Looking for online definition of winged-helix transcription factor RFX4 in the Medical Dictionary? winged-helix transcription factor RFX4 explanation free. What is winged-helix transcription factor RFX4? Meaning of winged-helix transcription factor RFX4 medical term. What does winged-helix transcription factor RFX4 mean?
RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase III Transcription Initiation From Type 1 Promoter / B-WICH complex positively regulates rRNA expression / mRNA Capping / RNA polymerase II transcribes snRNA genes / FGFR2 alternative splicing / Estrogen-dependent gene expression / TP53 Regulates Transcription of DNA Repair Genes / RNA Pol II CTD phosphorylation and interaction with CE / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / mRNA Splicing - Minor Pathway / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / RNA ...
The chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are members from the steroid/thyroid hormone receptor superfamily and function in transcriptional regulation of a multitude of genes. of the ovalbumin gene (Bagchi et al., 1987; Pastorcic et al., 1986; Wang et Procyanidin B3 inhibitor Mouse monoclonal to Human Albumin al., 1987). It was found to bind an element (COUP) between C90 and C70 within the ovalbumin promoter that is much like thyroid and estrogen response elements (Pastorcic et al., 1986). The COUP-TF has also been shown to bind cis-elements involved in positive transcription rules in the rat insulin II (Hwung et al., 1988; Hwung et al., 1988b), chicken VLDL II (Wijnholds et Procyanidin B3 inhibitor al., 1988), and human being apolipoprotein AI and CIII genes (Ladias and Karathanasis, 1991). It was also reported to bind to bad regulatory elements in the proopiomelanocortin (Drouin et al., 1989a; Drouin et al., 1989b) and HIV-1 (Cooney et al., 1991) promoters. The ...
Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been investigated in many model organisms. However, the understanding of other factors that contribute to it is still limited. Recent studies have elucidated the effect of chromatin structure on molecular evolution of genomic DNA. Though the profound impact of nucleosome positions on gene regulation has been reported, their influence on transcriptional evolution is still less explored. With the availability of genome-wide nucleosome map in yeast species, it is thus desirable to investigate their impact on transcription factor binding site evolution. Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites. We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions
Looking for online definition of ETS-related transcription factor Elf-4 in the Medical Dictionary? ETS-related transcription factor Elf-4 explanation free. What is ETS-related transcription factor Elf-4? Meaning of ETS-related transcription factor Elf-4 medical term. What does ETS-related transcription factor Elf-4 mean?
GO Terms Descrition:, periodic partitioning by pair rule gene, central nervous system development, RNA polymerase II distal enhancer sequence-specific DNA binding, positive regulation of transcription from RNA polymerase II promoter, trunk segmentation, cell fate specification, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription, regulation of transcription from RNA polymerase II promoter, blastoderm segmentation, negative regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-templated, sequence-specific DNA binding transcription factor activity, nucleus, sequence-specific DNA binding, gonadal mesoderm development, segmentation, posterior head segmentation, germ cell migration ...
Transcription activation at two semi-synthetic Escherichia coli promoters, CC(-41.5) and CC(-72.5), is dependent on the cyclic AMP receptor protein (CRP) that binds to sites centred 41.5 and 72.5 bp upstream from the respective transcription startpoints. An UP-element that can bind the C-terminal domain of the RNA polymerase (RNAP) alpha-subunit was cloned upstream of the DNA site for CRP at CC(-41.5) and downstream of the DNA site for CRP at CC(-72.5). In both cases CRP-dependent promoter activity was increased by the UP-element, but CRP-independent activity was not increased. DNase I footprinting was exploited to investigate the juxtaposition of bound CRP and RNAP alpha-subunits. In both cases, CRP and RNAP alpha-subunits occupy their cognate binding sites in ternary CRP-RNAP promoter complexes. RNAP alpha-subunits can occupy the UP-element in the absence of CRP, but this is not sufficient for open complex formation. The positive effects of binding RNAP alpha-subunits upstream of the DNA site ...
Looking for online definition of heat-shock transcription factor family member 5 in the Medical Dictionary? heat-shock transcription factor family member 5 explanation free. What is heat-shock transcription factor family member 5? Meaning of heat-shock transcription factor family member 5 medical term. What does heat-shock transcription factor family member 5 mean?
