avidity specificity and sensitivity of transcription factor dna binding in genome scale experiments
Báo cáo y học: "All motifs are not created equal: structural properties of transcription factor - dna interactions and the inference of sequence specificity" doc
... the binding specificities of transcription factors In attempting to analyze available binding matrixes in TRANSFAC [35], we were struck by how few examples there were of factors whose binding ... model of the sequences from A D) Information content of PWM from C Figure Clustering of information in transcription factor binding sites in TRANSFAC The information content of each position in ... biochemical nature of transcription factor- DNA (TF -DNA) interactions imposes constraints on the types of motifs that are likely to be transcription factor binding sites, and that our structural and biochemical...
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Báo cáo y học: "Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura" ppsx
... Predicted and aligned binding sites in pCRMs Predicted and aligned binding sites in pCRMs Predicted binding sites and aligned binding sites (see Materials and methods) in positive, ambiguous and negative ... pCRMs: the number of aligned binding sites; the density of aligned binding sites; the number of aligned plus preserved binding sites; and the density of aligned plus preserved binding sites All values ... based on binding- site clustering selectivityof evolutionary information greatly increases the specificity and Inclusion Inclusion of evolutionary information greatly increases the specificity and...
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algorithms for representation and discovery of transcription factor binding sites
... performance of all basic methods in discriminating between binding sites for the transcription factor of interest and binding sites of other transcription factors; however, weighting each match ... completely inside one another in the genome In these cases, when scoring the negative binding site, a true binding site for the transcription factor of interest is present; thus these corresponding binding ... 2.2.2 Approaches for representing and searching for transcription factor binding sites Four basic approaches for representing and searching for transcription factor binding sites were evaluated We...
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Tài liệu Báo cáo khoa học: TransLISA, a novel quantitative, nonradioactive assay for transcription factor DNA-binding analyses pdf
... interpretation of the results also depend on the research application, e.g screening or determining binding affinities for transcription factor DNA binding The results of measurements of HSF1 DNA- binding ... through the DNA- binding domain Stable binding requires simultaneous binding of all DNA- binding domains in a trimer to three adjacent 7372 nGAAn repeats Therefore, a functional HSE contains at least ... [11], exist for investigating transcription factors and transcriptional regulation, but the main purpose of using these methods is not in quantifying transcription factor DNA binding Our goal was...
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Báo cáo khoa học: Thermodynamic analysis of the unfolding and stability of the dimeric DNA-binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima and its E34D mutant pdf
... of DNA- binding protein HU from Bacilli Protein Eng 4, 11–22 16 Padas, P.M., Wilson, K.S & Vorgias, C.E (1992) The DNAbinding protein HU from mesophilic and thermophilic bacilli: gene cloning, overproduction ... structure and its thermal unfolding, and to describe some of the experimental and mathematical bases for future studies into strategies for increasing the thermal stability of proteins Materials and ... unfolding of both the wild-type HUTmar protein and its E34D mutant in acidic solutions (pH 4.00, 3.75 and 3.50) to improve the reversibility of unfolding and avoid postunfolding aggregation Judging...
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Tài liệu Báo cáo khoa học: Role of transcription factor activator protein 1 (AP1) in epidermal growth factor-mediated protection against apoptosis induced by a DNA-damaging agent doc
... MAP kinase signaling pathway TAM67 retains the DNA binding and leucine-zipper region of c-Jun, but it lacks the transactivation domain of c-Jun (amino acids 1–122) It thus blocks the binding of ... that AP1 DNA binding activity increased within h following EGF treatment and peaked at h following the treatment (Fig 5A) We also examined the effect of PD98059 on this binding activity and, as ... but retains the DNA binding and leucine-zipper region of c-Jun, it should function as a dominant-negative mutant of c-Jun to block wild-type c-Jun binding to the AP1 site [32] As shown in Fig...
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báo cáo khoa học: "The grapevine guard cell-related VvMYB60 transcription factor is involved in the regulation of stomatal activity and is differentially expressed in response to ABA and osmotic stress" ppt
... all the proteins included in the tree disclosed a highly conserved R2R3 DNA binding domain (Figure 1B) The identity between the R2R3 domain of AtMYB60 and VvMYB60 and VvMYB30 was 99%, and 90%, respectively ... 15-day-old pVvMYB60:GUS seedling (E) Magnification of leaf primordia in (D), showing staining of differentiating stomata (F) Detail of a pVvMYB60:GUS mature leaf, showing staining of fully differentiated ... (H) and (I) Histochemical analysis of GUS expression in pVvMYB60:GUS leaves in response to ABA (H) GUS staining of stomata in a control leaf (I), GUS staining of stomata following hours of exposure...
