ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C

Yousra Ben Zouari (1) , Anne M Molitor (1) , Natalia Sikorska (1) , Vera Pancaldi (2) , Tom Sexton (1)

1 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
2 CRCT - Centre de Recherches en Cancérologie de Toulouse

Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHiC profiles alongside epigenomic tracks.

Mots clés: Promoter-enhancer interactions; Chromatin loops; Capture Hi-C; Biological replicates; Gene regulation; Chromatin assortativity

Domaines: Biochimie, Biologie Moléculaire

Yousra Ben Zouari, Anne M Molitor, Natalia Sikorska, Vera Pancaldi, Tom Sexton. ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C. Genome Biology, 2019, 20 (1), pp.102. ⟨10.1186/s13059-019-1706-3⟩. ⟨hal-04083921⟩