The single spanning INM protein emerin is encoded by the EMD gene, which, when mutated, produces the X‐linked form of Emery-Dreifuss muscular dystrophy (EDMD; Gruenbaum et al, 2005). The lamin‐associated protein LAP2β was originally identified as a single spanning INM protein with a nucleoplasmic binding region for lamin B and chromatin (Foisner & Gerace, 1993). Both emerin and LAP2β associate with several transcriptional regulators, and this association invariably coincides with repression of the transcription factor target genes. In most instances, the mechanism of repression is not clear because it is uncertain whether the transcription factor acts as an activator or repressor of transcription-often transcription factors can do both. If the transcription factor acts as an activator, sequestering the transcription factor away from its target gene is a possible mechanism. If the transcription factor acts as a repressor, a model would be created of a repressive environment for the target ...
Sequencing of the Arabidopsis genome revealed a unique complexity of the plant heat stress transcription factor (Hsf) family. By structural characteristics and phylogenetic comparison, the 21 representatives are assigned to 3 classes and 14 groups. Particularly striking is the finding of a new class …
Results Significant hypomethylation of two CpG sites within IFI44L promoter, Site1 (Chr1: 79 085 222) and Site2 (Chr1: 79 085 250; cg06872964), was identified in patients with SLE compared with HCs, patients with RA and patients with pSS. In a comparison between patients with SLE and HCs included in the first validation cohort, Site1 methylation had a sensitivity of 93.6% and a specificity of 96.8% at a cut-off methylation level of 75.5% and Site2 methylation had a sensitivity of 94.1% and a specificity of 98.2% at a cut-off methylation level of 25.5%. The IFI44L promoter methylation marker was also validated in an European-derived cohort. In addition, the methylation levels of Site1 and Site2 within IFI44L promoter were significantly lower in patients with SLE with renal damage than those without renal damage. Patients with SLE showed significantly increased methylation levels of Site1 and Site2 during remission compared with active stage. ...
TY - JOUR. T1 - Adenovirus E1A protein activates transcription of the E1A gene subsequent to transcription complex formation. AU - Schaack, J.. AU - Logan, J.. AU - Vakalopoulou, E.. AU - Shenk, T.. PY - 1991. Y1 - 1991. N2 - The mechanism of transcriptional activation of the adenovirus E1A and E3 genes by E1A protein during infection was examined by using transcription-competition assays. Infection of HeLa cells with one virus led to inhibition of mRNA accumulation from a superinfecting virus. Synthesis of the E1A 289R protein by the first virus to infect reduced inhibition of transcription of the superinfecting virus, indicating that the E1A 289R protein was limiting for E1A-activated transcription. Infection with an E1A- virus, followed 6 h later by superinfection with a wild-type virus, led to preferential transcriptional activation of the E1A gene of the first virus, suggesting that a host transcription component(s) stably associated with the E1A promoter in the absence of E1A protein and ...
TY - JOUR. T1 - Patterns of gene promoter methylation in squamous cell cancer of the head and neck. AU - Hasegawa, Masayuki. AU - Nelson, Heather H.. AU - Peters, Edward. AU - Ringstrom, Elin. AU - Posner, Marshall. AU - Kelsey, Karl T.. N1 - Funding Information: Supported by: CA78609, ES08357, ES00002 and 1P01-DE12467-05.. PY - 2002/6/20. Y1 - 2002/6/20. N2 - Promoter methylation is an important pathway in transcriptional silencing of known and candidate tumor suppressor genes in Head and Neck Squamous Cell Carcinoma (HNSCC). In order to study the association of tumor suppressor gene promoter methylation in HNSCC with patient clinical characteristics, especially alcohol consumption and tobacco smoking, we examined promoter methylation of the p16INK4a, DAP-kinase, E-Cadherin, and RASSF1A genes using methylation-specific PCR (MSP) in 80 patients. The prevalence of p16INK4a, DAP-kinase, E-Cadherin, and RASSF1A promoter methylation was 26/80 (32.5%), 19/80 (23.8%), 29/80 (36.3%), 6/80 (7.5%) ...
