yin Yang 1 (YY1) is over-expressed and regulates tumor cell response to chemotherapeutic drugs. Thus, we hypothesized that YY1 may also be over-expressed in ALL and that its expression may be correlated with the expression of gp-170. We also hypothesized that the co-expression of YY1 and gp-170 may be of prognostic significance in high risk ALL patients. These hypotheses were examined with childhood ALL (n= 88) (of median age 8.2 years, range 0.21–16). The expression of YY1 and gp-170 was determined by IHC in tumor tissues and the frequency of YY1 positive cells was determined. For comparison, normal controls were also analyzed (n= 53). The findings demonstrate that were a significant increase in the frequency of positive cells in ALL compared to controls for both YY1 (38% vs. 8%, p= 0.0001) and for gp-170 (42% vs. 12%, p= 0.001). There was a good correlation between the expression of YY1 and gp-170 using Pearson's test, r=0.4, p=0.0001. We then examined if the co-expression of YY1 and gp-170 is also associated with decreased risk. Indeed, patients with low risk (L1) had significantly less frequency of positive cells compared to patients with high risk for both YY1 (40% vs. 30%, p=0.045) and for gp-170 (48% vs. 35%, p=0.0003). The strong correlation betweenYY1 and gp-170 expression suggested that there may be a cross-talk. TESS analysis demonstrated that the gp-170 proximal promoter contains four putative binding sites for the YY-1 protein. The gp-170 protein was cloned and we developed a luciferase reporter assay. Examination of the putative YY1 binding sites that were individually mutated revealed that mutation at the sites -1860 and -270 abolished activity. Mutation at the site -1420 abolished approximately 50% and mutation at -1230 abolished approximately 75%. Further, CHIP analysis demonstrated that YY1 binds directly to the gp-170 gene. Transfection of cells with YY1 siRNA inhibited the efflux of adriamycin from the cells confirming the regulation of gp-170 expression by YY1. Overall, the findings above demonstrate that both gp-170 and YY1 are over-expressed in childhood ALL and further over-expressed in patients with high risk. The findings suggest that YY1 may be a therapeutic target in MDR positive ALL and its inhibition may reverse resistance to chemotherapeutic drugs. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
1999 ◽  
Vol 94 (9) ◽  
pp. 3151-3160 ◽  
Author(s):  
Diana Catt ◽  
Shannon Hawkins ◽  
Ann Roman ◽  
Wen Luo ◽  
David G. Skalnik

CCAAT displacement protein (CDP) is a transcriptional repressor that restricts expression of the gp91phox gene to mature myeloid cells. CDP interacts with multiple sites within the −450 to +12 bp human gp91phox promoter, and down-regulation of CDP DNA-binding activity is required for induction of gp91phox transcription in mature phagocytes. Truncation of the gp91phox promoter to −102 to +12 bp removes 4 CDP-binding sites and reveals a promiscuous promoter activity that is active in some nonphagocytic cells. A cis-element at −90 bp is required for derepressed transcription and serves as a binding site for multiple transcriptional activators. We now report that this element also serves as a binding site for CDP. The affinity of CDP for this element is relatively weak compared with upstream CDP-binding sites within the promoter, consistent with the promiscuous transcriptional activity exhibited by the −102 to +12 bp gp91phox promoter fragment. Further analysis of the proximal promoter reveals an additional weak-affinity CDP-binding site centered at approximately −20 bp. Overexpression of cloned CDP represses the −102 to +12 bp gp91phox promoter, indicating that these proximal CDP-binding sites are functionally significant. The constellation of transcriptional activators and a repressor that interacts with the −90 bp cis-element is identical to that observed for a promoter element at −220 bp, reflecting the highly modular organization of the gp91phoxpromoter. These studies illustrate the complex interplay between transcriptional activators and a repressor that contribute to the myeloid-restricted expression of the gp91phox gene.


1992 ◽  
Vol 12 (6) ◽  
pp. 2758-2768 ◽  
Author(s):  
J M Allen ◽  
K A Forbush ◽  
R M Perlmutter

The lck gene encodes a protein tyrosine kinase that participates in lymphocyte-specific signal transduction pathways. Previous studies have established that lck transcription is regulated by two distinct promoter elements termed proximal (or 3') and distal (or 5'). The proximal promoter is active almost exclusively in thymocytes and becomes inactive later during T-cell maturation. To dissect the mechanisms responsible for lck gene regulation, we generated transgenic animals bearing 5' truncations in the proximal promoter element. Sequences between -584 and +37 with respect to the proximal promoter transcription start site act to direct tissue-specific and temporally correct transcription of either a tagged version of the lck gene itself or a heterologous reporter sequence (lacZ). This region contains binding sites for at least five distinct nuclear proteins, of which one is found only in cells that support proximal lck promoter activity and a second appears only in nonexpressing cells. Interestingly, the transcribed region of the lck gene contains positive control elements that can substantially boost expression from minimal (-130 bp) proximal promoter constructs. These results provide a basis for the biochemical dissection of transcriptional regulators that act at defined points during T-cell development.


