ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes
Fig 9
Genome-wide analysis reveals ZFP92 binds preferentially to B1/Alu SINE elements.
A) Pie chart showing the percentage distribution of different TE classes within the ZFP92 binding peaks obtained by CUT&RUN analysis. 93% of peaks have TEs with SINE elements being the largest group. The inset pie chart shows the family distribution of ZFP92-bound SINEs, with Alu/B1 family being most represented. B) Pie chart showing the distribution of ZFP92 binding peaks within different genomic features. C) Pie chart showing the distribution of different ENCODE Candidate Cis-Regulatory Elements (cCREs) within the ZFP92 binding peaks. enhD, distal enhancer signature; enhP, proximal enhancer-like signature; prom, promoter-like signature; CTCF, CTCF-only; K4m3, DNase-H3K4me3. D) UCSC Genome Browser view of Capn11 locus showing ZFP92 binding peaks and RNA-seq reads in WT and Zfp92 KO samples (GRCm38/mm10 assembly). The main peak containing the B1 SINE element is highlighted in gray, with red lines denoting amplicons and primer pairs that were used for qPCR shown in (E). E) qPCR on CUT&RUN chromatin samples with the primers shown in (D) to different regions of Capn11 locus and TE elements found there. (N = 3) Error bars: ± SEM. **p≤0.01; *p≤0.05. p-value is determined by an unpaired t-test. F) ZFP92 binding motif predicted by MEME analysis of ZFP92 binding peaks. Under the ZFP92 motif are the two similar motifs (ZNF460 and ZNF135) that were identified by TomTom analysis from the MEME suite. G) Pie chart showing the distribution of ZFP92 binding motif within TE elements in ZFP92 peaks. The inset pie chart shows the family distribution of SINEs with FP92 motif, with Alu/B1 family being most represented.