Journal: Nucleic Acids Research

Article Title: The Effects of Sequence Variation on Genome-wide NRF2 Binding—New Target Genes and Regulatory SNPs

doi: 10.1093/nar/gkw052

Figure Lengend Snippet: Testing the limits of NRF2 binding. Systematic multivariate ARE results by protein binding microarray for NRF2-MAFG heterodimer are shown. Tolerance for sequence variation was studied for positions 1–3 (white), 6–8 (grey) and 9–11 (dark grey) ( A ) and positions 1, 5 and 11 (seed sequences are shown in grey) ( B ). Results are depicted as measured binding relative to NQO1.ARE binding (black) (mean ± S.E.M., n = 45).

Article Snippet: The dilutions were dispensed in a 384-well plate (polypropylene plate No 267462, Nunc, N.Y, USA) and printed onto the avidin-coated glass slides with a microarray printer (BioRobotics MicroGrid II, BioRobotics Ltd, Cambridge, UK).

Techniques: Binding Assay, Protein Binding, Microarray, Sequencing

Journal: Nucleic Acids Research

Article Title: The Effects of Sequence Variation on Genome-wide NRF2 Binding—New Target Genes and Regulatory SNPs

doi: 10.1093/nar/gkw052

Figure Lengend Snippet: A SNP in FTL promoter has drastic effects of NRF2 binding and transcriptional activation. ( A ) A promoter analysis of the FTL gene at chr19 showing the location of experimentally verified NRF2 binding ARE together with dbSNP (v138) and ENCODE ChIP-seq data. ChIP-seq track displays combined MAFF and MAFK binding signals in H1-hESC (MAFK), K562 (MAFF, MAFK), HeLa-S3 (MAFK), HepG (MAFF, MAFK) and IMR90 (MAFK) cell lines. ( B ) Detailed view showing FTL ARE sequence and the SNP (rs113067944, A→C) position. ( C ) Protein binding microarray results for FTL.ARE.A and the SNP bearing FTL.ARE.C. Results are calculated as measured binding relative to NQO1.ARE binding (mean ± S.E.M, n = 39.). Scramble oligonucleotides served as negative control. ( D ) HEK-293T cells were transfected with NQO1-ARE and FTL-ARE bearing either allele A or allele C with and without NRF2 -expressing plasmids. Twenty-four h after transfection cells were treated with NRF2 inducer (L-SFN) for 16 h followed by luciferase activity measurements. An empty pGL3 promoter vector served as control and activities were normalized to β-galactosidase activity. Results are shown relative to control (mean± S.E.M, n = 4).

Article Snippet: The dilutions were dispensed in a 384-well plate (polypropylene plate No 267462, Nunc, N.Y, USA) and printed onto the avidin-coated glass slides with a microarray printer (BioRobotics MicroGrid II, BioRobotics Ltd, Cambridge, UK).

Techniques: Binding Assay, Activation Assay, ChIP-sequencing, Sequencing, Protein Binding, Microarray, Negative Control, Transfection, Expressing, Luciferase, Activity Assay, Plasmid Preparation, Control

Journal: Scientific Reports

Article Title: Identification of an Arg-Leu-Arg tripeptide that contributes to the binding interface between the cytokine MIF and the chemokine receptor CXCR4

doi: 10.1038/s41598-018-23554-5

Figure Lengend Snippet: Identification of the RLR sequence as a potential MIF binding region to the N-terminal peptide of CXCR4. ( a , b ) The peptide spot microarray method suggests that the RLR tripeptide at sequence position 87–89 may contribute to MIF/CXCR4 binding. A peptide spot array containing 15-mer spotted MIF peptides positionally shifted by three amino acids were probed with biotin-CXCR4(1–27). Graphs are plots of spotted MIF peptides over the intensity of the binding signal to biotin-CXCR4(1–27) as read-out by streptavidin Cy5.5 fluorescence. ( a ) Of five positionally shifted 15-mer peptides of the region 79–105 only peptides containing RLR interact with CXCR4(1–27). ( b ) Binding of RLR-containing MIF peptides is modulated by N-terminal extension, but residues N-terminal of RLR do not exhibit binding activity per se . ( c ) Structural model of MIF (as monomer and trimer) and position of the N-like loop (green) and the RLR sequence (red). Note: in the three-dimensional conformation of the monomer, RLR is located in the vicinity of the N-like loop of MIF. The trimeric structure shows that both the N-like loop and RLR are surface-exposed on the trimer (see also Fig. ).

Article Snippet: Analysis of interactions was performed using a microarray processing station (Intavis Slide Spotting Robot).

Techniques: Sequencing, Binding Assay, Microarray, Fluorescence, Activity Assay