Abstract
The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse.
Highlights
The organization of the genome in the cell nucleus has been shown to play a prominent role in the function of the cell
We prove the effectiveness of TADpole to investigate the chromatin hierarchy in capture high-throughput Chromosome Conformation Capture (Hi-C) data [40] where the chromosome topology is altered with local genomic inversions that drive gene misexpression associated to congenital malformations in mouse [41]
As the resolution of the Hi-C interaction map decreased, both the numbers of Topologically Associated Domains (TADs) and the mean TAD size in bins decreased with a 4-fold reduction
Summary
The organization of the genome in the cell nucleus has been shown to play a prominent role in the function of the cell. Fluorescence in-situ hybridization revealed that chromosomes are positioned in preferential areas of the nucleus called chromosome territories [12] This large-scale feature has been confirmed by high-throughput Chromosome Conformation Capture (Hi-C) experiments [13], that provided a genome-wide picture in which inter-chromosomal interactions are depleted relative to intra-chromosomal. In mammalian cells, concepts such as "metaTADs" [26] or "sub-TADs" [27] have been introduced The former is used to define a superior hierarchy of domains-withindomains that are modulated during cell differentiation [26] while the latter to emphasize how and where the cis-regulatory elements establish physical interactions that contribute to gene regulation [27]
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