Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency

Abstract

Higher-order chromatin structure is tightly linked to gene expression and therefore cell identity. In recent years, the chromatin landscape of pluripotent stem cells has become better characterized, and unique features at various architectural levels have been revealed. However, the mechanisms that govern establishment and maintenance of these topological characteristics and the temporal and functional relationships with transcriptional or epigenetic features are still areas of intense study. Here, we will discuss progress and limitations of our current understanding regarding how the 3D chromatin topology of pluripotent stem cells is established during somatic cell reprogramming and maintained during cell division. We will also discuss evidence and theories about the driving forces of topological reorganization and the functional links with key features and properties of pluripotent stem cell identity.

Keywords: 3D chromatin organization; ESC; bookmarking; enhancer-promoter interaction; iPSC; mitosis; reprogramming; transcription factors.

Figure 1

Reorganization of the 3D Genome during Self-Renewal and Cell Fate Change Schematic illustration of the 3D genomic reorganization that occurs during the cell cycle in self-renewing cells as well as during cell fate changes, such as differentiation and reprogramming. Examples of Hi-C heatmaps at 250-kb resolution are shown to illustrate the topological rewiring between cell types and during mitosis.

Figure 2

Dynamic Changes in Chromatin Architecture during Somatic Cell Reprogramming Changes in local chromatin state and TAD insulation are the earliest architectural changes that have been reported during iPSC reprogramming. Compartment switching begins to occur in tandem with new loop formation and continued changes in TAD insulation. Finally, transcriptional changes often occur concurrently or after topological reorganization.

Figure 3

Disruption of Cell-Type-Specifying Features Causes Temporary “Identity Crisis” during Mitosis Summary of the molecular changes that challenge cell identity during cell division. Transcription largely shuts down and most TFs and cofactors are dissociated from mitotic chromatin, except for a select few mitotic bookmarking factors. Histone modifications are variably lost (acetylation), gained (phosphorylation), or selectively maintained (bookmarked). Finally, the 3D chromatin architecture collapses from a cell-type-specific structure to a cell-type-invariant metaphase state. These features then must all be faithfully reset during G1 in the daughter cells in order to maintain proper cell identity.

Figure 4

Resetting of Chromatin Architecture during Mitotic Exit Schematic showing the resetting of different layers of chromatin architecture during the cell cycle. All of these features are disrupted in prometaphase (prometa), yet they reform with variable kinetics during mitotic exit. Compartments begin reorganizing during anaphase and telophase (ana/telo) and continue strengthening throughout S and G2. TADs are also rapidly reset, with smaller TADs in ana/telo building up to larger TADs in G1. TAD boundary insulation is strongest in G1 before weakening in S phase with the onset of DNA replication. Loops reform gradually and heterogeneously, with enhancer-promoter (Enh-Prom) contacts forming prior to CTCF/Cohesin-mediated structural loops. A few transient enhancer-promoter contacts are also observed during mitotic exit that are disrupted or lost later in the cell cycle.

Figure 5

Role of Mitotic Bookmarking in Transcriptional and Architectural Resetting during G1 Entry Model describing the role of mitotic bookmarking TFs and histone marks in the rapid resetting of pluripotency genes and the transient activation of lineage-specific genes. In PSCs, bookmarking factors (blue circles) are preferentially retained at stem cell-specific genes and enhancers during mitosis. This allows for fast recruitment of cofactors and transcriptional machinery (yellow ovals), resetting of enhancer-promoter contacts, and rapid transcriptional reactivation in G1 (arrows). Non-bookmarking TFs (green circles) must be recruited back to the chromatin during G1, resulting in a slower resetting of these sites. Lineage-specifying genes, often marked by PRC2 and bivalent histone marks (H3K4me3/H3K27me3) (pink circles), are transiently activated during G1. This could be caused by fluctuation of PRC2 components over the cell cycle, slower recruitment of other repressive factors (maroon ovals), and/or transient miswiring of chromatin loops.