Journal: JCI Insight

Article Title: Targeting and silencing of rhodopsin by ectopic expression of the transcription factor KLF15

doi: 10.1172/jci.insight.96560

Figure Lengend Snippet: (A) TRANSFAC analysis of the human rhodopsin promoter identifies transcription factors (TFs) predicted to bind the rhodopsin regulatory motif hRHO-cis (–88 to –58 from the transcription start site, TSS; Figure 2A and refs. 12, 13) including the TF KLF15 (orange arrow, minus strand). (B) Immunofluorescence analysis of Klf15 in C57BL6/J retina shows its absence in photoreceptors in the outer nuclear layer (ONL) and expression in the inner nuclear layer (INL) and in the ganglion cell layer (GCL). Scale bar: 50 μm. (C) qPCR of mRNA (2–ΔCt) shows that Klf15 is not expressed in porcine rods. Porcine rods transduced with AAV8-hGNAT1-eGFP (1 × 1012 genome copies [gc]) and FACS sorted show lack of expression of Klf15. For comparison the retina-specific cone-rod homeobox (Crx) and rod-specific neural retina leucine zipper (Nrl) TFs are shown. (D) Gel mobility shift titrations of hKLF15 and artificial ZF6-DB TF with the hRHO 65-bp oligonucleotide. In the saturation-binding experiments the nanomolar concentration of specific binding data were plotted against nanomolar increasing concentration of DNA ligand. KLF15 and the synthetic TF ZF6-DB show similar binding affinity for the target sequence (12, 13). (E) qPCR ChIP analysis of the human rhodopsin TSS region, after the transfection of hKLF15 in HEK293 cells, shows enrichment of binding in the Rho promoter region compared with eGFP-transfected cells. Data are shown as the mean ± SEM. **P < 0.01 by 2-tailed Student’s t test. n = 3 independent experiments.

Article Snippet: Plasmid construction The human KLF15 coding DNA sequence (CDS) and the murine KLF15 CDS were synthesized by Eurofins MWG.

Techniques: Immunofluorescence, Expressing, Transduction, Comparison, Mobility Shift, Binding Assay, Concentration Assay, Sequencing, Transfection

Journal: JCI Insight

Article Title: Targeting and silencing of rhodopsin by ectopic expression of the transcription factor KLF15

doi: 10.1172/jci.insight.96560

Figure Lengend Snippet: (A) Alignment of human, porcine, and murine rhodopsin (Rho) proximal promoter around the hRHO-cis. In red, the sequence recognized by KLF15 retrieved by TRANSFAC analysis (Figure 1A and Supplemental Table 1). (B) qPCR of mRNA levels (2–ΔΔCt) of adult porcine retina injected subretinally with AAV8-hGNAT1-hKLF15 (n = 6) or AAV8-hGNAT1-eGFP (n = 6) at a vector dose of 2 × 1010 genome copies (gc) 15 days after vector delivery shows significant repression of the Rho transcript; Gnat1, guanine nucleotide–binding protein 1; Arr3, arrestin 3. Data are shown as the mean ± SEM. ***P < 0.001; 2-tailed Student’s t test. (C) Western Blot analysis of porcine retinae injected with AAV8-hGNAT1-hKLF15 and AAV8-hGNAT1-eGFP shows the decrease in Rho protein consequent to KLF15 expression. (D) Rho (cyan) and KLF15 (red) immunofluorescence confocal analysis shows expression of hKLF15 in the outer nuclear layer (ONL) of injected retina (coinjected with AAV8-hGNAT1-eGFP, green) toward the nuclear interior of rod photoreceptor nuclei (euchromatin; see ref. 33), the collapse of the Rho-deprived outer-segment (OS), and partial retention of Rho in the cytoplasm. (E) Histological confocal immunofluorescence analysis of Gnat1 (red), which marks the soma of rods, confirmed rod-specific expression of hKLF15 upon transduction with AAV8-hGNAT1-hKLF15. Scale bars: 50 μm. (F) Venn diagrams showing pairwise intersection of differentially expressed genes (DEGs) between hKLF15 and ZF6-DB (12, 13). An adjusted P value (false discovery rate < 0.1), without filtering on fold change levels, resulted in 156 and 19 DEGs, in hKLF15- and ZF6-DB–treated retinae, respectively (12, 13). (G) Transcriptional activation and repression concordances among log fold changes of the genes in common between ZF6-DB and hKLF15.

