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

. 2022 Jul 23;13:4257. doi: 10.1038/s41467-022-31938-5

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

© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 6 — a Intra-chromosomal interactions over chromosome 1 detected by Hi-C and first principal component eigenvalue show that nuclear compartments composition was mostly unchanged during differentiation. b Heatmap showing eigenvalues of first principal component of Hi-C performed at 0 and 48 h. Less than 2% of all 250kb-bins changed their compartment during PrE differentiation (bottom cluster). Most 250 kb-bins did not change compartment (top cluster). Clusters are not represented to scale. Changes in compartments were associated with changes in H3K27ac but no changes were observed for H3K27me3 levels. Bins that changed from compartment B to A gained K27ac signal and bins that changed from B to A, lost this histone modification. Bins were sorted based on eigenvalue at 0 h. Examples of Epi and PrE-specific genes whose compartment localization changed during differentiation are shown. c, d In contrast to stable compartment status, interactions between gene promoters and their putative CREs were quickly remodeled within 16 h of GATA6 expression. PrE genes shown in c, quickly increased interactions with sites bound by GATA6 that gained H3K27ac during differentiation. Epi genes in contrast, reduced interactions with CRES that were occupied by NANOG at 0 h and that lost H3K27ac following GATA6 expression. Capture-C data is shown as the average signal of two replicates using bins of 1 kb. Green shaded area represents putative CREs showing increased interactions with PrE-specific genes while red shaded areas highlight Epi-CREs that lose interactions with putative Epi-specific genes. P values were calculated using the Wald test in DESeq2 and comparing Capture-C signal of 2 replicates over overlapping 5 kb windows across the regions shown in this figure. Comparisons were done between 0 h and either 16 h or 48 h. Adjusted p values using the FDR/Benjamini-Hochberg option in DE-Seq2 that were lower than 0.01 were considered as significant. Horizontal bars represent windows considered as statistically significantly different for these comparisons.