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bioRxiv · 10.1101/2020.07.21.214585

Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification

Galan, S.·Serra, F.·Marti-Renom, M. A.
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Abstract

Genome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains, which suggests that CTCF is essential in the 3D organization of chromatin. However, the systematic topological classification of pairwise CTCF-CTCF interactions has not been yet explored. Here, we developed a computational pipeline able to classify all CTCF-CTCF pairs according to their chromatin interactions from Hi-C experiments. The interaction profiles of all CTCF-CTCF pairs were further structurally clustered using self-organizing feature maps and their functionality characterized by their epigenetic states. The resulting clusters were then input to a convolutional neural network aiming at the de novo detecting chromatin loops from Hi-C interaction matrices. Our new method, called LOOPbit, is able to automatically detect significant interactions with a higher proportion of enhancer-promoter loops compared to any other callers. Our highly specific loop caller adds a new layer of detail to the link between chromatin structure and function.

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Galan, S., Serra, F., Marti-Renom, M. A.. 2020-07-22. Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification. https://doi.org/10.1101/2020.07.21.214585

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