Fig. 7: ZBTB43 binds at PPRs in prospermatogonia in vivo.
From: Z-DNA is remodelled by ZBTB43 in prospermatogonia to safeguard the germline genome and epigenome
a, Genome browser images of ZBTB43 ChIP–seq peaks (light green) obtained in purified 15.5 dpc prospermatogonia are displayed at 12 genomic locations. IgG lanes are shown as controls. The ChIP peaks align with the in vitro affinity sequencing peaks found in fully methylated genomic DNA (SssI) and in fully unmethylated genomic DNA (TKO) (dark green). MBP affinity-seq lanes are shown as controls. The scale of reads was normalized between experimental samples and their respective background control samples using the ‘group-autoscale’ function of IGV as marked on the right. b,c, Heatmap showing the ZBTB43 ChIP–seq peaks detected against IgG background in 100,000 (b) or 500,000 (c) purified prospermatogonia. The read intensities in three libraries, ZBTB43 antibody, IgG antibody and input DNA (as marked above), are plotted centred at the peak and using +1 kb and −1 kb flanking regions. d,e, Venn diagrams depicting the location of ZBTB43 ChIP–seq peaks mapped in 15.5 dpc prospermatogonia relative to the location of transcripts in the genome. In d, all genomic locations are plotted. In e, distal intergenic regions are excluded. f, The ZBTB43 ChIP–seq peaks detected in vivo are recognized by purified ZBTB43 protein in vitro. Heatmaps display the read intensities of ZBTB43-FL and the control MBP in affinity binding with unmethylated DNA (TKO) or methylated DNA (SssI). The plotted regions were centred at ChIP peaks called in 500,000 or 100,000 prospermatogonia against IgG, as indicated at the bottom. g, The ZBTB43 ChIP–seq peaks detected in prospermatogonia align with affinity-seq peaks and with predicted Z-DNA. Heat maps display the ChIP–seq log2 IP/IgG read intensities detected in 500 K or 100 K prospermatogonia (as marked at the top) along subset of genomic regions centred at ZBTB43-FL affinity-seq peaks in methylated DNA (SssI), unmethylated DNA (TKO) and at the subset of predicted Z-DNA sites (marked at the bottom) where overlap is found with ChIP–seq peaks. The ChIP–seq and affinity-sequencing results shown represent two independent biological replicates in a, f and g.
