Computational Methods for Assessing Chromatin Hierarchy

Abstract

The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects. Experimental requirements and considerations specific for each method were highlighted. For computational analysis, we summarized a common analysis strategy for both levels of chromatin assessment, focusing on the characteristic computing steps and the tools. The recently developed single-cell level techniques based on Hi-C and ATAC-seq present great potential to reveal cell-to-cell variability in chromosome architecture. A brief discussion on these methods in terms of experimental and data analysis features is included. We also touch upon the biological relevance of chromatin organization and how the combination with other techniques uncovers the underlying mechanisms. We conclude with a summary and our prospects on necessary improvements of currently available methods in order to advance understanding of chromatin hierarchy. Our review brings together the analyses of both higher- and primary-order chromatin structures, and serves as a roadmap when choosing appropriate experimental and computational methods for assessing chromatin hierarchy.

Keywords: 3C-technologies; 3D genome; ATAC-seq; Chromatin accessibility; Chromosome conformation capture; Hi-C.

Fig. 1

Genome organization in eukaryotes from higher to primary orders. Features of chromatin organization from higher- to primary-order. Techniques, experimental and computational procedures for assessment of chromatin hierarchy. The active circle represents TADs rich in genes and show early replication. The inactive circle represents TADs that harbor few genes and show late replication. *Among the chromatin accessibility profiling methods, only FAIRE-seq strictly requires crosslinking.

Fig. 2

Common computational analysis strategy and specific steps for assessing higher-order and primary-order chromatin structures. The common computational steps are outlined in the center. Steps specific to the higher-order or primary-order analysis are indicated on each side. The raw reads from 3C-based techniques follow the pipeline to the left to reveal higher-order chromatin interactions. The raw reads for chromatin accessibility analysis follow the pipeline to the right.