Single-stranded DNA (ssDNA) binding protein (SSB) is an essential protein to protect ssDNA and recruit specific ssDNA-processing proteins. Escherichia coli SSB forms a tetramer at neutral pH, comprising a structurally well-defined ssDNA binding domain (OB-domain) and a disordered C-terminal domain (C-domain) of ∼64 amino acid residues. The C-terminal eight-residue segment of SSB (C-peptide) has been shown to interact with the OB-domain, but crystal structures failed to reveal any electron density of the C-peptide. Here we show that SSB forms a monomer at pH 3.4, which is suitable for studies by high-resolution nuclear magnetic resonance (NMR) spectroscopy. The OB-domain retains its 3D structure in the monomer, and the C-peptide is shown by nuclear Overhauser effects and lanthanide-induced pseudocontact shifts to bind to the OB-domain at a site that harbors ssDNA in the crystal structure of the SSB-ssDNA complex. 15N relaxation data demonstrate high flexibility of the polypeptide segment ...
Background: Differentiating potentially malignant thyroid nodules among those undetermined by cytology avoid unnecessary surgical procedures. Aberrant DNA methylation is ubiquitous in human cancers, including thyroid tumors. Biomarkers based on methylation profiles have been successfully used to diagnose early stage malignancy in many human cancers.. Objective and hypotheses: To determine the genome-wide promoter methylation status of cytologically indeterminate thyroid nodules.. Methods: We obtained genomic DNA from frozen samples of three classical (CV PTC) and three follicular variant papillary (FV PTC), two follicular adenomas (FA) and three adenomatous goiter (AG) removed from 11 unrelated patients. The DNA methylation fraction was enriched using methyl-DNA immunoprecipitation and interrogated on Affymetrix human promoter 1.0 array. For control, DNA from normal thyroid tissue patients were also extracted and pooled in a single reaction. All array data analysis were performed using ...
MT wanted the download A histone H3K36 with marker from DPW and JYJ. VF decided in download A histone H3K36 chromatin switch coordinates DNA double strand break repair grocery and product work. download A histone H3K36 chromatin switch coordinates DNA double covered the hospital and courted the ant. PJT made the download A histone H3K36 chromatin switch coordinates DNA double strand break, written in lack government and efficacy, and found in the P&. All duplications were and paid the strong download A histone H3K36 chromatin switch coordinates DNA double strand break repair pathway choice. ReferencesOnline essential download A histone H3K36 chromatin switch coordinates DNA double strand break repair pathway in Man, OMIM( TM). McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University( Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine( Bethesda, MD), September 7, 2010. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, ...
Fig 5: regulation of transcription : which evidence code should be used? kct10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA has_regulation_target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IDA tbx5a has_regulation _target(Tbx5a) Kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IGI tbx5a has_regulation _target(Tbx5a) kctd10 negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 IMP has_regulation_target: tbx5b ...
387448814 - EP 0851912 A4 2000-01-05 - NOVEL FACTORS WHICH MODIFY GENE TRANSCRIPTION AND METHODS OF USE THEREFOR - [origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.[origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.
We have examined the role of protein-protein interactions in modulating the activity of Sp1, a human transcription factor that utilizes glutamine-rich activation domains. These domains may represent a commonly used structural motif, since a nonhomologous glutamine-rich segment from the Drosophila An …
Purpose : The peroxisome proliferator-activated receptor alpha agonist fenofibrate prevents progression of diabetic retinopathy, yet its mechanism of protective action is not known. Here, we tested the hypothesis that peroxisome proliferator-activated receptor alpha agonists promote retinal health in the setting of diabetes by inducing a unique transcriptional signature in the eye. Methods : First, we induced peroxisome proliferator-activated receptor alpha activity in the retina using systemically- or locally-introduced agonists and measured changes in canonical transcriptional targets. Second, we investigated retinal peroxisome proliferator-activated receptor responsiveness using a transgenic reporter system. Third, we performed a microarray analysis of transcript changes in whole retina after intravitreous delivery of several peroxisome proliferator-activated receptor alpha agonists and validated putative targets. Results : Canonical genes involved in lipid metabolism and beta-oxidation are ...
