Ultra-deep Hi-C during mouse neural differentiation

Using state-of-the-art techniques such as Hi-C, we have previously mapped chromatin interaction genome-wide with the highest resolution up to date using an in vitro neuronal differentiation system of embryonic stem cells into cortical neurons. In addition, we developed low-input Hi-C technology to reduce the number of cells required (less than 200 000) and used this method to explore the 3D chromatin organization of FACS-purified populations of progenitors and neurons directly from the mouse embryonic cortex. This combination of ultrahigh resolution and homogenous cell populations allowed us to study fine-scale regulatory contacts at an unprecedented level of detail in vivo.

Genome-wide maps of 3D chromatin interactions at various scales can be visualized as a 2D heatmap, where each axis represent the genomic coordinates and the color code indicates the interactions strength between two regions. Here, we have used HiGlass in order to visualize and synchronize the contact maps between the ultrahigh resolution datasets we published in Bonev et al , Cell (2017), showing the dynamic rewiring of the 3D genome at multiple scales.

Data was visualized using HiGlass

Data from Bonev et al, Cell 2017.
  • ES - Embryonic Stem Cells
  • NPC - Neural Progenitors
  • CN - Cortical Neurons
  • ncx NPC - Neocortical Progenitors (E14.5)
  • ncx CN - Neocortical Neurons (E14.5)