BackgroundChromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiation stages, sometimes in association with regulation of biological functions. The reliability and reproducibility of these findings are intrinsically related with the correct identification of these domains from high-throughput chromatin conformation capture (Hi-C) experiments.ResultsHere, we test and compare 22 computational methods to identify TADs across 20 different conditions. We find that TAD sizes and numbers vary significantly among callers and data resolutions, challenging the definition of an average TAD size, but strengthening the hypothesis that TADs are hierarchically organized domains, rather than disjoint structural elements. Performances of these methods differ based on data resolution and normalization strategy, but a core set of TAD callers consistently retrieve reproducible domains, even at low sequencing depths, that are enriched for TAD-associated biological features.ConclusionsThis study provides a reference for the analysis of chromatin domains from Hi-C experiments and useful guidelines for choosing a suitable approach based on the experimental design, available data, and biological question of interest.Electronic supplementary materialThe online version of this article (10.1186/s13059-018-1596-9) contains supplementary material, which is available to authorized users.

Hi-C chromatin maps of EZH2 WT and EZH2 Y646X lymphomas. EZH2 p.Tyr646* gain-of-function alterations lead to a genomewide increase in H3K27me3 (Supplementary Fig. 1a). To establish whether this global accumulation of H3K27me3 modifies the genome topology on a similarly broad scale, we performed high-throughput chromatin conformation capture (Hi-C) in two lymphoma cell lines (Karpas422 and WSU-DLCL2) expressing the mutant form of EZH2 (EZH2 Y646X) and a lymphoma cell line (OCI-Ly19) expressing the wild-type EZH2 (EZH2 WT) protein (Supplementary Table 1 and Supplementary Note). Contact maps of EZH2 Y646X and EZH2 WT cells were binned in regions of 50 kb and compared with multiple metrics (Fig. 1). For each pair of maps, we compared the overall distribution of chromosomal contacts by using the stratum-adjusted correlation coefficient (SCC) 24 (Fig. 1a); the fraction of 1-Mb regions assigned to the same compartment (A or B) 3 (Fig. 1b); the similarity among TADs 25-27 (Fig. 1c); and the fraction of bin interactions that were significant in both maps, also known as the cell interactome 28,29 (Fig. 1d). To build a reference scale of values for each metric, we compared Hi-C maps of EZH2 Y646X lymphoma cell lines with Hi-C maps of endothelial cells (HUVEC), fetal fibroblasts (IMR90), and normal lymphoblastoid cells (GM12878). Moreover, we used randomized contact maps or

Chromatin compartmentalization reflects biological activity. However, inference of chromatin sub-compartments and compartment domains from chromosome conformation capture (Hi-C) experiments is limited by data resolution. As a result, these have been characterized only in a few cell types and systematic comparisons across multiple tissues and conditions are missing. Here, we present Calder, an algorithmic approach that enables the identification of multi-scale sub-compartments at variable data resolution. Calder allows to infer and compare chromatin sub-compartments and compartment domains in >100 cell lines. Our results reveal sub-compartments enriched for poised chromatin states and undergoing spatial repositioning during lineage differentiation and oncogenic transformation.