The activity of the genome is regulated through controlling its structure and architecture. This occurs at different levels and scales, such as local chromatin composition, contact between cis-regulatory elements, the formation of topologically associated domains (TADs), and a “compartmentalized” structure in which active and inactive chromatin regions are segregated and interact like with like. Although it is clear that such controls are critical for transcription regulation and nuclear organization, these processes are poorly understood.
We recently developed ARC-C to interrogate genome architecture and regulatory interactions at high resolution (Huang et al 2018, BioRxiv). We identified >16,000 interactions that are significantly enriched in C. elegans L3 stage chromatin at 500bp resolution, 97% of which occur at regulatory elements. We also found that particular transcription factors (TFs) and chromatin regulators are enriched at interacting chromatin, making them excellent candidates for mediating interactions. These include cell-type specific TFs and cohesin components. Interrogating genome architecture, we found that chromatin marking domains defined by active or Polycomb modifications form topologically associating domains (TADs) that interact with A/B (active/inactive) compartment structure, similar to other animals.
We are using ARC-C in mutants and auxin degron lines to investigate the roles of transcription factors and chromatin regulators in controlling cell-type specific genome architecture, and genome editing to determine the roles of sequence features in mediating architecture. To study specific cell types, we FACS sort nuclei based on cell-type specific expression of nuclear envelope or pore targeted GFP.
