Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

Abstract

Summary Understanding the topological configurations of chromatin may reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in looping interactions at different length scales. CTCF/cohesin anchor long-range constitutive interactions that form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge shortrange enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales.

Genome-wide map of regulatory interactions in the human genome

“…These results agree with a study by Phillips-Cremins et al (2013) who investigated interactions in select regions of the mouse genome and found that > 80% of interactions were anchored by some combination of CTCF, MED12, or SMC1, a subunit of cohesin. Our analysis further revealed that CTCF and RAD21 were members of nearly every cobinding pattern that was enriched for interactions.…”

“…interactions (Kagey et al 2010;Hoffman et al 2013;Merkenschlager and Odom 2013;Phillips-Cremins et al 2013). CTCF, a canonical insulator protein, which is found at the majority (96.7%) of RAD21 sites in K562 cells, has also recently been implicated in long-range interactions (Handoko et al 2011).…”

Two independent modes of chromatin organization revealed by cohesin removal

“…The co-existence of two processes with different modes and scales of action can help explain the difficulties in the field in delineating and unambiguously classifying the different features of Hi-C maps, leading to a confusing plethora of denominations and definitions 7,8,12,40–42 . Our data demonstrates clearly the existence of local, cohesin-dependent, self-interacting domains identifiable as TADs.…”

LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration

“…As evident from the literature and argued by Taberlay et al [27], the available genome-wide assays for chromatin conformation analyses are unreliable for interpreting connectivity at distances >100 kb. However, the chromatin occupancies of the cohesin complex, which facilitates enhancer-promoter looping, may infer such interactions [27][28][29]. Therefore, we assessed the occupancy of Rad21, a member of cohesion complex, and Nipbl, a cohesin-loading factor.…”