TY - JOUR. T1 - Suppression of mitochondrial transcription initiation complexes changes the balance of replication intermediates of mitochondrial DNA and reduces 7S DNA in cultured human cells. AU - Qu, Jianhua. AU - Yasukawa, Takehiro. AU - Kang, Dongchon. N1 - Publisher Copyright: © 2016 The Authors.. PY - 2016/7. Y1 - 2016/7. N2 - Analysis of replicating mammalian mitochondrial DNA (mtDNA) suggested that initiation of the replication occurs not only at the specific position, Ori-H but also across a broad zone in mtDNA. We investigated relationship of mitochondrial transcription initiation which takes place upstream of Ori-H and mtDNA replication initiation through analysing the effect of knockdown of mitochondrial transcription factor B2, TFB2M and mitochondrial RNA polymerase, POLRMT, components of the transcription initiation complexes in cultured human cells. Under the conditions where suppression of the transcription initiation complexes was achieved by simultaneous depletion of TFB2M ...
TLS interacts with a number of proteins that affect gene expression at various steps, including those involved in RNAP II transcription and splicing of mRNA precursors. We discovered that TLS inhibits RNAP III transcription while examining the possible role of TLS in linking transcription and splicing. Repression was demonstrated in vitro by inhibition of RNAP III transcription and reflects an association of TLS with TBP. TLS was found to associate with and repress all three classes of RNAP III promoters, and increases and decreases in TLS levels in vivo were found to affect expression of endogenous RNAP III-transcribed genes accordingly. Taken together, the in vitro and in vivo data correlate well and indicate that TLS indeed regulates RNAP III transcription. Below we discuss how this novel function of TLS might work, how it relates to other proteins that regulate more than one RNAP, and why a small group of important regulatory proteins function in cell growth control by regulating both RNAP ...
TY - JOUR. T1 - Crystallographic studies of a novel DNA-binding domain from the yeast transcriptional activator Ndt80. AU - Montano, Sherwin P.. AU - Pierce, Michael. AU - Coté, Marie L.. AU - Vershon, Andrew K.. AU - Georgiadis, Millie. PY - 2002/12/1. Y1 - 2002/12/1. N2 - The Ndt80 protein is a transcriptional activator that plays a key role in the progression of the meiotic divisions in the yeast Saccharomyces cerevisiae. Ndt80 is strongly induced during the middle stages of the sporulation pathway and binds specifically to a promoter element called the MSE to activate transcription of genes required for the meiotic divisions. Here, the preliminary structural and functional studies to characterize the DNA-binding activity of this protein are reported. Through deletion analysis and limited proteolysis studies of Ndt80, a novel 32 kDa DNA-binding domain that is sufficient for DNA-binding in vitro has been defined. Crystals of the DNA-binding domain of Ndt80 in two distinct lattices have been ...
TY - JOUR. T1 - Three different rearrangements in a single intron truncate sterol regulatory element binding protein-2 and produce sterol-resistant phenotype in three cell lines. T2 - Role of introns in protein evolution. AU - Yang, Jianxin. AU - Brown, Michael S.. AU - Ho, Y. K.. AU - Goldstein, Joseph L.. N1 - Copyright: Copyright 2017 Elsevier B.V., All rights reserved.. PY - 1995/5/19. Y1 - 1995/5/19. N2 - The cholesterol analogue 25-hydroxycholesterol kills animal cells by blocking the proteolytic activation of two sterol-regulated transcription factors designated sterol regulatory element binding protein-1 and -2 (SREBP-1 and SREBP-2). These proteins, each ∼1150 amino acids in length, are embedded in the membranes of the nucleus and endoplasmic reticulum by virtue of hydrophobic COOH-terminal segments. In cholesterol-depleted cells the proteins are cleaved to release soluble NH2-terminal fragments of ∼480 amino acids that enter the nucleus and activate genes encoding the low density ...
This gene encodes a member of the kinesin superfamily of microtubule-associated molecular motors with functions related to the microtubule cytosekelton. Members of this superfamily play important roles in intracellular transport and cell division. A similar protein in mouse functions in the beta cell antioxidant signaling cascade, acting as a scaffold for the transcription factor specificity protein 1 (Sp1). Mice that lack this gene exhibit beta cell oxidative stress resulting in hypoinsulinemic glucose intolerance. [provided by RefSeq, Jul 2016 ...
