The CTCF Anatomy of Topologically Associating Domains

Abstract

Topologically associated domains (TADs) are defined as regions of self-interaction. To date, it is unclear how to reconcile TAD structure with CTCF site orientation, which is known to coordinate chromatin loops anchored by Cohesin rings at convergent CTCF site pairs. We first approached this problem by 4C analysis of the FKBP5 locus. This uncovered a CTCF loop encompassing FKBP5 but not its entire TAD. However, adjacent CTCF sites were able to form 'back-up' loops and these were located at TAD boundaries. We then analysed the spatial distribution of CTCF patterns along the genome together with a boundary identity conservation 'gradient' obtained from primary blood cells. This revealed that divergent CTCF sites are enriched at boundaries and that convergent CTCF sites mark the interior of TADs. This conciliation of CTCF site orientation and TAD structure has deep implications for the further study and engineering of TADs and their boundaries.

CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

“…Finally, our finding of the asymmetry of CTCF-dependent chromatin boundaries at the scale of several nucleosomes may provide the missing mechanistic explanation for the asymmetry of chromatin boundaries at the scale of hundreds to thousands of nucleosomes reported recently (80,81). As we showed, TAD boundaries often contain several directed CTCF motifs (Figure 7F, Supplementary Figure S18).…”