Deciphering hierarchical organization of topologically associated domains through change-point testing

Background The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromosome conformation capture, such as Hi-C, have revealed topologically associating domains (TADs) that are defined by biased chromatin interactions within them. Results We introduce a novel method, HiCKey, to decipher hierarchical TAD structures in Hi-C data and compare them across samples. We first derive a generalized likelihood-ratio (GLR) test for detecting change-points in an interaction matrix that follows a negative binomial distribution or general mixture distribution. We then employ several optimal search strategies to decipher hierarchical TADs with p values calculated by the GLR test. Large-scale validations of simulation data show that HiCKey has good precision in recalling known TADs and is robust against random collisions of chromatin interactions. By applying HiCKey to Hi-C data of seven human cell lines, we identified multiple layers of TAD organization among them, but the vast majority had no more than four layers. In particular, we found that TAD boundaries are significantly enriched in active chromosomal regions compared to repressed regions. Conclusions HiCKey is optimized for processing large matrices constructed from high-resolution Hi-C experiments. The method and theoretical result of the GLR test provide a general framework for significance testing of similar experimental chromatin interaction data that may not fully follow negative binomial distributions but rather more general mixture distributions.

Automated summary

The study introduces a novel method, HiCKey, for deciphering hierarchical TAD structures in Hi-C data and comparing them across samples. The GLR test was used to detect change-points in interaction matrices and calculate p values, showing that HiCKey has good precision in recalling known TADs and is robust against random chromatin interactions. Multiple layers of TAD organization were identified among human cell lines, with most having no more than four layers, and TAD boundaries were found to be significantly enriched in active chromosomal regions compared to repressed regions.