Fig. 5: Reprogramming Zfp266 KO MEFs results in chromatin opening at OSK bound, B1 SINE containing loci. | Nature Communications

Fig. 5: Reprogramming Zfp266 KO MEFs results in chromatin opening at OSK bound, B1 SINE containing loci.

From: B1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors

Fig. 5

A ATAC-seq volcano plot of Zfp266 KO vs Wt reprogramming at 72 h. Green and red dots indicate more open regions (MORs) and more closed regions in Zfp266 KO reprogramming, respectively (FDR < 0.05). B Significance and fold enrichment ratio of transposable element (TE) families within Zfp266 KO MEF MORs. Green dots indicate significantly enriched SINEs, blue dots indicate other significantly enriched TEs. The p-values were calculated by the cumulative hypergeometric distribution. C Number of Zfp266 KO reprogramming MORs with TEs. D De novo motif discovery analysis on Zfp266 KO reprogramming MORs. The motifs correspond to parts of the B1 SINE consensus sequence are indicated by matching colors. E Overlap between Zfp266 KO MEF and Zfp266 KO reprogramming MORs. F Motif enrichment analysis with Zfp266 KO reprogramming MOR summits and percentages of MORs with KLF, SOX, OCT (POU) family and OCT4::SOX2 motifs. G Classification of Zfp266 KO reprogramming MORs based on ATAC-seq signals in MEF and reprogramming 72 h. H Reprogramming 48 h OSKM ChIP-Seq heatmap at Zfp266 KO reprogramming MORs. I KLF, SOX, OCT (POU) family, OCT4::SOX2 and SINE motif distribution within Zfp266 KO reprogramming MORs. 70 bp from the summit is highlighted in pink. The colors of B1 SINE motifs correlate to those in D. J Orientation-biased distribution of B1 SINEs within Zfp266 KO reprogramming MORs. Head of B1 SINE tends to locate on the MOR summit side. 70 bp from the summit is highlighted in pink. K Numbers of SINEs located on the plus (1, 3) or minus (2, 4) strand either upstream (1, 2) or downstream (3, 4) of the MOR summits in reprogramming MORs (left top). KLF4/SOX3 motif enrichment in each group with midpoint of B1 SINE in the centre (right four panels). L Nucleosome dyad frequency at B1 SINEs within reprogramming MORs using MNase-seq data with MEFs (GSM1004654) (top) and KLF4 and SOX3 motif enrichment at the same regions (bottom). M A model of nucleosome wrapped by B1 SINE with KLF and SOX motifs at the head and tail.

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