Skip to main content
. Author manuscript; available in PMC: 2015 Jul 14.
Published in final edited form as: Dev Cell. 2014 Jul 3;30(1):11–22. doi: 10.1016/j.devcel.2014.05.024

Figure 6. Nuclease-resistant footprints over CTCF motifs represent bona fide CTCF binding in ES cells.

Figure 6

A. Abundance of short MNase footprints over CTCF binding sites in ES cells correlates with CTCF ChIP-Seq enrichment. CTCF motifs are split into quintiles according to ChIP-seq signal (Chen et al., 2008). B. As in (A), but for mononucleosome-length footprints. Flanking nucleosomes are more strongly positioned when CTCF ChIP-seq signal is highest. C. Western blots of CTCF and EGFP esiRNA knockdown in mESCs, probed with anti-CTCF and β-actin antibodies. D. qRT-PCR of CTCF mRNA abundance. E. Aggregation plot for <80 bp and 135–165 bp digestion products in EGFP KD ES cells, aligned using CTCF motifs. F. Knockdown of CTCF in ES cells results in loss of <80bp footprint enrichment over CTCF motifs, with an associated increase in nucleosome occupancy over the CTCF motif and loss of surrounding nucleosome positioning. See also Figures S4–5.