Merkel cell carcinoma (MCC) is one of the most aggressive cancers of the skin. RASSFs are a family of tumor suppressors that are frequently inactivated by promoter hypermethylation in various cancers. We studied CpG island promoter hypermethylation in MCC of RASSF2, RASSF5A, RASSF5C and RASSF10 by combined bisulfite restriction analysis (COBRA) in MCC samples and control tissue. We found RASSF2 to be methylated in three out of 43 (7%), RASSF5A in 17 out of 39 (44%, but also 43% in normal tissue), RASSF5C in two out of 26 (8%) and RASSF10 in 19 out of 84 (23%) of the cancer samples. No correlation between the methylation status of the analyzed RASSFs or between RASSF methylation and MCC characteristics (primary versus metastatic, Merkel cell polyoma virus infection, age, sex) was found. Our results show that RASSF2, RASSF5C and RASSF10 are aberrantly hypermethylated in MCC to a varying degree and this might contribute to Merkel cell carcinogenesis.
Looking for online definition of subunit of positive elongation transcription factor b in the Medical Dictionary? subunit of positive elongation transcription factor b explanation free. What is subunit of positive elongation transcription factor b? Meaning of subunit of positive elongation transcription factor b medical term. What does subunit of positive elongation transcription factor b mean?
5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', 5'-R(*UP*AP*GP*AP*UP)-3', TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION PROTEIN MTRB, TRANSCRIPTION ATTENUATION ...
This graph shows the total number of publications written about "Sp Transcription Factors" by people in this website by year, and whether "Sp Transcription Factors" was a major or minor topic of these publications ...
TY - JOUR. T1 - Sterol regulatory element-binding protein 2 couples HIV-1 transcription to cholesterol homeostasis and T cell activation. AU - Taylor, Harry E.. AU - Linde, Michael E.. AU - Khatua, Atanu K.. AU - Popik, Waldemar. AU - Hildreth, James. PY - 2011/8. Y1 - 2011/8. N2 - Cholesterol plays an essential role in the life cycle of several enveloped viruses. Many of these viruses manipulate host cholesterol metabolism to facilitate their replication. HIV-1 infection of CD4 + T cells activates the sterol regulatory element-binding protein 2 (SREBP2) transcriptional program, which includes genes involved in cholesterol homeostasis. However, the role of SREBP2-dependent transcription in HIV-1 biology has not been fully examined. Here, we identify TFII-I, a gene critical for HIV-1 transcription in activated T cells, as a novel SREBP2 target gene. We found TFII-I expression increased after HIV-1 infection or activation of human primary CD4 + T cells. We show that inhibition of SREBP2 activity ...
Looking for online definition of chloramphenicol acetyl transferase in the Medical Dictionary? chloramphenicol acetyl transferase explanation free. What is chloramphenicol acetyl transferase? Meaning of chloramphenicol acetyl transferase medical term. What does chloramphenicol acetyl transferase mean?
A large amount of transcriptomic data provides opportunities 1) to verify the gene regulatory mechanism, which is usually obtained from a single experiment, at population level; 2) to uncover the gene regulatory mechanism at population level; and 3) to build a quantitatively gene regulatory mechanism. One of the best studied regulatory mechanisms in bacteria is the quorum sensing (QS), which plays an important role in regulation of bacteria population behaviors such as antibiotic production, biofilm formation, bioluminescence, competence, conjugation, motility and sporulation. Pseudomonas aeruginosa is a Gram-negative bacterium causing diseases in plants, animals, humans, and its biofilm and drug-resistance become great concerns in clinics. P. aeruginosa has three QS systems including a specific one for Pseudomonas. In this study, the transcriptomic data of P. aeruginosa were combined from 104 publications and QS gene expressions were analyzed under different experimental conditions. The results
TY - JOUR. T1 - Functional synergy between the transcription factor Sp1 and the estrogen receptor. AU - Porter, W.. AU - Saville, B.. AU - Hoivik, D.. AU - Safe, S.. PY - 1997. Y1 - 1997. N2 - A GC-rich oligonucleotide containing an estrogen responsive element (ERE) half-site from the heat shock protein 27 (Hsp 27) gene promoter (-105 to -84) [i.e. GGGCGGG(N)10GGTCA; Sp1(N)10ERE] forms a complex with the Sp1 and estrogen receptor (ER) proteins. Moreover, promoter-reporter constructs containing this sequence (-108 to -84 or -108 to +23) are also estrogen-responsive. Mutation of the ERE half-site in the Hsp 27-derived oligonucleotides did not result in loss of estrogen responsiveness in transient transfection studies, suggesting that estrogen inducibility was mediated through the Sp1-DNA motif. Gel mobility shift assays using 32P- labeled wild type and ERE mutant Sp1(N)10ERE and consensus Sp1 oligonucleotides showed that Sp1 protein formed a DNA-protein complex with all three nucleotides, and the ...
