Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains

Mapping nucleolar-associated domains (NADs) is challenging as the nucleolus is membrane-less. Here the authors adapted the DNA adenine methyltransferase identification (DamID) method by engineering a nucleolar histone that can mark genomic contacts with the nucleolus through DNA methylation (m6A) and characterized NADs in mouse embryonic stem cells (ESCs) and derived neural progenitors (NPCs). Eukaryotic chromosomes are folded into hierarchical domains, forming functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks contributing to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for the identification of nucleolar associated domains (NADs). Here we have established DamID- and HiC-based methodologies to generate accurate genome-wide maps of NADs in embryonic stem cells (ESCs) and neural progenitor cells (NPCs), revealing layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs show higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation into NPCs, chromosomes around the nucleolus acquire a more compact, rigid architecture with neural genes moving away from nucleoli and becoming unlocked for later activation. Further, histone modifications and the interaction strength within A and B compartments of NADs and LADs in ESCs set the choice to associate with NL or nucleoli upon dissociation from their respective compartments during differentiation. The methodologies here developed will make possible to include the nucleolar contribution in nuclear space and genome function in diverse biological systems.

Automated summary

The authors developed a method to map nucleolar-associated domains using DNA methylation, and characterized these domains in mouse embryonic stem cells and neural progenitor cells. They found distinct chromatin states and changes in genome architecture during differentiation.