Fig. 5: SNIP1-bound regions are co-occupied by PRC2 on NPC chromatin.
From: SNIP1 and PRC2 coordinate cell fates of neural progenitors during brain development
a–d Co-immunoprecipitation followed by WB to examine the interaction between SNIP1 and PRC2. (a) SNIP1, (b) JARID2, (c) EZH2, or (d) EED was immunoprecipitated in the NPC nuclear extract. RBBP5 was a negative control. Source data are provided as a Source Data file. e Heatmaps aligning chromatin peaks enriched with SNIP1, SUZ12, and EZH2 in NPCs. Peaks from SNIP1 CUT&RUN–reChIP with IgG, EZH2, and H3K27me3 were aligned to SNIP1-bound peaks. Intensity for 5 or 10 kb on either side of 23,188 SNIP1-bound peaks are shown. A dark color indicates high intensity and a light color indicates low intensity. f Tracks of SNIP1 CUT&RUN–reChIP with IgG, EZH2, and H3K27me3 are visualized by Integrative Genomics Viewer (IGV). Mcm7, Chr5: 138,169,717 − 138,173,621. Aen, Chr7: 78,894,526 − 78,898,271. Lhx8, Chr3: 154,325,066 − 154,334,835. Eomes, Chr9: 118,474,178 − 118,480,775. g Profile plots comparing the median binding intensity of SNIP1, PRC2, and H3K27me3/ac in Snip1Nes-KO vs. control NPCs at the SNIP1 targets. Regions were considered true SNIP1 targets when SNIP1 levels were reduced in Snip1Nes-KO vs. control NPCs with p < 0.05. h, i Motifs of SNIP1- and SUZ12-bound regions where their levels significantly reduced in Snip1Nes-KO NPCs with fold-change >2 and p < 0.05. HOMER de novo analysis was performed and the five motifs with lowest p-values and had vertebrate motif matches are listed here. j, k Volcano plots of transcription factors whose binding to our differentially expressed genes (FDR < 0.05) has been reported. Genes were searched against ENCODE and ChEA consensus TFs from ChIP-X database using Enrichr56. Darker colors show smaller p-values and large points passed p-value < 0.05. Transcription factors in bold were found in our CUT&RUN motif analyses in Fig. 5h, i.
