Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2019 Mar;29(3):383–395. doi: 10.1101/gr.240572.118

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 2019 Veil et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

PMC Copyright notice

Figure 3. — Pou5f3, SoxB1, and Nanog bind to the high nucleosome affinity regions (HNARs). (A–C) Mean predicted nucleosome occupancy plots on the indicated motifs bound by respective TF (magenta) versus unbound random motif matches (gray). (D) Mean predicted nucleosome occupancy plot centered on Pou5f3 pre-MBT TF binding peaks (magenta) versus random sequences (gray). (E) Pou5f3 binds to the regions of high predicted nucleosome occupancy and propeller twist on the enhancers of pou5f3 and vox. (PT°) Propeller twist; (nuc) in vitro nucleosome occupancy prediction, tick marks every 1 kb. (F) Propeller twist summary plot of random zebrafish, yeast, and human genomic regions aligned at the base pair with maximal predicted nucleosome occupancy within 320 bp [nucmax]. Yellow x-axis gridlines 10 bp apart. (G) Scheme of the PT periodic oscillations in 300 bp around [nucmax]. (H) Scheme of the oriented PT plot aligned at [nucmax]. (I) Oriented PT plot of PSN group (red) and control genomic regions (gray). (J) Scheme of medial and lateral strong nucleosome footprints at HNAR. Central 300-bp periodic frame supports alternative medial, lateral one, and lateral two nucleosome positions with decreasing strength (m > l1 > l2 = random footprint); in random sequence, only medial footprint is supported (bottom). (K,M) Symmetric (K) and oriented (M) smoothened PT plots (80-bp moving average) of PSN and control genomic regions, aligned at [nucmax]. (L,N) Distribution of nanog and pou:sox motifs in the PSN group for K and M, respectively. Motif density in base-pair motif per base-pair sequence.