Characterizing chromatin folding coordinate and landscape with deep learning

Genome organization is critical for setting up the spatial environment of gene transcription, and substantial progress has been made towards its high-resolution characterization. The underlying molecular mechanism for its establishment is much less understood. We applied a deep-learning approach, variational autoencoder (VAE), to analyze the fluctuation and heterogeneity of chromatin structures revealed by single-cell super-resolution imaging and to identify a reaction coordinate for chromatin folding. This coordinate monitors the progression of topologically associating domain (TAD) formation and connects the seemingly random structures observed in individual cohesin-depleted cells as intermediate states along the folding pathway. Analysis of the folding landscape derived from VAE suggests that well-folded structures similar to those found in wild-type cells remain energetically favorable in cohesin-depleted cells. The interaction energies, however, are not strong enough to overcome the entropic penalty, leading to the formation of only partially folded structures and the disappearance of TADs from contact maps upon averaging. Implications of these results for the molecular driving forces of chromatin folding are discussed.