PT  - JOURNAL ARTICLE
AU  - Silvia Galan
AU  - François Serra
AU  - Marc A. Marti-Renom
TI  - Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification
AID  - 10.1101/2020.07.21.214585
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2020.07.21.214585
4099  - http://biorxiv.org/content/early/2021/02/15/2020.07.21.214585.short
4100  - http://biorxiv.org/content/early/2021/02/15/2020.07.21.214585.full
AB  - 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.Competing Interest StatementThe authors have declared no competing interest.