New targets in this one-sample data set, all three predicted sites in Zfp423 introns 3 and 5 were called as peaks and enriched relative to other sites in a 400 kb window encompassing the 10781694 Zfp423 gene, providing further evidence for the prior hypothesis of selective binding by Zfp423 at these sites and for the potential of a conserved autoregulatory circuit at Zfp423. The intron 5 site was among the top 30 scores on chromosome 8 using the peak-finding algorithm in Homer. Moreover, the peak was composed of two adjacent, facing sets of forward and reversestrand reads, with the modes for each strand separated by approximately the model distance of the sheared chromatin used for constructing the sequencing library.Zfp423 Intron 5 Title Loaded From File Fragment has Enhancer Activity in P19 CellsTo test whether the strongly-bound site in intron 5 has enhancer activity, we cloned it and several derivatives into a plasmid with a basal promoter driving firefly luciferase as a reporter, cotransfected each construct with a single Renilla luciferase reporter as a transfection control into P19 cells, and measured the ratio of luciferase activities for replicate transfections with each of three independent DNA preparations for each intron 5 construct (Figure 4). The base construct included a 740 bp fragment fully encompassing the vertebrate-conserved sequence, 16985061 in the same orientation relative to the direction of transcription as it occurs in Zfp423 (Figure 4A). This showed substantial enhancer activity relative to the base vector, pGL4-TAL (Figure 4B). Shorter fragments derived from the 740 bp sequence also showed activity, including a fragment with the overlapping Zfp423/Ebf predicted binding sites mutated (Figure 4C). Having independent DNA preparations with substantial replication measures for each tested construct allowed us to compare relative enhancer strengths compared to the pGL4-TAL base vector transfected on the same day for each experiment with a robust statistical comparison (Figure 4D). Placing the full 740 bp sequence in the reverse orientation showed even higher activity in this assay, while placing it 39 to the reporter showed essentially the same activity level as the initial construct, satisfying the classical criteria for a transcriptionalFigure 2. Cell culture models express Zfp423 and its binding partners. (A) Inverted gel images from semi-quantitative RT-PCR show expression of ZNF423 and EBF family members in IMR32 (neuroblastoma), as well as D238 (medulloblastoma) cell lines. ZNF423 was not detected from either U87 or U251 (glioblastoma) lines. Cycle numbers are indicated to the left. (B) Among four neuroblastoma cell lines, RT-qPCR shows high relative expression of ZNF423 in IMR32 and SK-N-SH cells. Graph shows average and standard deviation for technical replicates of a single experiment. (C) Graph shows RT-qPCR expression values for Zfp423 and Ebf RNAs in P19 cells, normalized to the geometric mean of Gapdh, Pitpna, and Ppig as reference genes. Error bars indicate range in technical replicates only. Title Loaded From File Analysis of an independent second culture showed similar results. (D) RT-qPCR expression values from postnatal day 3 mouse cerebellum as a primer control, normalized and scaled as in (C). Note significantly higher expression levels in tissue compared to P19. (E) Western blots show detection of Zfp423 in 25 mg total cellular protein from IMR32 or P19 cells, detected with a goat polyclonal antibody (E20) and visualized by infrared imaging. The doublet app.New targets in this one-sample data set, all three predicted sites in Zfp423 introns 3 and 5 were called as peaks and enriched relative to other sites in a 400 kb window encompassing the 10781694 Zfp423 gene, providing further evidence for the prior hypothesis of selective binding by Zfp423 at these sites and for the potential of a conserved autoregulatory circuit at Zfp423. The intron 5 site was among the top 30 scores on chromosome 8 using the peak-finding algorithm in Homer. Moreover, the peak was composed of two adjacent, facing sets of forward and reversestrand reads, with the modes for each strand separated by approximately the model distance of the sheared chromatin used for constructing the sequencing library.Zfp423 Intron 5 Fragment has Enhancer Activity in P19 CellsTo test whether the strongly-bound site in intron 5 has enhancer activity, we cloned it and several derivatives into a plasmid with a basal promoter driving firefly luciferase as a reporter, cotransfected each construct with a single Renilla luciferase reporter as a transfection control into P19 cells, and measured the ratio of luciferase activities for replicate transfections with each of three independent DNA preparations for each intron 5 construct (Figure 4). The base construct included a 740 bp fragment fully encompassing the vertebrate-conserved sequence, 16985061 in the same orientation relative to the direction of transcription as it occurs in Zfp423 (Figure 4A). This showed substantial enhancer activity relative to the base vector, pGL4-TAL (Figure 4B). Shorter fragments derived from the 740 bp sequence also showed activity, including a fragment with the overlapping Zfp423/Ebf predicted binding sites mutated (Figure 4C). Having independent DNA preparations with substantial replication measures for each tested construct allowed us to compare relative enhancer strengths compared to the pGL4-TAL base vector transfected on the same day for each experiment with a robust statistical comparison (Figure 4D). Placing the full 740 bp sequence in the reverse orientation showed even higher activity in this assay, while placing it 39 to the reporter showed essentially the same activity level as the initial construct, satisfying the classical criteria for a transcriptionalFigure 2. Cell culture models express Zfp423 and its binding partners. (A) Inverted gel images from semi-quantitative RT-PCR show expression of ZNF423 and EBF family members in IMR32 (neuroblastoma), as well as D238 (medulloblastoma) cell lines. ZNF423 was not detected from either U87 or U251 (glioblastoma) lines. Cycle numbers are indicated to the left. (B) Among four neuroblastoma cell lines, RT-qPCR shows high relative expression of ZNF423 in IMR32 and SK-N-SH cells. Graph shows average and standard deviation for technical replicates of a single experiment. (C) Graph shows RT-qPCR expression values for Zfp423 and Ebf RNAs in P19 cells, normalized to the geometric mean of Gapdh, Pitpna, and Ppig as reference genes. Error bars indicate range in technical replicates only. Analysis of an independent second culture showed similar results. (D) RT-qPCR expression values from postnatal day 3 mouse cerebellum as a primer control, normalized and scaled as in (C). Note significantly higher expression levels in tissue compared to P19. (E) Western blots show detection of Zfp423 in 25 mg total cellular protein from IMR32 or P19 cells, detected with a goat polyclonal antibody (E20) and visualized by infrared imaging. The doublet app.
