Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries.

ABSTRACT: The metazoan genome is compartmentalized in areas of highly interacting chromatin known as topologically associating domains (TADs). TADs are demarcated by boundaries mostly conserved across cell types and even across species. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. In this study, we first use fused two-dimensional lasso as a machine learning method to improve Hi-C contact matrix reproducibility, and, subsequently, we categorize TAD boundaries based on their insulation score. We demonstrate that higher TAD boundary insulation scores are associated with elevated CTCF levels and that they may differ across cell types. Intriguingly, we observe that super-enhancers are preferentially insulated by strong boundaries. Furthermore, we demonstra

SUBMITTER: Gong Y 

PROVIDER: S-EPMC5803259 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature