CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

Abstract

Three-dimensional organization of the genome has emerged as an important player in transcriptional regulation [1][2][3][4][5][6][7] . In mammals, CTCF and the cohesin complex create sub-megabase structures with elevated internal chromatin contact frequencies, called topologically associating domains (TADs) [8][9][10][11] . Although TADs are generally considered important for transcriptional regulation, ablation of TAD organization by disrupting CTCF or the cohesin complex only caused modest gene expression changes [12][13][14][15] . In contrast, CTCF is required for cell cycle regulation 16 , early embryo development and for the formation of various adult cell types 17 . To uncouple the role of CTCF in cell state transitions and cell proliferation we studied the effect of CTCF be efficiently converted by exogenous CEBPA expression into functional induced macrophages (iMacs) with only one cell division on average (Fig. 1a; Supplementary Note 1) 26 . Using this system, we analyzed a time-series of transdifferentiating cells for genome-wide changes in 3D genome organization (in-situ Hi-C), enhancer activity (ChIP-seq of histone modifications), chromatin accessibility (ATAC-seq) and gene expression (RNA-seq).We first determined genome segmentation into A and B compartments on the basis of the first eigenvector values of a principal component analysis (PCA) on the Hi-C correlation matrix ('PC1 values'). Overall, although most of the genome remained stable, around 14% of A or B compartment regions were dynamic during transdifferentiation, showing transcriptional changed correlating with the altered compartmentalization state (Fig. 1b-f, Extended Data Fig. 1a-d; Supplementary Note 2). Next, we used chromosome-wide insulation potential 27 to identify between 3,100-3,300 TAD borders per time point (Fig. 1g). Boundaries were highly reproducible between biological replicates (Jaccard index>0.99) and enriched in binding sites for CTCF (Extended Data Fig. 1e). Genome-wide insulation scores analysed by PCA over time revealed progressive changes, reflecting a transdifferentiation trajectory (Extended Data Fig. 1f). While 70% of TAD borders were stable across all stages, 18% were lost or gained and 12% were transiently altered (Fig. 1g). CTCF binding was significantly more enriched at stable than at dynamic boundaries (Fig. 1h), as observed earlier 28 . Furthermore, while lost borders showed some CTCF occupancy in B cells that decreased in iMacs, gained borders were depleted for CTCF in both cell states (Fig. 1h), indicating CTCF-independent mechanisms driving local insulation. The dynamic rearrangement of TAD borders during transdifferentiation is illustrated by the DDX54 locus (Fig. 1i), in which a new boundary appears in iMacs without apparent changes in CTCF binding. Furthermore, border gain or loss did not correlate with changes in local gene expression (Extended Data Fig. 1g), indicating that transcription is not a driver of the observed changes. However, whereas motif analysis at ATAC-seq peaks within stable borders indee...

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

“…2), among which many lineage-specific genes that are dynamically regulated during development. These observations are consistent with recent reports, showing that CTCF is required for the expression of a subset of lineage-specific genes during cell differentiation 32 and for fast transcriptional responses to external stimuli 45 .…”

Severe COVID-19 associated variants linked to chemokine receptor gene control in monocytes and macrophages

“…CCR2, CCR5) and putative enhancer elements (Fig.1g) -a conformation often used for complex tissue-specific gene regulation 14 . In support, all three ACRs were bound by the architectural CCCTC-binding factor CTCF 14 and acute CTCF depletion in in vitro generated macrophages 15 resulted in chromatin hub disruption and CCR1/CCR2/CCR5but not CCR3 -downregulation ( Fig.1h-i, Supplementary Fig.1f-g). Importantly, CCR1 as well as CCR2 are critical mediators of monocyte/macrophage polarization and tissue infiltration 16 , which are pathogenic hallmarks of severe COVID-19 2 .…”

“…Immune cell-specific gene expression data was obtained using the DICE online platform (https://dicedatabase.org/) and visualized as averaged values (from n=81-91 individuals) using Morpheus (https://software.broadinstitute.org/morpheus/). RNA-Seq, ChIP-Seq and in-situ Hi-C from in vitro generated ('induced') macrophages (prior to and after auxin-inducible CTCF degradation) were obtained from GSE140528 and analyzed as previously described 15 .…”

A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis

“…3d) at this enhancer were also increased in OLG-EAE. CTCF has been recently shown to be required for acute inflammatory responses in macrophages 27 and an increase in CTCF mediated promoter-enhancer interactions at the MHC-I and MHC-II loci was previously observed in B-cells 28,29 . Therefore, we profiled CTCF with Cut&Run upon treatment with IFN γ and observed increased binding of CTCF in enhancers and at the promoters of many immune genes (Fig.…”