Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization

Area of Science:

• Cell Biology
• Genomics
• Epigenetics

Background:

• Mammalian chromosomes are organized into topologically associating domains (TADs).
• TADs reside in either active (A) or inactive (B) subnuclear compartments, correlating with replication timing (RT).
• A compartments replicate early, while B compartments replicate late.

Purpose of the Study:

• To investigate the dynamic changes in A/B compartments and their relationship with replication timing during mouse embryonic stem cell (mESC) differentiation.
• To understand the mechanisms driving these organizational changes, such as boundary shifting.
• To explore the implications for cellular reprogramming and pluripotency states.

Main Methods:

• Genome-wide analysis of A/B compartment changes and replication timing during mESC differentiation.
• Single-cell Repli-seq to confirm compartment dynamics at the individual cell level.
• Comparison of differentiation profiles with reprogramming and other stem cell types (e.g., EpiSCs).

Main Results:

• A/B compartment changes and RT shifts occur genome-wide and coordinately during mESC differentiation.
• A to B compartment transitions are tightly linked with early to late RT shifts.
• B to A compartment transitions precede late to early RT shifts and transcriptional activation.
• Compartment changes are primarily mediated by boundary shifting, affecting adjacent TADs.
• Single-cell Repli-seq revealed gradual, uniform changes in differentiating mESCs, transiently resembling epiblast-derived stem cells (EpiSCs).

Conclusions:

• A/B chromosome compartments and replication timing are dynamically regulated during cellular differentiation.
• Boundary shifting is a key mechanism for altering TAD compartmentalization.
• These findings offer insights into the gradual changes in chromosome organization during differentiation and reprogramming towards a primed pluripotent state.