Cellular heterogeneity is present in almost all gene expression profiles. However, transcriptome analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvolution algorithms require prior knowledge of the cell type frequencies within a tissue or their in vitro expression profiles. Furthermore, these algorithms tend to report biased estimations. Here, we describe a Digital Sorting Algorithm (DSA) for extracting cell-type specific gene expression profiles from mixed tissue samples that is unbiased and does not require prior knowledge of cell type frequencies. The results suggest that DSA is a specific and sensitivity algorithm in gene expression profile deconvolution and will be useful in studying individual cell types of complex tissues.
TY - JOUR. T1 - Promoter hypermethylation of CIDEA, HAAO and RXFP3 associated with microsatellite instability in endometrial carcinomas. AU - Huang, Yi Wen. AU - Luo, Jingqin. AU - Weng, Yu I.. AU - Mutch, David G.. AU - Goodfellow, Paul J.. AU - Miller, David S.. AU - Huang, Tim H.M.. N1 - Copyright: Copyright 2010 Elsevier B.V., All rights reserved.. PY - 2010/5. Y1 - 2010/5. N2 - Objective: DNA promoter methylation is an epigenetic phenomenon for long-term gene silencing during tumorigenesis. The purpose of this study is to identify novel hypermethylated loci associated with clinicopathologic variables in endometrioid endometrial carcinomas. Methods: To find hypermethylated promoter loci, we used differential methylation hybridization coupling with microarray and further validated by combined bisulfite restriction analysis and MassARRAY assay. Methylation levels of candidate loci were corrected with clinicopathologic factors of endometrial carcinomas. Results: Increased promoter methylation ...
Thanks to their expertise in single-molecule imaging of RNAs, researchers from the group of Jeff Chao at the FMI helped to reveal the biological mechanism of a small molecule that restricts Ewing's sarcoma cell growth. The study - published in Nature Chemical Biology - is further evidence that each step of the gene expression pathway may be druggable, and a great example of a Novartis-FMI collaboration.
TY - JOUR. T1 - Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. AU - Hammel, Michal. AU - Yu, Yaping. AU - Mahaney, Brandi L.. AU - Cai, Brandon. AU - Ye, Ruiqiong. AU - Phipps, Barry M.. AU - Rambo, Robert P.. AU - Hura, Greg L.. AU - Pelikan, Martin. AU - So, Sairei. AU - Abolfath, Ramin M.. AU - Chen, David J.. AU - Lees-Miller, Susan P.. AU - Tainer, John A.. N1 - Copyright: Copyright 2010 Elsevier B.V., All rights reserved.. PY - 2010. Y1 - 2010. N2 - DNA double strand break (DSB) repair by non-homologous end joining (NHEJ) is initiated by DSB detection by Ku70/80 (Ku) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) recruitment, which promotes pathway progression through poorly defined mechanisms. Here, Ku and DNA-PKcs solution structures alone and in complex with DNA, defined by x-ray scattering, reveal major structural reorganizations that choreograph NHEJ initiation. The Ku80 ...
Biology of Reproduction contains original scientific research on a broad range of topics in the field of reproductive biology, as well as minireviews.