Article Snippet: Plasmid construction The human KLF15 coding DNA sequence (CDS) and the murine KLF15 CDS were synthesized by Eurofins MWG.

Techniques: Sequencing, Injection, Plasmid Preparation, Binding Assay, Western Blot, Expressing, Immunofluorescence, Transduction, Activation Assay

Journal: JCI Insight

Article Title: Targeting and silencing of rhodopsin by ectopic expression of the transcription factor KLF15

doi: 10.1172/jci.insight.96560

Figure Lengend Snippet: (A) Electroretinography (ERG) traces from a representative mouse injected with AAV carrying hKLF15, mKlf15, or eGFP measured at increasing luminances (cd⋅s/m2). (B) ERG analysis on P347S mice subretinally injected at postnatal day 14 (P14) with AAV8-hGNAT1-hKLF15 (n = 12), AAV8-hGNAT1-mKlf15 n = 9), AAV8-hGNAT1-eGFP (n = 14), or not injected (n = 6) and analyzed at P30. Retinal responses in both scotopic (dim light) and photopic (bright light) showed that both a- and b-wave amplitudes, evoked by increasing light intensities, were more preserved in hKLF15- and mKlf15-injected eyes compared with eGFP control eyes. (C) Immunofluorescence staining of P347S mouse retina, injected at P14 with AAV8-hGNAT1-hKLF15, AAV8-hGNAT1-mKlf15, or AAV8-hGNAT1-eGFP and analyzed at P30. hKLF15- and mKlf15-treated retinae show KLF15-positive expression toward the periphery of rod photoreceptor nuclei, an inverted pattern compared with pig (Figure 2D and ref. 33), and higher preservation of the outer nuclear layer (ONL) compared with eGFP controls. INL, inner nuclear layer. (D) qPCR of mRNA levels (2–ΔCt normalized to the mGnat1 gene) demonstrates that hKLF15 and mKLF15 downregulate human RHO-P347S expression without changing the endogenous wild-type murine rhodopsin transcript.

Article Snippet: Plasmid construction The human KLF15 coding DNA sequence (CDS) and the murine KLF15 CDS were synthesized by Eurofins MWG.

Techniques: Injection, Control, Immunofluorescence, Staining, Expressing, Preserving

Journal: PLoS ONE

Article Title: Structural Differences between Human Proteins and Aero- and Microbial Allergens Define Allergenicity

doi: 10.1371/journal.pone.0040552

Figure Lengend Snippet: The percent identity levels between human proteins (x-axis) a representative helminth ( B. malayi , A ), protozoan ( P. falciparum , B ) and fungus ( C. albicans , C ) protein (y-axis). Correlations were evaluated by Spearman rank test. Each dot represents one allergen and the squared-dot at the origin of the axis represents allergens that had neither homologues in humans nor in the microbes: (A) n = 222, (B) n = 247 and (C) n = 210 allergens.

Article Snippet: Fasta files with translated CDS annotated protein sequences for Brugia malayi , Loa loa and Wuchereria bancrofti (all version 1) were downloaded from the Broad Institute ( http://www.broadinstitute.org/annotation/genome/filarial_worms/MultiDownloads.html ), Schistosoma mansoni fasta file (version GeneDB v 4.0 h) was downloaded from Sanger Institute ( ftp://ftp.sanger.ac.uk/pub/pathogens/ ), Plasmodium falciparum (PlasmoDB 6.4) from Plasmodb ( http://plasmodb.org/common/downloads/ ), Trypanosoma cruzi CL Brener (TriTrypDB-2.2) and Leishmania major Friedlin (TriTrypDB-2.2) from Tritrypdb ( http://tritrypdb.org/common/downloads/ ), Toxoplasma gondii ME-49 (ToxoDB 6.0) from Toxobd ( http://toxodb.org/common/downloads/ ).

Techniques: