3D Chromatin Organization During Differentiation

Phillips-Cremins et al did a study of chromatin interaction organization in their new publication Architectural Protein Subclasses Shape 3D organization of genomes during Lineage Commitment. They looked at the topology of the interactions in differentiation related cell types as well as the factors that were enriched at these sites.  It is important to look at the 3D organization of chromatin to understand regulatory networks, because TF binding at a distal enhancer can affect the regulation of expression at an interacting promoter.

In this paper, they used 5C to make chromatin interaction maps in ES and ES-derived Neural Progenitor Cells (NPCs) to determine cell type specificity.  The 5C primers were located in six 1-2 Mb sized genomic regions around developmentally regulated genes (Oct4, Nanog, Nestin, Sox2, Klf4, and Olig1-Olig2).  They found that topological features in the 5C data was similar to those found in Hi-C data (Dixon et al 2012), and the replicates within a cell type were highly correlated.

Chromatin interactions are thought to be mostly between regions within a topologically associating domain (TAD), a genomic area on the scale of a megabase.  These TADs are thought to be conserved across organisms and cell types.  Looking at the 5c interactions, the complex set of TADs are visible, but they also find that within these TADs, there is a hierarchy including more fine grained sub-topologies (sub-TADs) in which chromatin interactions are more frequent.  Within these sub-TADs, interaction dynamics varied, suggesting that the small-scale interaction frequencies are specific to the function of the genomic region.

Using a stringent threshold to identify interactions, they found 83 ES-cell-specific interactions, 260 interactions that exist in both cell types, and 165 NPC specific interactions.  This demonstrates that these interactions are cell type specific.  There were a few epigenomic marks frequently found at interacting regions including H3K4me1, H3K27ac, and low levels of H3K4me3.  Greater than 80% of significant interactions were marked by some combination of CTCF, Med12 (Mediator), or Smc1 (Cohesin) in ES cells.  However, only 40% of interactions were occupied by some combination of Oct4, Nanog, and/or Sox2, suggesting that these are not as important in chromatin interaction architecture.  They test the importance of Smc1 and Med12 by knocking out these genes.  Knockdown of Med12 and Smc1 results in an alteration of the chromatin interaction landscape. They performed a knockout of Med12 and Smc1 and found no interaction between Olig1 and the enhancer region that was present in wild type.

This work is very interesting to the ongoing study of chromatin architecture.  This 5c map highlights the topology of the chromatin interactions in regions around key differentiation related genes.  These interactions change during cell type differentiation.  The identification of Smc1, Med12, and CTCF as important factors for interactions suggests that there may be a subset of proteins greatly responsible for chromatin organization.