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Fig. 6 | BMC Biology

Fig. 6

From: UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells

Fig. 6

UBN1- and UBN2-mediated H3.3 deposition is involved in neuron progenitor cell differentiation. a RT-qPCR of Tuj-1 in WT and FID/AAA-mutated mES cells during NPC differentiation. The expression level of Tuj1 was normalized to GAPDH and day 0. b Immunofluorescence shows expression of Nanog and Tuj-1 in WT and FID/AAA-mutated cells during NPC differentiation. Scale bar, 20 μm. c Dot plot shows the relationship between the dynamics of H3.3 at promoter regions and gene expression during NPC differentiation. H3.3 read density was counted within promoters (TSS ± 500 bp) to calculate fold change from ES cell to NPC by HOMER. The Red dots represent the genes with upregulated expression and increased H3.3 signal at promoters. The thresholds for H3.3 fold change and gene expression are 1.5 and 2 respectively. PCC, Pearson’s correlation coefficient. d Venn diagram shows the relationship between the “both-up” genes and downregulated genes in NPCs derived from FID/AAA-mutated mES cells. e The top 10 enriched biological function terms from GO analysis of the 44 genes by DAVID. Lmx1b, Zic2, and Zfp521 are the enriched genes related to “regulation of transcription, DNA-templated”. A full list of significantly enriched terms is in Additional file 1: Figure S6E. f Genome tracks show H3.3 deposition at promoters of Zfp152, Zic2, Lmx1b, and Polr2a during NPC differentiation of WT mES cells. g RT-qPCR of gene expression of Zfp152, Zic2, Lmx1b, and Polr2a during NPC differentiation of WT and FID/AAA-mutated mES cells. The gene expression levels were normalized to GAPDH. Standard deviations were derived from three replicates. h ChIP-qPCR of H3.3 deposition at the promoters of Zfp152, Zic2, Lmx1b, and Polr2a during NPC differentiation in WT and FID/AAA-mutated cells. The qPCR value was normalized to 1% input of each sample. Standard deviation was derived from three replicates

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