In grey lowercase. (D) As one estimate of the significance level for apparent shifts between constructs, normalized expression values were compared by ANOVA, followed by Tukey’s Honest 10781694 Significant Differences pair-wise comparisons. Calculated p-values are indicated in the intersection between construct designations. Potential scaling differences between sequential experiments on different days (indicated by gaps between cells in the table) may violate some assumptions of the test. (E) ChIP-qPCR performed for transfected plasmids shows a higher enrichment index compared to input and IgG controls (calculated as DDCT for carrying the wild-type site than for the mutated sites shown in (C). The pairwise comparison was significant at p = 0.007 by ttest or 0.03 by the nonparametric equivalent (Wilcoxon signed rank test). doi:10.1371/journal.pone.0066514.gknockdown of Ebf1 and Zfp423 was somewhat less effective. It is notable that the cell culture model used for these extensive enhancer activity studies, P19, expresses lower levels of Zfp423 RNA than developing neural tissues, suggesting that the response we see to ,2.4X higher levels of ZNF423 in the culture model (Figure 5H) may indeed be relevant to levels achieved in developing cells. We propose that this site might play a role in either limiting Zfp423 accumulation or, more 16985061 provocatively, providing a developmental ratchet in which Zfp423 alone or in progressive complexes with one or more binding partners serves to turn off its own expression, to allow the cell to exit an immature cell state and Autophagy facilitate developmental progression. Our results also provide some information on predictive algorithms for transcription factor binding. While many of the sites we examined do not appear occupied under the narrow conditions tested, we do find compelling evidence for binding at several sites, and Epigenetic Reader Domain particularly strong evidence for binding in both mouse and human at a clearly functional site in intron 5. Regardless of whether the other predicted sites are occupied under conditions or not, the predictive approach need not be perfect to be a useful guide for early experiments where legitimate targets are not defined. In this example, the occurrence of clustered motifs for transcription factors known to interact in a complex facilitated the identification of an apparent autoregulatory site for a key transcription factor important for the development of both mice and humans. All together, our results strongly support both Zfp423 occupancy and functional enhancer activity for at least one predicted conserved segment. As most enhancers are cell-type specific [20], further analysis of genome-wide binding in a wider variety of cellular contexts will be required to test the generality of such predictions.software package. Monoclonal antibodies against b-actin (AC-74, Sigma) and GAPDH (GT239, GeneTex) were used to verify equal loading by detection of internal standards.Cell LinesNeuroblastoma IMR32 [21] was originally obtained from ATCC [22] and passaged in the authors’ laboratory to obtain a more adherent phenotype for ChIP. Medulloblastoma line D238 [23] was obtained from ATCC. Cell lines or cDNA from and glioblastoma U87 and U251 [24,25] were obtained from Dr. Frank Furnari. Mouse P19 cells [26] were obtained from the laboratory of Dr. Michael G. Rosenfeld.Chromatin ImmunoprecipitationCells were crosslinked in 1 formaldehyde, sonicated, and subjected to standard ChIP purification with the indicated antibodi.In grey lowercase. (D) As one estimate of the significance level for apparent shifts between constructs, normalized expression values were compared by ANOVA, followed by Tukey’s Honest 10781694 Significant Differences pair-wise comparisons. Calculated p-values are indicated in the intersection between construct designations. Potential scaling differences between sequential experiments on different days (indicated by gaps between cells in the table) may violate some assumptions of the test. (E) ChIP-qPCR performed for transfected plasmids shows a higher enrichment index compared to input and IgG controls (calculated as DDCT for carrying the wild-type site than for the mutated sites shown in (C). The pairwise comparison was significant at p = 0.007 by ttest or 0.03 by the nonparametric equivalent (Wilcoxon signed rank test). doi:10.1371/journal.pone.0066514.gknockdown of Ebf1 and Zfp423 was somewhat less effective. It is notable that the cell culture model used for these extensive enhancer activity studies, P19, expresses lower levels of Zfp423 RNA than developing neural tissues, suggesting that the response we see to ,2.4X higher levels of ZNF423 in the culture model (Figure 5H) may indeed be relevant to levels achieved in developing cells. We propose that this site might play a role in either limiting Zfp423 accumulation or, more 16985061 provocatively, providing a developmental ratchet in which Zfp423 alone or in progressive complexes with one or more binding partners serves to turn off its own expression, to allow the cell to exit an immature cell state and facilitate developmental progression. Our results also provide some information on predictive algorithms for transcription factor binding. While many of the sites we examined do not appear occupied under the narrow conditions tested, we do find compelling evidence for binding at several sites, and particularly strong evidence for binding in both mouse and human at a clearly functional site in intron 5. Regardless of whether the other predicted sites are occupied under conditions or not, the predictive approach need not be perfect to be a useful guide for early experiments where legitimate targets are not defined. In this example, the occurrence of clustered motifs for transcription factors known to interact in a complex facilitated the identification of an apparent autoregulatory site for a key transcription factor important for the development of both mice and humans. All together, our results strongly support both Zfp423 occupancy and functional enhancer activity for at least one predicted conserved segment. As most enhancers are cell-type specific [20], further analysis of genome-wide binding in a wider variety of cellular contexts will be required to test the generality of such predictions.software package. Monoclonal antibodies against b-actin (AC-74, Sigma) and GAPDH (GT239, GeneTex) were used to verify equal loading by detection of internal standards.Cell LinesNeuroblastoma IMR32 [21] was originally obtained from ATCC [22] and passaged in the authors’ laboratory to obtain a more adherent phenotype for ChIP. Medulloblastoma line D238 [23] was obtained from ATCC. Cell lines or cDNA from and glioblastoma U87 and U251 [24,25] were obtained from Dr. Frank Furnari. Mouse P19 cells [26] were obtained from the laboratory of Dr. Michael G. Rosenfeld.Chromatin ImmunoprecipitationCells were crosslinked in 1 formaldehyde, sonicated, and subjected to standard ChIP purification with the indicated antibodi.
