Additional file 4: Figure S3. of Suppression of AGR2 in a TGF-β-induced Smad regulatory pathway mediates epithelial-mesenchymal transition

The effect of AGR2 expression on vimentin cellular localization. A scale bars correspond to 20 μm. (PDF 319 kb

Additional file 3: Figure S2. of Suppression of AGR2 in a TGF-β-induced Smad regulatory pathway mediates epithelial-mesenchymal transition

The effect of PD98059 inhibitor on TGF-β induced nuclear accumulation of Smad2/Smad3 complex. (PDF 352 kb

Additional file 2: Table S1. of Suppression of AGR2 in a TGF-β-induced Smad regulatory pathway mediates epithelial-mesenchymal transition

Sequences of the primers used in quantitative PCR analysis. (PDF 213 kb

Additional file 10: Table S3. of A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues

Biological functions enriched in ΔNp63 and TAp63 networks by IPA. Column A provides the diseases/biological functions, column B provides the p value of enrichment for the functions (calculated by Fisher’s exact test) and columns C and D provide the number and details of molecules that are involved in that function. (CSV 2 kb

Additional file 7: Figure S5. of A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues

p63 isoform expression as estimated by Analysis Pipeline 2. Heatmap depicting the expression of p63 isoforms in FPKM (fragments per kilobase of transcript per million), across representative p63 expressing cell-lines. (PDF 44 kb

Additional file 5: Figure S3. of A global analysis of the complex landscape of isoforms and regulatory networks of p63 in human cells and tissues

ΔNp63α is the predominant isoform in both proliferating and differentiating keratinocytes. Line chart depicting expression of p63 isoforms in human keratinocytes at three time points during differentiation: Day 0(DK0), Day3 (DK3) and Day 6(DK6). ΔNp63α levels are attenuated during keratinocyte differentiation whereas TAp63 expression is not detectable at any time points under these conditions. Also shown are expression pattern of differentiation markers, FLG and EHF. FPKM: fragments per kilobase of transcript per million. (PDF 30 kb

Binding of IFI16 protein to supercoiled DNAs.

<p>(A) 100 ng sc pBluescript (lane 1–6) and sc pCMYC (lane 7–12) were incubated with increasing concentrations of IFI16 (molar ratio DNA:protein 1:0 / 1:1.25 / 1:2.5 / 1:5/ 1:10 / 1:20) in binding buffer (5 mM Tris-HCl, pH 7.0; 1 mM EDTA, 50 mM KCl and 0.01% Triton X-100) on ice for 15 min. The electrophoresis ran for 3 h at 100 V at 4°C. (B) 100 ng linear pBluescript (lane 1–6) and linear pCMYC (lane 7–12) were incubated with increasing concentrations of IFI16 (molar ratio DNA: protein 1:0 / 1:1.25 / 1:2.5 / 1:5/ 1:10 / 1:20) in binding buffer (5 mM Tris-HCl, pH 7.0; 1 mM EDTA, 50 mM KCl and 0.01% Triton X-100) on ice for 15 min. The electrophoresis ran for 3 h at 100 V at 4°C.</p

H/D exchange of IFI16 in response to DNA interaction.

<p>(A) H/D exchange of IFI16 in response to DNA interaction was analyzed in four reactions: IFI16 protein without DNA as a control, IFI16 with single stranded DNA oligonucleotide (SS DNA), IFI16 with double stranded DNA oligonucleotide (DS NHE III) and IFI16 with DNA forming quadruplex structure (Q NHEIII). H/D exchange was quenched at 900 s after addition of deuterium. The graph shows percentage deuteration of individual amino acids of IFI16 calculated as weighted average of corresponding peptides [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157156#pone.0157156.ref053" target="_blank">53</a>]. Shaded area of the graph shows the areas not covered by peptides. The deuteration spectrum is aligned with the domain structure of IFI16 and with prediction of disordered regions (FoldIndex [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157156#pone.0157156.ref054" target="_blank">54</a>]). (B) Structure of the first HIN-A domain (PDB 2OQ0) corresponding to amino acids 198–389 of IFI16 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157156#pone.0157156.ref014" target="_blank">14</a>]. (C) Complex of the second HIN-B domain with DNA (PDB 3RNU) corresponding to amino acids 516–710 of IFI16 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157156#pone.0157156.ref023" target="_blank">23</a>]. In (B) and (C) the helical linker peptide exhibiting the most significant changes in percentage of deuteration in the presence of quadruplex DNA is highlighted in red.</p

CD spectroscopy of quadruplexes and their stabilization by IFI16.

<p>(A) CD spectra of oligonucleotide HTEL in TE buffer after denaturation (blue line), in TE buffer + 50 mM NaCl (red line) and in TE buffer + 50 mM KCl (green line). (B) CD spectra of oligonucleotide NHEIII in TE buffer after denaturation (blue line), in TE buffer + 50 mM NaCl (red line) and in TE buffer + 50 mM KCl (green line). The schematic drawings represent quadruplex structures of HTEL and NHEIII sequences. (C) The effect of recombinant IFI16 on HTEL quadruplex formation in potassium ions. CD spectra description: HTEL oligonucleotide in TE buffer (blue line), HTEL in TE buffer with 50 mM KCl (red line), HTEL in TE buffer + protein buffer with final concentration 3.4 mM KCl (green line), HTEL in TE buffer + IFI16 in protein buffer at molar ratio 1:1 and final concentration 3.4 mM KCl (violet line), IFI16 protein in protein buffer with final concentration 3.4 mM KCl in TE buffer (black line). (D) The effect of recombinant IFI16 on NHEIII quadruplex formation in potassium ions. The same description of curves as in C (NHEIII instead of HTEL). (E) The effect of recombinant IFI16 on HTEL quadruplex formation in sodium ions. CD spectra description: HTEL oligonucleotide in TE buffer (blue line), HTEL in TE buffer with 50 mM NaCl (red line), HTEL in TE buffer + protein buffer with final concentration 3.2 mM NaCl (green line), HTEL in TE buffer + IFI16 in protein buffer at molar ratio 1:2 and final concentration 3.2 mM NaCl (violet line), IFI16 protein in protein buffer with final concentration 3.2 mM NaCl in TE buffer (black line). (F) The effect of recombinant IFI16 on NHEIII quadruplex formation in sodium ions. The same description of curves as in E (NHEIII instead of HTEL).</p

DNA sequences of oligonucleotides.

<p>DNA sequences of oligonucleotides.</p