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Báo cáo y học: "Explicit equilibrium modeling of transcription-factor binding and gene regulation" pdf
... binding of proteins X and Y to DNA can be separated thermodynamically into the formation of an XY dimer and the binding of that dimer to DNA; this is thermodynamically equivalent to protein X binding ... consists of windows i and j; it is analogous to Ka,eff,X,i, the equilibrium constant for monomeric X binding to site i in that it is the product of an intrinsic binding affinity, Ka,XY,i,j, and a ... GOMER assumes that the intrinsic binding affinity of the dimer, Ka,XY,i,j, is the product of the binding constants of the two proteins, X and Y, for their respective sites, i and j Thus: Ka,eff,XY,i,j...
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Dual roles of transcription factor zic3 in regulating embryonic stem cell pluripotency and differentiation
... regulatory chain motifs48 The 12 Figure Functional domains of a transcription factor The amino acid sequence of a prototypical transcription factor is illustrated, containing a DNA- binding domain (DBD), ... transcriptional cofactor with the Gli proteins, with interactions occurring at the zinc-finger domain105,120 A Zic3 DNAbinding sequence has been identified, although its binding affinity is significantly ... stimuli and increased stability of gene expression in ES cells In addition to transcription factor binding targets, a recent study was conducted to determine protein interaction patterns of key...
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Tài liệu Báo cáo khoa học: Hsp105b upregulates hsp70 gene expression through signal transducer and activator of transcription-3 pdf
... N-terminal ATPase domain binds ADP ⁄ ATP, and can hydrolyze ATP; the central b-sheet domain directly binds peptide substrates; and the C-terminal a-helix domain regulates substrate binding [4–6] ... 30 min, and the remaining DNA was precipitated with 30 lL of a 50% slurry of Ultralink streptavidin gel (Pierce, Rockford, IL, USA) at °C for h Bound fractions were washed five times with binding ... times with binding buffer, and DNA- bound proteins were eluted with binding buffer containing mgÆmL)1 biotin; this was followed by SDS ⁄ PAGE and western blotting Chromatin immunoprecipitation HeLa-tet...
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Tài liệu Báo cáo khoa học: Efficient killing of SW480 colon carcinoma cells by a signal transducer and activator of transcription (STAT) 3 hairpin decoy oligodeoxynucleotide – interference with interferon-c-STAT1-mediated killing pdf
... eliminating any possible effects as a result of the introduction of DNA within cells, and indicating that, in itself, the interaction of ODN with STAT3 induced these effects (i.e inhibition of ... functions of STAT1 and STAT3 differ considerably and this must depend at some point on the specific recognition of a DNA- binding motif Specific inhibition of STAT3 by DNA- binding targeting may require ... distinct functions in cells STAT3 is mostly involved in cell survival and proliferation, and STAT1 is involved in anti-viral and immune defence and cell death, in response to interferons, including...
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Tài liệu Báo cáo khoa học: Unusual metal specificity and structure of the group I ribozyme fromChlamydomonas reinhardtii23S rRNA pptx
... pre-RNA, and the binding of a minimum of n Mg2+ ions leads to formation of the active complex, whereas binding of a minimum of m Mn2+ ions forms the inactive complex The sizes of the active and inactive ... dependence of this effect indicates that the nucleotide is acting via the G 2638 binding site in P7 An obvious explanation for this result is that binding of GMP prevents an inhibitory Mn2+ from binding ... fraction of metal -binding sites in RNA [29] An alternative explanation for GMP-induced folding of the ribozyme in Mn2+ is that binding of the cosubstrate to its site induces a conformational change in...
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Báo cáo khoa học: Eukaryotic class 1 translation termination factor eRF1 ) the NMR structure and dynamics of the middle domain involved in triggering ribosome-dependent peptidyl-tRNA hydrolysis pptx
... C domain of eRF1 interacts with the C domain of eRF3 [15–18], and the binding of both factors is essential for fast kinetics of the termination of translation [1] However, in a simplified in vitro ... coli in vivo can be explained by their competitive inhibition at the ribosome -binding site [32] Together, the M and C domains of human eRF1, in the absence of the N domain, are able to bind to ... eRF3 of fission yeast RNA 4, 958–972 Ebihara K & Nakamura Y (1999) C-terminal interaction of translational release factors eRF1 and eRF3 of fission yeast: G-domain uncoupled binding and the role of...
