Three-dimensional genome structures play a key role in gene regulation and cell functions. Characterization of genome structures necessitates single-cell measurements. This has been achieved for haploid cells but has remained a challenge for diploid cells. We developed a single-cell chromatin conformation capture method, termed Dip-C, that combines a transposon-based whole-genome amplification method to detect many chromatin contacts, called META (multiplex end-tagging amplification), and an algorithm to impute the two chromosome haplotypes linked by each contact. We reconstructed the genome structures of single diploid human cells from a lymphoblastoid cell line and from primary blood cells with high spatial resolution, locating specific single-nucleotide and copy number variations in the nucleus. The two alleles of imprinted loci and the two X chromosomes were structurally different. Cells of different types displayed statistically distinct genome structures. Such structural cell typing is crucial for understanding cell functions.

Cells integrate multiple measurement modalities to navigate their environment. Soluble and substrate-bound chemical gradients and physical cues have all been shown to influence cell orientation and migration. Here we investigate the role of asymmetric hydraulic pressure in directional sensing. Cells confined in microchannels identified and chose a path of lower hydraulic resistance in the absence of chemical cues. In a bifurcating channel with asymmetric hydraulic resistances, this choice was preceded by the elaboration of two leading edges with a faster extension rate along the lower resistance channel. Retraction of the "losing" edge appeared to precipitate a final choice of direction. The pressure differences altering leading edge protrusion rates were small, suggesting weak force generation by leading edges. The response to the physical asymmetry was able to override a dynamically generated chemical cue. Motile cells may use this bias as a result of hydraulic resistance, or "barotaxis," in concert with chemotaxis to navigate complex environments. Chemotactic cells, such as neutrophils and Dictyostelium, integrate chemical cues over the cell surface to move up an attractant gradient (1-5). Stiffness gradients, sensed by adhesion receptors, can also orient migration (durotaxis) (6-9). Cells must balance these and other environmental inputs to determine a direction of polarization and migration (10). Given the complex environment in tissues, it is likely that there are still unknown inputs to directional decision-making.Microfluidics provides a programmable environment for single cells in which chemical and physical cues can be precisely controlled in space and time, and polarization and migration quantified (11). In particular, cellular confinement has been instrumental in observing many novel cellular behaviors such as integrin-independent motility (12) and EGF gradient sensing (13). Additionally, cellular confinement into narrow microchannels (<10 μm) is thought to mimic the tissue environment better than stiff 2D substrates covered with low-viscosity medium.Here we use confinement to investigate the role of cell-generated hydraulic pressure in directional decisions. We show that, under strong confinement, migrating neutrophil-like cells push the column of water ahead of the cell, generating a hydraulic pressure. Cells selectively move toward a path of lower hydraulic pressure when presented with multiple paths. The morphological and signaling dynamics of this decision-making process revealed potential mechanisms that diverge from the classical PI3K-mediated chemotactic pathway. Remarkably, this physical input can outcompete conventional chemotactic signals, suggesting an important role in directing migration through tissues. ResultsTo challenge single cells with complex hydraulic environments, we used microfluidic devices that harbor bifurcating, fibronectincoated channels, derived from designs described by Ambravaneswaran et al. (14). These channels are 6 μm or smaller in width and 3 μm in height, forcing ...