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. 2020 Apr 16;9:e57519. doi: 10.7554/eLife.57519

Figure 4. MiDAC directly targets positive and negative regulators of neurite outgrowth during neural differentiation.

(A–J) qPCR from manual ChIP experiments against (A, F) DNTTIP1, (B, G) ELMSAN1, (C, H) HDAC1, (D, I) H3K27ac and (E, J) H4K20ac from WT, Dnttip1 KO1 and Elmsan1 KO1 NE targeting select promoter, putative enhancer and intragenic control regions of (A–E) Slit3 or (F-J) Spry4 loci as highlighted in Figure 3F and G. IgG was used as a control antibody. Unpaired t-test was performed throughout where **, p≤0.01; and ns, p>0.05 is not significant.

Figure 4.

Figure 4—figure supplement 1. MiDAC directly targets positive and negative regulators of neurite outgrowth during neural differentiation.

Figure 4—figure supplement 1.

(A–J) qPCR from manual ChIP experiments against (A, F) DNTTIP1, (B, G) ELMSAN1, (C, H) HDAC1, (D, I) H3K27ac and (E, J) H4K20ac from WT, Dnttip1 KO1 and Elmsan1 KO1 NE targeting select promoter, putative enhancer and intragenic control regions of (A–E) the Ntn1 or (F-J) the Id1 loci as highlighted in Figure 3—figure supplement 1E and F. IgG was used as a control antibody. Unpaired t-test was performed throughout where **, p≤0.01; and ns, p>0.05 is not significant.
Figure 4—figure supplement 2. MiDAC does not transcriptionally regulate the genes of the ROBO3 and UNC5B receptors of the SLIT3 and NTN1 signaling pathways.

Figure 4—figure supplement 2.

(A, B) ChIP-seq profiles of the (A) Robo3 and (B) Unc5b loci for DNTTIP1 in WT, Dnttip1 KO1 and Elmsan1 KO1 mESCs and for HDAC1 in WT mESCs. Promoter regions used for manual ChIP experiments in (C) and (E) are highlighted by orange boxes. DNTTIP1 ChIP-seq peaks were determined based on the average of two replicates each from WT mESCs and based on the average of two replicates each from the Dnttip1 KO1 and Elmsan1 KO1 clone, respectively. HDAC1 ChIP-seq data were obtained from GSE55437. (C) qPCR from manual ChIP experiments against DNTTIP1, ELMSAN1 and HDAC1 from WT, Dnttip1 KO1 and Elmsan1 KO1 NE targeting the promoter of the Robo3 locus as highlighted in (A). IgG was used as a control antibody. (D) qRT-PCR for Robo3 mRNA in WT, Dnttip1 KO1 and Elmsan1 KO1 NE after 12 days of differentiation. Expression was normalized to Gapdh. (E) qPCR from manual ChIP experiments against DNTTIP1, ELMSAN1 and HDAC1 from WT, Dnttip1 KO1 and Elmsan1 KO1 NE targeting the promoter of the Unc5b locus as highlighted in (B). IgG was used as a control antibody. (F) qRT-PCR for Unc5b mRNA in WT, Dnttip1 KO1 and Elmsan1 KO1 NE after 12 days of differentiation. Expression was normalized to Gapdh.