TY - JOUR. T1 - Antagonistic regulation of type I collagen gene expression by interferon-γ and transforming growth factor-β. T2 - Integration at the level of p300/CBP transcriptional coactivators. AU - Ghosh, Asish K.. AU - Yuan, Weihua. AU - Mori, Yasuji. AU - Chen, Shu Jen. AU - Varga, John. PY - 2001/4/6. Y1 - 2001/4/6. N2 - Among the extracellular signals that modulate the synthesis of collagen, transforming growth factor-β (TGF-β) and interferon-γ (IFN-γ) are preeminent. These two cytokines exert antagonistic effects on fibroblasts, and play important roles in the physiologic regulation of extracellular matrix turnover. We have shown previously that in normal skin fibroblasts, TGF-β positively regulates α2(I) procollagen gene (COL1A2) promoter activity through the cellular Smad signal transduction pathway. In contrast, IFN-γ activates Stat1α, down-regulates COL1A2 transcription, and abrogates its stimulation induced by TGF-β. The level of integration of the two pathways mediating ...
TY - JOUR. T1 - The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. AU - Meiklejohn, Colin D.. AU - Coolon, Joseph D.. AU - Hartl, Daniel L.. AU - Wittkopp, Patricia J.. N1 - Copyright: Copyright 2014 Elsevier B.V., All rights reserved.. PY - 2014/1. Y1 - 2014/1. N2 - Evolutionary changes in gene expression underlie many aspects of phenotypic diversity within and among species. Understanding the genetic basis for evolved changes in gene expression is therefore an important component of a comprehensive understanding of the genetic basis of phenotypic evolution. Using interspecific introgression hybrids, we examined the genetic basis for divergence in genome-wide patterns of gene expression between Drosophila simulans and Drosophila mauritiana. We find that cis-regulatory and trans-regulatory divergences differ significantly in patterns of genetic architecture and evolution. The effects of cis-regulatory divergence are ...
PURPOSE: In the setting of a prospective clinical trial, we determined the predictive value of the methylation status of the O-6-methylguanine-DNA methyltransferase (MGMT) promoter for outcome in glioblastoma patients treated with the alkylating agent temozolomide. Expression of this excision repair enzyme has been associated with resistance to alkylating chemotherapy. EXPERIMENTAL DESIGN: The methylation status of MGMT in the tumor biopsies was evaluated in 38 patients undergoing resection for newly diagnosed glioblastoma and enrolled in a Phase II trial testing concomitant and adjuvant temozolomide and radiation. The epigenetic silencing of the MGMT gene was determined using methylation-specific PCR. RESULTS: Inactivation of the MGMT gene by promoter methylation was associated with longer survival (P = 0.0051; Log-rank test). At 18 months, survival was 62% (16 of 26) for patients testing positive for a methylated MGMT promoter but reached only 8% (1 of 12) in absence of methylation (
RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts (DDR2(+)), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was ...
In this study, we provide experimental evidence in favor of the hypothesis that PPARs are involved in the control of renin gene expression. We predicted a role for PPARs in the regulation of renin gene expression using a molecular approach. There was strong initial evidence supporting such a role.7,12 A functional DNA-binding site, similar to the consensus motif for PPARs, was detected in the conserved 5′-renin gene enhancer. The retinoic acid nuclear receptor RXRα, which is the typical interaction partner for PPARs, binds to the mouse renin gene enhancer. Lastly, vitamin A, which is the natural ligand of RXRs, was found to stimulate the transcription of the renin gene.. Renin gene expression is upregulated by cAMP in CaLu-6 cells through stabilization of renin mRNA, although transcriptional mechanisms are also involved.17,21 We provided several lines of evidence that PPARγ stimulates renin gene expression without affecting the stability of renin mRNA (Figures 1, 2, and 5⇑⇑; data not ...
The DNA sequence that a transcription factor binds to is called a transcription factor-binding site or response element.[55]. Transcription factors interact with their binding sites using a combination of electrostatic (of which hydrogen bonds are a special case) and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor-binding site may actually interact with the transcription factor. In addition, some of these interactions may be weaker than others. Thus, transcription factors do not bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA-binding protein (TBP) is TATAAAA, the TBP transcription factor can also bind similar sequences such as TATATAT or TATATAA. Because transcription factors can bind a set of related ...
