Full size image We validated Chem-map for the BET inhibitor JQ1 in human leukemia K562 cells, as JQ1 interactions have been characterized using Click-Chem-seq in the same cell line5. In parallel, we mapped the genome-wide binding sites of the inhibitor’s main target BRD4 using a specific...
Full size image We computed the number of connectors Nc, within and between TADs, by averaging the connectivity values ξm for monomers in each TAD obtained from fitting the EP (Eqs. (3) and (5)) to all 302 monomers. After averaging we obtained the connectivity matrix Ξ, and used it ...
Activating mutations in the tyrosine kinase JAK2 cause myeloproliferative neoplasms, clonal blood stem cell disorders with a propensity for leukaemic transformation. LIF signalling through JAK-STAT enables ES cell self-renewal. Here we show that mouse ES cells carrying the human JAK2V617F mutation coul...
DNA Methylation and Chromatin Map of the Developing Brain Revealed with Single-Cell Multiomics November 22, 2024 Maps can tell you where to go and what landmarks you’ll find along the way. In the same way, a new multiomic map describes how DNA methylation and 3D chromatin conformation chan...
The lysis stage extracts the crosslinked protein–DNA complexes from cells or tissue and brings them into solution. At this stage, cellular components are liberated by dissolving the cell membrane with detergent-based solutions. Because pr...
At this stage, cellular components are liberated by dissolving the cell membrane with detergent-based solutions. Because protein–DNA interactions occur primarily in the nuclear compartment, removing cytosolic proteins can help reduce backgro...
3DCoop is an approach for computational inference of cell type-specific TR cooperation in 3D chromatin (and 1D mode without 3D information), by incorporating 3D chromatin interactions (required for 3D mode) and TR footprinting. Chromatin loops detected by 3C-based technologies (Hi-C, PCHi-C, Ch...
The ability of formaldehyde to form DNA-protein and protein-protein cross-links had been previously characterized (Brutlag et al., 1969; Ilyin and Georgiev, 1969; Van Lente et al., 1975; Jackson, 1978), applied to whole-cell fixation to study chromatin dynamics (Jackson and Chalkley...
Here, we use Caenorhabditis elegans to investigate the impact of fasting on the large-scale genome organization using live imaging within tissues of intact animals, at single-cell resolution. Results Fasting induces a 3D genome reorganization in the intestine To investigate whether a complete lack of...
Full size image Visualization of single-cell gene expression profiles from gd7, Tollrm9/rm10 and Toll10B embryos revealed that specific clusters were depleted in these mutant embryos (Fig. 2c and Extended Data Fig. 3b,c). Cells from clusters representing mesoderm cell fates were almost complete...