Figure 3.

NFI associates with histone modification H3K4me3. In vivo NFI sites were defined with the threshold of 6 tags yielding 4,794 sites. In vivo NFI sites were separated into two categories: one group (808 sites) mapping to regions +/− 5 kb from transcription start sites (TSS) and another group outside these regions (3,986 sites). The average ChIP-Seq tag counts for different histone modifications were calculated in windows of 100 bp for a region of 10 kb up- and down- stream of the in vivo NFI sites. Tag counts were normalized globally, as a fold-increase over the genome average tag count in a window of 100 bp. In vivo Nanog sites were separated into two categories: mapping into regions +/− 5 kb from transcription start sites (TSS) and outside these regions. The average ChIP-Seq tag counts for different histone modifications were calculated as for NFI. (A) In vivo NFI sites inside TSS +/− 10 kb. (B) In vivo NFI sites outside TSS +/−10 kb. (C) In vivo Nanog sites inside TSS +/− 10 kb. (D) In vivo Nanog sites outside TSS +/− 10 kb.