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

. 2018 Feb 6;11:6. doi: 10.1186/s13072-018-0174-4

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

© The Author(s) 2018

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

PMC Copyright notice

Fig. 6 — CpG methylation induces a DNA shape change that explains its effect on Pbx-Hox binding. a Schematic representation of Pbx-Hox heterodimer bound to DNA (PDB ID 1PUF), and of the effect of CpG methylation on binding. Pbx (green) and Hox (blue) homeodomains bind up- and downstream of the central spacer region (indicated in red), respectively. CpG methylation at offsets 6/7 and 10/11 reduces binding, whereas methylation at offset 9/10 enhances binding. Methyl group readout was previously identified as underlying mechanism for the latter offset [13]. b Scatter-plot representation of relative binding affinities of methylated versus unmethylated sequences for Pbx-HoxA1 complex. Sequences carrying a single methylation event and their corresponding unmethylated part were considered. Green, magenta, and blue points correspond to methylation at offsets 6/7, 9/10, and 10/11, respectively. Sequences containing CpG dinucleotides at other offsets (relatively weakly affected by methylation) are colored gray. c Alternative representation of the data in b, showing the effect of methylation on binding free energy, denoted as ΔΔΔG/RT. Positive (e.g., offsets 6/7 and 10/11) and negative (e.g., offset 9/10) shifts from the dashed line (indicating no methylation effect) reflect reduced and enhanced binding (on logarithmic scale) due to methylation. CpG dinucleotides at offsets 6/7 and 10/11 produce the same hexamer context for A₄ and A₈ (NNAYCG/NGAYCG) and, hence, were assigned a common color, dark-cyan. d Analysis of the methylation-induced change in MGW at positions A₄ and A₈ within the Pbx-Hox binding site (NNGAYNNAYNNN), for the different hexameric/pentameric contexts that the Pbx-Hox heterodimer may encounter within its binding sequence. Coloring corresponds to that of labels and rectangular patches in c. Statistically significant widening of minor groove (first two boxes) plausibly explains the observed reduced binding due to methylation at CpG offsets 6/7 and 10/11. No significant change in MGW upon methylation was observed for offset 9/10