Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia.

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...

Rhesus macaque (Macaca mulatta) and long-tailed macaque (Macaca fascicularis) are the 2 most commonly used primate model species in biomedical sciences. Although morphological studies have revealed a weak hybridization at the interspecific contact zone, in the north of Indochina, a molecular study has suggested an ancient introgression from rhesus to long-tailed macaque into the Indo-Chinese peninsula. However, the gene flow between these 2 taxa has never been quantified using genetic data and theoretical models. In this study, we have examined genetic variation within and between the parapatric Chinese rhesus macaque and Indo-Chinese long-tailed macaque populations, using 13 autosomal, 5 sex-linked microsatellite loci and mitochondrial DNA sequence data. From these data, we assessed genetic structure and estimated gene flow using a Bayesian clustering approach and the "Isolation with Migration" model. Our results reveal a weak interspecific genetic differentiation at both autosomal and sex-linked loci, suggesting large population sizes and/or gene flow between populations. According to the Bayesian clustering, Chinese rhesus macaque is a highly homogeneous gene pool that contributes strongly to the current Indo-Chinese long-tailed macaque genetic makeup, whether or not current admixture is assumed. Coalescent simulations, which integrated the characteristics of the loci, pointed out 1) a higher effective population size in rhesus macaque, 2) no mitochondrial gene flow, and 3) unilateral and male-mediated nuclear gene flow of approximately 10 migrants per generation from rhesus to long-tailed macaque. These patterns of genetic structure and gene flow suggest extensive ancient introgression from Chinese rhesus macaque into the Indo-Chinese long-tailed macaque population.