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Elizabeth Ing-Simmons, Juan M. Vaquerizas (Max Planck Institute for Molecular Biomedicine, Muenster, Germany)
Embryonic development and differentiation are driven by gene expression that varies across space and time, which must be tightly controlled to ensure the correct development of an organism. To allow this level of control, DNA must be packaged into the nucleus in a way that allows genes to be precisely activated and deactivated. This occurs through packaging of DNA into chromatin, and through the higher-order organisation of the chromatin. This 3D organisation of the genome is increasingly recognised as an important contributor to the regulation of gene expression. The development of sequencing-based methods to investigate 3D chromatin conformation at high resolution has led to many new insights, but the large quantities of data produced by these techniques pose challenges for effective analysis and visualisation. Interactions and structural features of interest span orders of magnitude in size and contact frequency, and researchers must selectively choose which features to visualise. We present strategies to overcome the challenges of visualising 3D chromatin organisation data in two dimensions, and describe visualisation approaches that facilitate biological interpretation.