Galan Martínez, Silvia, 1992-Serra, FrançoisMarti-Renom, Marc A.2022-04-072022-04-072022Galan S, Serra F, Marti-Renom MA. Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification. NAR Genom Bioinform. 2022 Mar 8;4(1):lqac021. DOI: 10.1093/nargab/lqac0212631-9268http://hdl.handle.net/10230/52841Genome-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 other callers. Our highly specific loop caller adds a new layer of detail to the link between chromatin structure and function.application/pdfeng© Silvia Galan, François Serra, Marc A. Marti-Renom 2022. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly citedGenòmicaCromatinaEpigenèticainfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/nargab/lqac021info:eu-repo/semantics/openAccess