Chromatin accessibility classification of TAD boundaries discloses new architectural proteins

Abstract

3D genome organization is crucial to modulate gene expression. Topologically Associated Domains (TADs) isolate genes and their regulatory elements within the same topological neighborhood, avoiding crosstalk between regulatory elements. Perturbation of domain boundaries causes aberrant genomic contacts and gene expression misregulation. Architectural proteins such as CTCF and the cohesin complex are critical to form boundaries. However, we still lack a complete understanding of what makes a boundary more effective at insulating genomic contacts than others. To understand how domains are structured, we experimentally classified boundaries according to their chromatin accessibility as a proxy of protein occupancy in K562 human cells. We found that highly accessible boundaries are occupied by more proteins, are more robust contact insulators, have a more conserved CTCF DNA-binding motif and are more conserved across cell types in contrast to less accessible ones. By exploring the proteins enriched at boundaries with different accessibility, we found that CTCF and cohesin, together with REST, form a module, and ZFN316, together with EMSY, form another module, and both modules occupy boundaries very frequently. Finally, by using CRISPR-Cas9 mediated genetic edition of ZNF316 DNA-binding motif at a robust domain boundary, we demonstrate that ZNF316 can block chromatin contacts in the absence of CTCF. Our results emphasize the importance of protein combination and abundance to support boundary strength and propose ZNF316 as a novel architectural protein. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/629025v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@16a816corg.highwire.dtl.DTLVardef@157064aorg.highwire.dtl.DTLVardef@5ded2aorg.highwire.dtl.DTLVardef@7d95ed_HPS_FORMAT_FIGEXP M_FIG C_FIG