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: BMC Plant Biology

Article Title: Genome-wide survey of the bHLH super gene family in Brassica napus

doi: 10.1186/s12870-020-2315-8

Figure Lengend Snippet: Sequence characteristics of the bHLH domains in different DNA-binding types. Multiple sequence alignments were conducted with the bHLH domains of all candidate proteins and then was conducted with the domains of proteins of a given DNA-binding type. The number in bracket indicates the amount of BnabHLHs in a certain category. Protein secondary structures are illustrated under the sequences. Red asterisks indicate the residues with over 90% similarity; black asterisks indicate residues with over 70% similarity. Black triangles at the top of the sequence indicates the E-box recognition sites; red triangles indicate the G-box recognition sites. The bHLH domains with at least five basic residues but no E-box/G-box binding sites are classified as non-E-box binding genes, otherwise it is a non-DNA binding gene (atypical gene)

Article Snippet: The corresponding CDS and DNA sequences of candidate bHLH genes in B. napus were obtained from Genoscope database as well.

Techniques: Sequencing, Binding Assay

Journal: BMC Plant Biology

Article Title: Genome-wide survey of the bHLH super gene family in Brassica napus

doi: 10.1186/s12870-020-2315-8

Figure Lengend Snippet: Phylogenetic relationships, DNA-binding types, intron insertion patterns, and architecture of conserved protein motifs in 35 bHLH subfamilies. a Phylogenetic relationships of 769 bHLHs from B. napus (602) and Arabidopsis (167). The phylogenetic tree is generated based on the alignment of bHLH domains of the corresponding bHLH proteins with 1000 bootstrap replicates. The subfamilies marked in grey are newly identified in this study as compared to the results in Arabidopsis . b DNA-binding types and intron insertion types of BnabHLHs in each subfamily. The illustration of intron insertion patterns is shown in Fig. . c Architecture of conserved protein motifs of BnabHLHs in each subfamily by MEME analysis. Blocks with a black background indicate the bHLH domain. Blocks with a solid line represent the motif distributed in all proteins in a certain subfamily, while those with a dotted line represent the motif distributed in a part of members in a given subfamily

Article Snippet: The corresponding CDS and DNA sequences of candidate bHLH genes in B. napus were obtained from Genoscope database as well.

Techniques: Binding Assay, Generated