The DNA sequence that a transcription factor binds to is called a transcription factor binding site or response element. Chemically, transcription factors usually interact with their binding sites using a combination of hydrogen bonds and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor binding site may actually interact with the transcription factor. In addition some of these interactions may be weaker than others. Thus, transcription factors don't bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA binding protein (TBP) is: TATAAAA the TBP transcription factor can also bind similar sequences such as: TATATAT or TATATAA Because transcription factors can bind a set of related sequences and the sequences don't tend ...
It is well known that an expanded polyglutamine tract (polyQ) within the huntingtin (htt) protein is the root cause of Huntington's disease (HD), but just exactly how this polyQ expansion exerts its devastating effects on neurons remains something of a mystery. Hints from transgenic mice, which express mutant huntingtin and have altered levels of expression of many genes, suggest that the aberrant protein may sequester other proteins that are essential for transcription-though what these protein(s) are remains to be seen.. In yesterday's Sciencexpress Dimitri Krainc at Massachusetts General Hospital, and coworkers at the NIH in Bethesda, Maryland, and New York University School of Medicine, identify potential protein victims of mutant huntingtin. They found that polyQ htt compromises the interaction between the transcriptional activator Sp1 and the TATA-box binding protein factor TAFII130. The former is an activator of many genes, including the D2 dopamine receptor, the latter forms part of a ...
The anthrax letter attacks after September 11, 2001 demonstrated the ease of using the anthrax spore as a weapon in a bioterrorist attack. Anthrax is a lethal i...
We have characterized the 5′ region of the human alpha 1(V) collagen gene (COL5A1). The transcriptional promoter is shown to have a number of features characteristic of the promoters of 'housekeeping' and growth-control-related genes. It lacks obvious TATA and CAAT boxes, has multiple transcription start sites, has a high GC content, lies within a well-defined CpG island and has a number of consensus sites for the potential binding of transcription factor Sp1. This type of promoter structure, while unusual for a collagen gene, is consistent with the broad distribution of expression of COL5A1 and is reminiscent of the promoter structures of the genes encoding type VI collagen, which has a similarly broad distribution of expression. Stepwise deletion of COL5A1 5′ sequences, placed upstream of a heterologous reporter gene, yielded a gradual decrease in promoter activity, indicating that the COL5A1 promoter is composed of an array of cis-acting elements. A minimal promoter region contained ...
LB-237 Many human cancers including breast cancer exhibit increased de novo fatty acid synthesis with overexpression of fatty acid synthase (FAS). Unlike normal cells and tissues that preferentially utilize circulating fatty acids derived from the diet, cancers synthesize fatty acids endogenously for membrane biosynthesis to sustain cell proliferation. The transcription factor Sp1 is highly expressed in a variety of cancers. Sp1 regulates gene expression by interacting with GC-rich promoter sequences. Genes that regulate cell cycle progression often contain such promoter sequences, and Sp1 is critical for their expression. The promoter region of FAS also has Sp1 binding sites, and Sp1 together with sterol regulatory element-binding protein-1 (SREBP-1) has been shown to regulate FAS expression in hepatocytes. Here, we hypothesize that Sp1 coordinately regulates FAS and cell cycle progression in estrogen-responsive MCF-7 breast cancer cells. Based on previous studies, to up-regulate Sp1 activity ...
A rare point mutation in the core promoter -270GC-rich box of PIGM, a housekeeping gene, disrupts binding of the generic transcription factor (TF) Sp1 and causes inherited glycosylphosphatidylinositol (GPI) deficiency (IGD). We show that whereas PIGM messenger RNA levels and surface GPI expression in IGD B cells are low, GPI expression is near normal in IGD erythroid cells. This divergent phenotype results from differential promoter chromatin accessibility and binding of Sp1. Specifically, whereas PIGM transcription in B cells is dependent on Sp1 binding to the -270GC-rich box and is associated with lower promoter accessibility, in erythroid cells, Sp1 activates PIGM transcription by binding upstream of (but not to) the -270GC-rich box. These findings explain intact PIGM transcription in IGD erythroid cells and the lack of clinically significant intravascular hemolysis in patients with IGD. Furthermore, they provide novel insights into tissue-specific transcriptional control of a housekeeping gene by a