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Báo cáo khoa học: Insulin induces heme oxygenase-1 through the phosphatidylinositol 3-kinase/Akt pathway and the Nrf2 transcription factor in renal cells pptx
... oxidative insult Insulin is a polypeptide hormone that regulates glucose, lipid and protein metabolism and promotes cell growth and differentiation On ligand binding, the insulin receptor tyrosine kinase ... with increasing concentrations of human insulin resulted in a four-fold induction of HO-1 after h (Fig 1A) Maximal induction of HO-1 protein was achieved at concentrations of 200 nm insulin A ... treated in a similar manner with insulin (200 nm) for increasing periods of time (Fig 1E) A robust induction of HO-1 protein was observed Insulin-mediated induction of HO-1 is PI3K dependent In our...
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Báo cáo khoa học: Initiation of JC virus DNA replication in vitro by human and mouse DNA polymerase a-primase ppt
... especially in the synthesis of products greater than four nucleotides in length Murine DNA polymerase a-primase is absolutely inactive in initiating SV40 DNA replication in an assay consisting of purified ... containing the SV40 origin of DNA replication (B) The JCV system uses JCV TAg and pJC389 DNA with the JCV origin The cell extracts were supplemented with 0.5 and 1.0 DNA polymerase units of the indicated ... carried out with naked plasmid DNA Nucleosomes may interfere with the initiation of replication and evidence exists that the binding of transcription factors to sites in the regulatory regions adjacent...
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Báo cáo khoa học: A novel splicing variant form suppresses the activity of full-length signal transducer and activator of transcription 5A pot
... transactivation domain and the tyrosine residue (Tyr694) phosphorylated by Janus protein tyrosine kinase or other tyrosine kinases, although the DNA- binding domain and SH2 domain remained intact The frameshift ... composed of a a-helical coiled-coil domain, a DNA- binding domain, an SH2 domain, and a C-terminal transactivation domain The deletion of exon 18 (52 bp) in the STAT5A_DE18 mRNA results in a translational ... TATA -binding protein, and NF-Y, resulting in reduced expression of their target genes [28,29] This inhibition of functional transcription factors may be associated with the normal functions of...
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Báo cáo khoa học: Synergistic co-operation of signal transducer and activator of transcription 5B with activator protein 1 in angiotensin II-induced angiotensinogen gene activation in vascular smooth muscle cells potx
... of STAT5B binding and of c-Jun binding to DNA was detected, respectively, by electrophoretic mobility shift assays (EMSAs) using radiolabeled oligonucleotides containing either a STAT5B -binding ... specific inhibitor of the JAK-STAT pathway) for 16 h [24], indicating that the activation of STAT5B and c-Jun may be involved in Ang II-induced AGT mRNA expression (Fig 1C) DNA- binding activity of ... treated with Ang II for 0.5, 1, and h, and the DNA- binding activity of STAT5B and of AP-1 increased in a time-dependent manner The specificities of two DNA protein complexes were demonstrated by...
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Báo cáo khoa học: Domains of ERRcthat mediate homodimerization and interaction with factors stimulating DNA binding potx
... interaction of fusion proteins containing the DNA- binding domain of the androgen and glucocorticoid receptor with andro- DNA binding of ERRc (Eur J Biochem 269) 4097 53 54 55 56 57 58 59 60 gen and glucocorticoid ... in vitro translated protein ERRc-218, lacking amino acids forming the LBD and the C-terminal part of the hinge region, still binds to DNA, and the addition of serum results in increased binding ... Localization of the ERRc domain involved in the enhanced DNA binding (A) Schematic view of truncated ERRc and fusion proteins of GCNF and ERRc used in this study The position of the N-terminal A/B-domain,...
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Báo cáo y học: "Attenuation of murine antigen-induced arthritis by treatment with a decoy oligodeoxynucleotide inhibiting signal transducer and activator of transcription-1 (STAT-1)" ppt
... Darnell JE Jr, Stein RB, Rosen J: Spacing of palindromic half sites as a determinant of selective STAT (signal transducers and activators of transcription) DNA binding and transcriptional activity ... regulatory factor (IRF)-1 and CD40 in murine arthritic knee joints Total RNA was isolated from joint STAT-3, interferon regulatory factor (IRF)-1 and CD40 in murine arthritic knee joints capsules including ... joints were removed in toto, skinned, fixed in 4.5% phosphate-buffered formalin, decalcified in EDTA, embedded in paraffin, cut into µm thick frontal sections, and stained with hematoxylin-eosin...
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