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

. 2023 Feb 8;220(4):e20221288. doi: 10.1084/jem.20221288

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

This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

PMC Copyright notice

Figure 6. — T_EFF-acquired CTCF binding activates effector transcriptional program. (A) Volcano plot showing differential ChrAcc sites between WT and Ctcf^−/− early T_EFF cells isolated on 4 dpi, with values denoting site numbers. (B) Distribution of CTCF binding sites in WT T_EFF cells (both dynamic and constitutive) in differential ChrAcc sites between Ctcf^−/− and WT early T_EFF cells. (C) Scatterplot showing distribution between dynamic CTCF binding sites (in WT T_EFF vs. T_N comparison) and differential ChrAcc sites (in WT vs. Ctcf^−/− T_EFF comparison), where the 1,709 sites in quadrant i and the 1,873 sites in quadrant iii are defined as congruous and incongruous sites, respectively. (D) Heatmaps showing DEGs (in WT vs. Ctcf^−/− early T_EFF comparison) and associated differential ChrAcc sites (overlapping with congruous or incongruous CTCF binding) between WT and Ctcf^−/− T_EFF cells. The DEGs were grouped based on gene expression patterns defined in WT T_EFF vs. T_N comparison in Fig. 1 F, with select genes marked. (E) Tracks of CTCF CUT&RUN, ATAC-seq, and Tcf1 ChIP-seq at the Tbx21 gene locus. Orange bars denote T_EFF-acquired CTCF binding sites linked to CTCF-dependent ChrAcc in T_EFF cells, and open bars with dotted line denote CTCF binding sites that depended on Tbet and Runx3 (TRKO, Tbx21^−/−Runx3^−/−). (F) Tbet expression in T_EFF cells in which sgRNAs targeting Tbx21 −8 kb enhancer (marked in E, Chr.11) or Thy1 constitutive CTCF binding site (Chr.9) were retrovirally delivered together with dCas9-KRAB-MeCP2. Values in half-stacked histographs (left) denote gMFI, and cumulative data are means ± SD (right) from two independent experiments. ***, P < 0.001 by two-tailed Student’s t test. gMFI, geometric mean fluorescence intensity. (G) Top motifs in the congruous CTCF sites (defined in quadrant i in C), with the incongruous sites as background based on HOMER analysis. (H) Volcano plot showing differential CTCF binding sites between WT and Tbx21^−/−Runx3^−/− (TRKO) early T_EFF cells isolated on 4 dpi, with values denoting site numbers. (I) Heatmap showing CTCF binding strength at the congruous CTCF sites in WT and Tbx21^−/−Runx3^−/− (TRKO) early T_EFF cells.