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

Abstract

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.

dcHiC: differential compartment analysis of Hi-C datasets

“…When comparing dcHiC to existing approaches, we showed that it identifies regions with higher differences in replication timing, Lamin B1 signals, and differentially expressed genes, suggesting better prioritization of relevant biological regions. Even though differences of compartmentalization between ESC and NPC generally aligned with changes in Lamin B1 association, a recent work highlighted the importance of nucleolus association in revealing layers of compartmentalization with distinct repressive chromatin states [63]. Our initial analysis showed that over 10% of all significant compartment differences we found between ESC and NPC belongs to nucleolus associated domains (NADs) that were deemed exclusive to either ESC or NPC [63] providing an explanation for a subset of differences in compartmentalization during differentiation .…”

“…Even though differences of compartmentalization between ESC and NPC generally aligned with changes in Lamin B1 association, a recent work highlighted the importance of nucleolus association in revealing layers of compartmentalization with distinct repressive chromatin states [63]. Our initial analysis showed that over 10% of all significant compartment differences we found between ESC and NPC belongs to nucleolus associated domains (NADs) that were deemed exclusive to either ESC or NPC [63] providing an explanation for a subset of differences in compartmentalization during differentiation . Expanding to a three-way (n=3) mouse neuronal differentiation model, we showed that dcHiC continues to systematically identify critical biological marker genes and can recover cell-specific functions from differential compartment analysis alone.…”

dcHiC: differential compartment analysis of Hi-C datasets

“…When comparing dcHiC to existing approaches, we showed that it identifies regions with higher differences in replication timing, Lamin B1 signals, and differentially expressed genes, suggesting better prioritization of relevant biological regions. Even though differences in compartmentalization between ESCs and NPCs are generally aligned with changes in the lamin B1 association, a recent work highlighted the importance of nucleolus association in revealing layers of compartmentalization with distinct repressive chromatin states [63]. Our initial analysis showed that over 10% of all significant compartment differences we found between ESC and NPC belong to nucleolus-associated domains (NADs) that were deemed exclusive to either ESC or NPC [63], providing an explanation for a subset of differences in compartmentalization during differentiation.…”

“…Even though differences in compartmentalization between ESCs and NPCs are generally aligned with changes in the lamin B1 association, a recent work highlighted the importance of nucleolus association in revealing layers of compartmentalization with distinct repressive chromatin states [63]. Our initial analysis showed that over 10% of all significant compartment differences we found between ESC and NPC belong to nucleolus-associated domains (NADs) that were deemed exclusive to either ESC or NPC [63], providing an explanation for a subset of differences in compartmentalization during differentiation. Expanding on a three-way (n=3) mouse neuronal differentiation model, we showed that dcHiC continues to systematically identify critical biological marker genes and can recover cell-specific functions from differential compartment analysis alone.…”

Characterizing the variation in chromosome structure ensembles in the context of the nuclear microenvironment

“…A logical follow up question is what factors might contribute to the extent of structural variation. There are various essential factors such as epigenetic marks, associated structural proteins, and nuclear lamina associations that vary in a cell-type specific manner and contribute to the organization of 3D genome (40)(41)(42). Therefore, investigating the role of these different factors in the variation of chromosome structural ensemble is of high importance.…”