2002 ◽  
Vol 1 (4) ◽  
pp. 548-557 ◽  
Author(s):  
Jimmy O. O. Sjöstrand ◽  
Andreas Kegel ◽  
Stefan U. Åström

ABSTRACT We studied the silencing of the cryptic mating-type loci HMLα and HMRa in the budding yeast Kluyveromyces lactis. A 102-bp minimal silencer fragment was defined that was both necessary and sufficient for silencing of HMLα. Mutagenesis of the silencer revealed three distinct regions (A, B, and C) that were important for silencing. Recombinant K. lactis ribosomal DNA enhancer binding protein 1 (Reb1p) could bind the silencer in vitro, and point mutations in the B box abolished both Reb1p binding and silencer function. Furthermore, strains carrying temperature-sensitive alleles of the REB1 gene derepressed the transcription of the HMLα1 gene at the nonpermissive temperature. A functional silencer element from the K. lactis cryptic HMRa locus was also identified, which contained both Reb1p binding sites and A boxes, strongly suggesting a general role for these sequences in K. lactis silencing. Our data indicate that different proteins bind to Kluyveromyces silencers than to Saccharomyces silencers. We suggest that the evolution of silencers is rapid in budding yeasts and discuss the similarities and differences between silencers in Saccharomyces and Kluyveromyces.


Development ◽  
2001 ◽  
Vol 128 (11) ◽  
pp. 2163-2173 ◽  
Author(s):  
Ana Busturia ◽  
Alan Lloyd ◽  
Fernando Bejarano ◽  
Michael Zavortink ◽  
Hua Xin ◽  
...  

Silencing of homeotic gene expression requires the function of cis-regulatory elements known as Polycomb Response Elements (PREs). The MCP silencer element of the Drosophila homeotic gene Abdominal-B has been shown to behave as a PRE and to be required for silencing throughout development. Using deletion analysis and reporter gene assays, we defined a 138 bp sequence within the MCP silencer that is sufficient for silencing of a reporter gene in the imaginal discs. Within the MCP138 fragment, there are four binding sites for the Pleiohomeotic protein (PHO) and two binding sites for the GAGA factor (GAF), encoded by the Trithorax-like gene. PHO and the GAF proteins bind to these sites in vitro. Mutational analysis of PHO and GAF binding sequences indicate that these sites are necessary for silencing in vivo. Moreover, silencing by MCP138 depends on the function of the Trithorax-like gene, and on the function of the PcG genes, including pleiohomeotic. Deletion and mutational analyses show that, individually, either PHO or GAF binding sites retain only weak silencing activity. However, when both PHO and GAF binding sites are present, they achieve strong silencing. We present a model in which robust silencing is achieved by sequential and facilitated binding of PHO and GAF.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4187-4187
Author(s):  
Marina Kreutz ◽  
Achim Ehrnsperger ◽  
Michael Rehli ◽  
Reinhard Andreesen

Abstract MADDAM (Metalloprotease And Disintegrin Dendritic Cell Antigen Marker, ADAM19), a human metalloprotease belonging to the ADAM-family, is strongly expressed during in vitro differentiation of monocytes into dendritic cells (DC), whereas differentiation of monocytes into macrophages (MAC) is associated with a loss of MADDAM transcription. To investigate the mechanisms underlying this cell-type specific expression pattern we defined the transcriptional start site and the proximal promoter of the MADDAM gene. Gene bank analysis of the CpG island promoter and first intron revealed putative binding sites for several transcription factors, including VDR, NF-kB and Sp1-family factors. EMSA demonstrated binding of Sp1, Sp3, NF-kB and VDR to their putative binding sites in the proximal promoter region and mutation of these elements led to a decreased reporter activity of the proximal promoter in luciferase assays. A minimal promoter construct of 150-bp showed weak reporter activity in primary monocyte-derived MAC and a threefold higher activity in monocyte-derived DC, indicating that differential binding of transcription factors contributes to the cell-type specific regulation of MADDAM. Transfection of monocytic THP-1 cells with the 150-bp fragment also resulted in significant reporter activity, despite the lack of endogenous MADDAM expression. Interestingly, Trichostatin A (TSA), a known inhibitor of histone deacetylation, lead to a dose dependent induction of MADDAM mRNA in THP-1 cells. Chromatin immunoprecipitation (ChIP) assays demonstrate increased levels of acetylated histones H3 and H4 in DC as compared to MAC, indicating an important role of histone acetylation in the cell-type specific regulation of the MADDAM gene.


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