Nature 488, 116C120. of increased compartmentalization and TAD boundary strength in adult 6b-Hydroxy-21-desacetyl Deflazacort HSCs. In contrast, intra-TAD chromatin interactions are much more dynamic and wide-spread, involving over a thousand gene promoters and distal enhancers. These developmental-stage-specific enhancer-promoter interactions are mediated by different sets of transcription factors, such as TCF3 and MAFB in fetal HSCs, versus NR4A1 and GATA3 in adult HSCs. Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. In Brief A developmental transition occurs between fetal and adult hematopoietic stem cells. How the 3D genome folding contributes to this transition is usually poorly comprehended. Chen et al. show global genome business is largely conserved, but a large fraction of enhancer-promoter interactions is usually reorganized and regulate genes contributing to the phenotypic differences. Graphical Abstract INTRODUCTION During development, hematopoietic stem cells (HSCs) first appear in major arteries of the mouse embryo at embryonic day 11 (E11) and migrate to the fetal liver (FL) at E12 where they expand in number by 10- to 30-fold (Ema and Nakauchi, 2000). Right before birth, FL HSCs migrate to bone marrow (BM) to take up permanent residence. The physiological properties and functions of FL and adult BM HSCs are distinct. FL HSCs must support rapid blood development and hence rapidly expand, while BM HSCs support homeostatic blood production and respond to injury and external stress. Phenotypic differences between FL and BM HSCs enable them to fulfill these different physiological needs. Most (>70%) BM HSCs exist in a quiescent G0 state (Passegu et al., 2005; Wilson et al., 2008) to prevent HSC exhaustion, whereas the majority of FL Rabbit Polyclonal to RAB41 HSCs are actively cycling (Bowie et al., 2006). Second, the relative lineage outputs of lymphoid and myeloid cells change between FL and BM HSCs and during the process of aging. FL HSCs tend to have balanced lymphoid and myeloid lineage outputs whereas BM HSCs tend to have a myeloid-biased lineage output that becomes more prevalent during the aging process in mouse (Benz et al., 2012; Busch et al., 2015). Finally, FL HSCs more robustly engraft mice when transplanted and display a greater self-renewal activity when stimulated to proliferate Hi-C (Rao et al., 2014). We also conducted Capture-C (Hughes et al., 2014) to investigate the dynamics of promoter-centric chromatin interactions, focusing on 4,052 promoters that are highly expressed in HSCs compared to a compendium of 20 other mouse tissues (Figures 1A, S2A, and S2B; Table S2; STAR Methods). Using several metrics, we confirmed that our Hi-C and Capture-C data have sufficient sequencing depth and high reproducibility (Figures S2CCS2F; Table S3). To understand the relationship between the epigenome and 3D genome business, we also generated chromatin immunoprecipitation sequencing (ChIP-seq) data for four histone marks, H3K4me1, H3K4me3, H3K27ac, and H3K27me, as well as assay for transposase-accessible chromatin using sequencing (ATAC-seq) data (Physique 1A). These data also have sufficient sequencing depth and high reproducibility (Figures S2G and S2H). Open in a separate window Physique 1. Limited Change in Global 3D Genome Business during Fetal-to-Adult HSC Transition(A) Schematic diagram of experimental design. (B) Fraction of genomic regions with compartment switching during fetal to adult transition. B A, 6b-Hydroxy-21-desacetyl Deflazacort regions switching from compartment B to compartment A; static, regions without compartment switching. (C) Gene expression change is usually correlated with compartment switching. (D and E) Increased compartmentalization during fetal to adult transition. (D) Shown are log ratios of observed versus expected contact frequencies between TADs from the same (A versus A, B versus B) or different compartments (A versus B). (E) An example heatmap of contact frequencies along chromosome 2, showing increased contacts among regions of the same compartment. Compartment assignment is usually indicated along the top and left. Several examples of more frequent interactions between the same compartments are highlighted by rectangles. Color is usually proportional to the difference in contact frequency (BM HSC-FL HSC). Panel was generated by Juicebox. (F) Scatterplot of TAD boundary strength in 6b-Hydroxy-21-desacetyl Deflazacort FL HSCs and BM HSCs. Boundaries with significantly increased and decreased strength (FDR <0.1) are highlighted in blue and red, respectively. (G) 3D distance is larger between adjacent TADs with increased boundary strength during the fetal-to-adult transition. y axis, difference in 3D distance of adjacent TADs between BM HSCs and FL HSCs. Normalized distance was calculated based on the 3D structure model of each chromosome. (H) An example TAD boundary with.